This is the 2nd in a series of 3 posts on metabolic emergencies. Last month’s post covered hypoglycemia. Today’s post will cover two distinct causes of hyperammonemia with different laboratory findings.

As a reminder, early-bird registration for our 30-hour ABGC Board Review Bootcamp (June 11-July 23) for the Aug 2026 exam ends Mon June 1st at 11:59pm ET! If you are interested in taking the course, make sure to sign up before this time to take advantage of the $100 discount. Please also consider forwarding this email to anyone in your network who might be interested.

Feel free to reach out (daniel@studyrare.com) with any questions about the course or this post. I hope you have a great week!

-Daniel

Question 106

A 3-day-old boy born at term presents with poor feeding, vomiting, and lethargy. He is hypothermic, hypotonic, and tachypneic. Labs show plasma ammonia 820 μmol/L (elevated), and a venous blood gas shows a pH of 7.52. Plasma amino acids show low citrulline and elevated glutamine. Urine organic acids show elevated orotic acid. Which of the following enzymes is most likely deficient in this patient?

Question 107

A 4-day-old presents with lethargy and poor feeding. Her laboratory studies show elevated plasma ammonia, a pH of 7.18, and elevated propionylcarnitine (C3). Laboratory studies show elevated methylmalonic acid and methylcitrate. Which of the following most strongly distinguishes this patient from one with a urea cycle disorder?

Explanations

Question 106: D) Ornithine transcarbamylase

Question 107: B) Anion gap acidosis

Hyperammonemia is a neonatal metabolic emergency

Ammonia is a toxic molecule that is produced continuously, both by the catabolism of dietary and endogenous protein and by intestinal bacteria. The liver clears it through the urea cycle, which converts ammonia to urea. Urea is then removed from the body in the urine. When the urea cycle is unable to keep pace, ammonia accumulates in the blood. This is dangerous because ammonia, unlike most metabolites, readily crosses the blood-brain barrier. Within astrocytes, ammonia is incorporated into glutamine, an osmotically active molecule whose accumulation draws water into the brain and produces cerebral edema, seizures, and coma. If it is not corrected promptly, hyperammonemia can progress to brainstem herniation and death.

The blood gas separates the two major causes of hyperammonemia

Both patients in this post are neonates with hyperammonemia who present in a similar fashion (poor feeding, vomiting, lethargy). The laboratory finding that separates them is the acid-base status on the venous blood gas, which divides the differential into two broad categories.

The first category is the urea cycle disorders (UCDs), in which the defect lies within the urea cycle itself (Question 106). Because ammonia stimulates the respiratory center, these infants hyperventilate and characteristically develop a respiratory alkalosis (pH > 7.45). The second category is the organic acidemias, in which an organic acid that accumulates upstream secondarily impairs the urea cycle (Question 107). These infants develop an anion gap metabolic acidosis from the accumulating organic acid. The presence or absence of acidosis can help narrow the differential diagnosis in a neonate with hyperammonemia.

The urea cycle

The urea cycle operates in the liver and spans the mitochondrial matrix and the cytosol. It comprises six enzymes and one allosteric activator (NAG):

1. NAGS (N-acetylglutamate synthase) produces N-acetylglutamate (NAG), a molecule that activates CPS1.

2. CPS1 (carbamoyl phosphate synthetase 1) combines ammonia and bicarbonate into carbamoyl phosphate. This is the rate-limiting step.

3. OTC (ornithine transcarbamylase) combines carbamoyl phosphate and ornithine to form citrulline.

4. ASS1 (argininosuccinate synthetase) combines citrulline and aspartate to form argininosuccinate.

5. ASL (argininosuccinate lyase) cleaves argininosuccinate into arginine and fumarate.

6. ARG1 (arginase) hydrolyzes arginine into urea and ornithine, regenerating the cycle.

Loss of function of each of the enzymes in the urea cycle is associated with a separate disorder. All of the urea cycle disorders are inherited in an autosomal recessive manner, with the exception of OTC deficiency, which is X-linked.

Ornithine transcarbamylase (OTC) deficiency

The patient in Question 106 has OTC deficiency (Choice D). OTC is a mitochondrial enzyme that combines carbamoyl phosphate and ornithine to form citrulline. When OTC is deficient, carbamoyl phosphate accumulates and is converted to orotic acid (a pyrimidine precursor), which is excreted in the urine. The combination of a low plasma citrulline, elevated urinary orotic acid, and a respiratory alkalosis in a hyperammonemic neonate is essentially diagnostic of OTC deficiency.

💡 Remember that OTC converts Ornithine To Citrulline.

OTC deficiency classically presents in a healthy, full-term male infant who decompensates within the first several days of life. Because the gene is X-linked, heterozygous females can also become symptomatic, with severity determined by the degree of skewed X-inactivation in the liver. Some present in infancy, while others remain asymptomatic until they experience a stressor (e.g., large protein load, postpartum state, or severe illness). A family history of unexplained neonatal deaths among male relatives, or longstanding protein avoidance in the mother, can be an important clue.

Unlike many of the organic acidemias, OTC deficiency is not reliably detected by standard newborn screening, because the diagnostic finding is a low citrulline rather than an elevation. As a result, affected infants often decompensate before any screening result returns, which underscores the importance of recognizing the clinical picture.

Methylmalonic acidemia

The patient in Question 107 has methylmalonic acidemia (MMA), an organic acidemia caused by deficiency of methylmalonyl-CoA mutase or by defects in its cobalamin (vitamin B12) cofactor. Methylmalonyl-CoA is an intermediate in the catabolism of propionyl-CoA, which is itself derived from Valine, Odd-chain fatty acids, Methionine, Isoleucine, and Threonine (“VOMIT”). When the mutase is deficient, both methylmalonyl-CoA and propionyl-CoA accumulate.

This accumulation has two consequences. First, the accumulating organic acids consume bicarbonate and produce an anion gap metabolic acidosis. This acidosis helps distinguish MMA from a urea cycle disorder (Choice B), because urea cycle disorders are associated with respiratory alkalosis. Second, accumulated propionyl-CoA inhibits N-acetylglutamate synthase (NAGS), so that the activator of CPS1 is not produced and the urea cycle stalls. The hyperammonemia in MMA is therefore secondary and occurs despite urea cycle enzymes that are otherwise functional.

Additional features that support an organic acidemia rather than a urea cycle disorder include ketonuria (which is inappropriate in a young infant), neutropenia, thrombocytopenia, and an elevated lactate. The plasma acylcarnitine profile shows an elevated propionylcarnitine (C3), and urine organic acids show methylmalonic acid, 3-hydroxypropionate, and methylcitrate. Newborn screening detects most cases through an elevated C3 on the dried blood spot, although a neonate may decompensate before the results are available. These findings would not be present in a urea cycle disorder.

Acute management of hyperammonemia

Acute hyperammonemia is treated by stopping all protein intake for 24 to 48 hours, providing high-calorie dextrose (D10) with or without intralipid to reverse catabolism, and administering nitrogen scavengers (sodium benzoate and sodium phenylacetate, given IV as Ammonul) that provide alternative routes for nitrogen excretion. Hemodialysis is the most effective acute therapy and is indicated when ammonia exceeds 500 µmol/L or when the patient does not respond rapidly to medical management.

Incorrect answers

Question 106

Carbamoyl phosphate synthetase 1 (CPS1) deficiency (Choice A) also produces severe neonatal hyperammonemia with a low citrulline, but the urinary orotic acid is normal or low because no carbamoyl phosphate is generated to be diverted into pyrimidine synthesis. Argininosuccinate synthetase (ASS1) deficiency (Choice B) causes citrullinemia type I, in which the unprocessed substrate accumulates and produces an elevated, rather than low, plasma citrulline. Propionyl-CoA carboxylase deficiency (Choice C) causes propionic acidemia, an organic acidemia that would present with an anion gap metabolic acidosis and an elevated propionylcarnitine (C3), neither of which are described in the question stem.

Question 107

Hyperammonemia (Choice A) is a feature of both urea cycle disorders and the classic organic acidemias. Elevated blood urea nitrogen (Choice C) is not expected in either condition, because impaired ureagenesis in both UCDs and organic acidemias typically produces a low or normal BUN (note that chronic kidney disease can develop later in MMA but does not produce an elevated BUN in the acute neonatal presentation). The age of onset (Choice D) is likewise unhelpful, because both the classic urea cycle disorders and the organic acidemias typically present in the first few days of life, once protein feeding begins and the nitrogen load rises.

Learning Objective

Hyperammonemia is a neonatal metabolic emergency, and the acid-base status of a patient can help narrow the differential diagnosis in a patient with hyperammonemia. A respiratory alkalosis points to a urea cycle disorder, while an anion gap metabolic acidosis points to an organic acidemia. Acute management of hyperammonemia centers on stopping protein, giving dextrose-containing fluids, nitrogen scavengers, and hemodialysis for severe cases.

2025 ABMGG General Exam Blueprint | V. Single gene inheritance > d) Single gene disorders > Metabolic disorders

2023 ABGC Exam Content Outline | Domain 1C. Genetic Conditions. (OTC deficiency is listed on the ABGC self-study guide)

Additional resources

1. Urea cycle disorder overview (GeneReviews)

2. Ornithine transcarbamylase deficiency (GeneReviews)

3. Isolated methylmalonic acidemia (GeneReviews)

This is the 1st in a new series of 3 posts on metabolic emergencies. Today's post will cover two distinct causes of hypoglycemia with different laboratory findings and treatment options.

We were also happy to announce that registration for the ABGC Board Review Bootcamp is now open! The bootcamp will take place from June 11th - July 23rd, 2026 and is for genetic counselors preparing for the August 2026 ABGC board exam. Our course includes 30 hours of live instruction that cover all 5 domains on the ABGC content outline, plus access to a 500-question qbank for additional practice. Early-bird pricing of $399 is available through June 1st ($499 regular price thereafter). You can sign up and learn more about the bootcamp at our website: www.studyrare.com/abgc-bootcamp

Please feel free to reach out (daniel@studyrare.com) with any questions about the course or this post. I hope you have a great week!

-Daniel

Questions

Question 104

A 9-month-old boy presents to the emergency department with a seizure after a febrile illness. He has had decreased oral intake over the past 2 days. Physical exam reveals a lethargic infant with hepatomegaly. Laboratory studies show a glucose of 28 mg/dL (low), elevated venous lactate, elevated triglycerides, and elevated uric acid. Glucose levels do not respond to glucagon. Which of the following enzymes is MOST likely deficient in this patient?

Question 105

A 14-month-old girl presents to the emergency department with lethargy after a 24-hour febrile illness with poor oral intake. Laboratory studies show a glucose of 22 mg/dL (low), and serum beta-hydroxybutyrate is also low. An acylcarnitine profile shows elevated medium-chain acylcarnitine species. Newborn screening was declined at birth. Which of the following BEST describes the primary mechanism of hypoglycemia in this patient?

Explanations

Question 104: B) Glucose-6-phosphatase

Question 105: C) Impaired fatty acid oxidation

Hypoglycemia and inborn errors of metabolism

Hypoglycemia is one of the most common metabolic emergencies. It is dangerous because the brain runs almost entirely on glucose (with ketones as its only backup fuel), and prolonged hypoglycemia causes seizures, coma, and permanent neurologic injury if untreated. While many cases in children have multifactorial causes, recurrent or unusually severe hypoglycemia should prompt a workup for an inborn error of metabolism. This post walks through several pathways that help maintain blood glucose between meals, a decision tree used to narrow the differential diagnosis, and two classic IEM causes of pediatric hypoglycemia: GSD Ia and MCAD deficiency.

Three pathways maintain fasting glucose

Three pathways keep blood glucose stable between meals. Disruption of any one of them can cause hypoglycemia. These pathways function at different times after a meal (see “Bonus” section at the end of this post for more details). The two diseases covered in this post each affect different pathways:

1. Glycogenolysis - the liver breaks down glycogen to release glucose. First line of defense while fasting, lasts roughly 12 hours in older children (much shorter in infants).

2. Gluconeogenesis - the liver makes new glucose from lactate, glycerol, and amino acids. Starts to increase as glycogen runs low.

3. Fatty acid beta-oxidation (FAO) - once glycogen is depleted, the body oxidizes fatty acids. FAO does not make glucose directly, but it produces the ATP, NADH, and acetyl-CoA* that power gluconeogenesis. It also generates ketone bodies (e.g., beta-hydroxybutyrate) that serve as an alternative fuel for the brain.

*Acetyl-CoA activates pyruvate carboxylase, the enzyme that catalyzes the 1st step of gluconeogenesis.

Insulin shuts down energy production

Insulin is the master off-switch for all three pathways. When you eat, insulin rises and shuts down glycogenolysis, gluconeogenesis, and lipolysis (the mobilization of fat that feeds FAO), and also promotes glycogenesis (production of glycogen). It also promotes the uptake of glucose from the bloodstream into cells. As a result, glucose levels in blood drop. During fasting, insulin falls and these pathways turn back on. This is why inappropriately elevated insulin in a patient with hypoglycemia is so dangerous: all three pathways are blocked simultaneously, and the body cannot even make ketones as a backup fuel.

💡 Remember: insulin drives glucose into cells, lowering glucose in the bloodstream.

Ketones help narrow the differential diagnosis

When you see a hypoglycemic child, one useful lab test to consider sending is ketones (e.g., beta-hydroxybutyrate). While fasting, there is less glucose available, and so the body instead mobilizes fat and makes ketones for energy. So during hypoglycemia, ketones should be high. Low ketones in the setting of hypoglycemia is pathologic and helps narrow the differential, as seen in the diagram below:

Low ketones (hypoketotic) → 2 possibilities:

• Hyperinsulinism - insulin is suppressing lipolysis (the mobilization of fat), so the body cannot make ketones. Insulin is inappropriately elevated (should be low because glucose is low).

• FAO disorder - the body tries to make ketones (via FAO) but the pathway is broken. Insulin is appropriately low.

High ketones (ketotic) → body responded correctly, but glucose production still failed:

• Lactate high - points to GSD I or a gluconeogenesis defect (glucose-6-phosphate is backed up or cannot be formed).

• Lactate normal - points to idiopathic ketotic hypoglycemia, hormone deficiency (growth hormone or cortisol), or the milder GSDs (types 0, III, VI, IX).

The two cases in this post sit on opposite sides of the diagnostic algorithm. Question 104 presents a case of ketotic hypoglycemia (right half), while question 105 presents a case of hypoketotic hypoglycemia (left half).

Glycogen storage disease Ia (Von Gierke)

The patient in Question 104 has glycogen storage disease type Ia (GSD Ia), caused by deficiency of glucose-6-phosphatase (G6Pase) (Choice B). This enzyme catalyzes the final step of both glycogenolysis and gluconeogenesis, which is the conversion of glucose-6-phosphate (G6P) to free glucose. Without G6Pase, glucose cannot be released into the bloodstream from either pathway, and patients become hypoglycemic once feeds space out or when they cannot eat during illness.

The combination of fasting hypoglycemia, lactic acidosis, hypertriglyceridemia, and hyperuricemia in a patient with hepatomegaly should raise concern for GSD Ia.

As seen in Question 104, patients with GSD Ia do not respond to glucagon (a medication given to hypoglycemic patients to raise blood glucose). But why? Glucagon is a hormone with the opposite action to insulin and stimulates glycogenolysis (glycogen breakdown), which generates more G6P. But without G6Pase, G6P has nowhere to go and instead shunts into lactate. The absent glucose response to glucagon (often with a paradoxical rise in lactate) is a classic finding in GSD Ia and places the patient on the ketotic, high-lactate branch of the decision tree.

Management of GSD Ia includes frequent feeds and uncooked cornstarch (a slow-release glucose polymer that provides 4-6 hours of glucose). Patients should avoid fructose and galactose, as both are converted inside cells to G6P, which cannot be released and instead worsens the lactate and triglyceride load. Hepatic imaging for adenomas (which carry a risk of malignant transformation) is indicated, and liver transplant is an option for patients with severe complications.

Medium-chain acyl-CoA dehydrogenase (MCAD) deficiency

The patient in Question 105 has medium-chain acyl-CoA dehydrogenase (MCAD) deficiency, the most common fatty acid oxidation disorder. The classic presentation of MCAD is a previously well infant or toddler who decompensates during an illness (e.g. viral gastroenteritis) with poor oral intake. Between episodes, patients are asymptomatic.

MCAD catalyzes the first step of beta-oxidation for medium-chain fatty acyl-CoAs (C6–C12). During prolonged fasting, fatty acid oxidation becomes an important fuel source. This process generates cellular energy directly and produces ketones that serve as an alternative fuel for the brain. MCAD deficiency blocks this process, so patients present with hypoketotic hypoglycemia, which is low blood sugar without the expected compensatory rise in ketones (mechanism described in figure below). It is the hallmark of FAO disorders and the reason MCAD sits on the hypoketotic branch of the decision tree.

A plasma acylcarnitine profile is a useful biochemical test when diagnosing a suspected FAO disorder. In MCAD deficiency, medium-chain species (particularly C8, octanoylcarnitine) are elevated. Newborn screening uses a similar test and catches most cases before a clinical crisis. Scenarios like the one in Question 105 can arise when comprehensive NBS is declined or otherwise not available.

Management includes avoiding fasting (exact duration varies by age) and ensuring patients follow an emergency protocol (dextrose-containing fluids orally or IV) during illness. No dietary fat restriction is needed for patients with MCAD, unlike long-chain FAO disorders (VLCAD, LCHAD, CPT I/II), which typically do require fat restriction.

Incorrect answers

Question 104

(Choice A) Deficiency of acid alpha-glucosidase causes Pompe disease (GSD II), which is a lysosomal and glycogen storage disorder. Pompe presents with severe hypotonia and hypertrophic cardiomyopathy in the infantile form, not fasting hypoglycemia with lactic acidosis.

(Choice C) MCAD deficiency does cause fasting hypoglycemia, but the metabolic profile here (lactic acidosis, hyperuricemia, hypertriglyceridemia) points more specifically to GSD I. In MCAD deficiency, lactate and triglycerides are normal, and the hallmark is hypoketotic hypoglycemia.

(Choice D) Deficiency of muscle glycogen phosphorylase causes McArdle disease (GSD V), which presents with exercise intolerance and rhabdomyolysis in adolescents and adults. It does not cause fasting hypoglycemia or hepatomegaly. The defect is confined to skeletal muscle, which has a different glycogen phosphorylase isoform than the liver.

Question 105

(Choice A) Congenital hyperinsulinism (increased insulin secretion) can cause hypoglycemia with suppressed ketones, since insulin inhibits lipolysis. However, hyperinsulinism does not cause elevated medium-chain acylcarnitines. The acylcarnitine profile in this patient points specifically to a block in fatty acid beta-oxidation.

(Choice B) Defects in gluconeogenesis (e.g., fructose-1,6-bisphosphatase deficiency) cause fasting hypoglycemia with lactic acidosis. Fatty acid oxidation is intact in these disorders, and the body can therefore still produce ketones. We would expect elevated, not suppressed, beta-hydroxybutyrate.

(Choice D) Impaired glycogenolysis is the mechanism for most glycogen storage disorders (GSD). Patients with GSD do not present with hypoketotic hypoglycemia, as the breakdown of fatty acids into ketone bodies is not impaired.

Learning Objective

GSD Ia and MCAD deficiency both present with severe fasting hypoglycemia in infancy but result from defects in different metabolic pathways. The ketone level at the time of hypoglycemia helps narrow the differential diagnosis in an undiagnosed patient. GSD Ia presents with ketotic hypoglycemia and lactic acidosis (G6Pase block shunts G6P into lactate, triglycerides, and urate), while MCAD presents with hypoketotic hypoglycemia (the FAO pathway is broken, so the body cannot make ketones or sustain gluconeogenesis). GSD Ia is managed with frequent feeds and cornstarch, while MCAD is managed by avoiding fasting, especially during illness.

2025 ABMGG General Exam Blueprint | V. Single gene inheritance > d) Single gene disorders > Metabolic disorders (glycogen storage diseases, fatty acid oxidation disorders); IX. Population screening > Newborn screening

2023 ABGC Exam Content Outline | Domain 1C. Genetic Conditions. (Both MCAD and GSD are conditions listed on the ABGC self-study guide)

Additional resources

1. Glycogen storage disease type I (GeneReviews)

2. MCAD deficiency (GeneReviews)

3. Recognition, assessment and management of hypoglycaemia in childhood (BMJ)

Consider reviewing our earlier post (Question 3), which covers the related GSD Ib subtype and its treatment with empagliflozin.

Bonus: energy sources during fasting

The pathways discussed in this post do not all contribute equally at every point during a fast. Dietary glucose covers the first 1-2 hours. Hepatic glycogen then takes over for the next several hours, with gluconeogenesis becoming more and more dominant as glycogen stores are depleted. With prolonged fasting, fat-derived fuels (free fatty acids from adipose plus ketones from the liver) eventually become the largest contributor. Note that these durations are all shorter in infants, which is part of why a healthy 9-month-old cannot tolerate fasting nearly as long as an adult, who can fast for days without decompensating.

Try mapping the IEMs discussed in this post onto this chart. GSD Ia shrinks the glycogen and gluconeogenesis bands, so patients become symptomatic relatively quickly once dietary glucose runs out (hence the need for near-continuous glucose sources like cornstarch). In contrast, MCAD shrinks the fat-derived fuels band, so patients become symptomatic later in the fast, once FAO should have taken over. This video walks through this framing in more detail (min ~5:30-10:30).

I am traveling to Baltimore this week for the ACMG conference. The conference does not suggest official “tracks” based on your interest, so here are two I would build myself from the trainee perspective. These are not exhaustive, so use these as starting points as you plan which sessions to attend.

The conference schedule is here and the abstracts are available here. Note that abstract number is preceded by a letter: “O” is for Oral presentation, and “P” is for Poster presentation.

If you are looking for more general advice on how to have a productive conference, this link will download a PDF of a paper (”How to Conference”) with a few tips for introverts (myself included).

If you will be at the meeting, I hope to meet you in person!

Sincerely,

Daniel

Track 1: Trainees and Mentorship

These sessions are explicitly targeted towards trainees, students, and early-career professionals. Consider attending these if you want to network with peers and seek new mentors. I personally plan to attend several of these.

Tuesday 3/10

6:00 - 7:30 PM | Camden Lobby, Level 300 Welcome Reception for Trainees, Residents, Fellows, and Students

The title is self-explanatory. In past years, there has been free food and drinks. It is one of the easiest rooms of the week to walk into alone. Go if you can.

Wednesday 3/11

8:00 - 9:30 AM | Room 318-323, Level 300 Early Genetics Trainee Forum -- Mastering the Challenges of Diagnosing and Managing Overgrowth, Connective Tissue, and Mitochondrial Disorders

This one will be worth waking up early for. Each of these three classes of disorders can be tricky to diagnose using standard genetic testing approaches. In some cases, specialized testing may be required beyond the traditional exome or genome (e.g., targeted deep sequencing for overgrowth disorders). Diagnosing these disorders accurately is increasingly important because of a growing number of targeted treatments that are available or in clinical trials. Feeling comfortable with sending the appropriate testing once one of these disorders is suspected sets you apart as a genetics provider and helps provide the patient with the best care possible.

10:00 AM - 12:00 PM | Exhibit Hall AB, Level 100 Presidential Plenary Session -- The Future of Expanded Newborn Genomic Screening: Promise and Practice

Right now, newborn screening catches a defined list of conditions, mostly through biochemical assays. The question is whether we should be adding broad genomic sequencing to that process and screening for hundreds or thousands of conditions at birth instead of dozens. I anticipate that this plenary will cover this topic and the practical challenges of doing that at scale. It is going to be one of the defining policy questions in our field over the next decade and one where geneticists can play a central role alongside public health experts. Walk straight from the Trainee Forum into this one.

Thursday 3/12

9:00 - 10:00 AM | Exhibit Hall AB, Level 100 TED-Style Talks

I wanted to highlight the talk by Shoumita Dasgupta on mentorship in genomic medicine. Mentorship is one of those things people talk about in the abstract but rarely give you a concrete framework for. Even if you are a trainee now, it is likely that you are or will be a mentor to somebody soon in the future. Dr. Dasgupta is a distinguished author, speaker, and geneticist.

10:15 - 11:30 AM | Exhibit Hall C-E, Level 100 Speed Mentoring Session

This is a good place to practice your 2-minute “elevator pitch” as well as see what different career trajectories in genetics can look like. The folks who volunteer for this have a genuine interest in mentoring and helping others at an early career stage. If a conversation feels like a dead end, apply the five W’s of journalism (who, what, where, when, why) to jump-start the conversation. Don’t forget to exchange contact information (e.g., email, LinkedIn) with those who you made a genuine connection with.

11:45 AM - 1:00 PM | Room 314-317, Level 300 Early Career Genetic Mentor Luncheon

Walk over from the speed mentoring session to this luncheon. You will again have a chance to meet with potential mentors as well as other early career trainees over lunch.

Friday 3/13

1:30 - 3:00 PM | Room 314-317, Level 300 Student Workshop: Pathways to Careers Within Medical Genetics and Genomics

This session will likely be relevant not just for students but also for folks who are mentors. Even if you are a recent graduate, these paths might look different from what they were when you went through the process. I anticipate a discussion about the different ABMGG training pathways and certifications. The breadth of the field is apparent in the training structure itself -- it is one of the few subspecialties where you could have completed any prior residency beforehand and that also welcomes PhDs.

5:30 - 7:00 PM | Rooms 307-310, 318-323, and 324-326, Level 300 Diagnostic Challenges Sessions (Pediatric/Prenatal, Laboratory, and Adult/Cancer)

These are real cases, presented to the audience, where you work through the diagnostic logic alongside the experts on stage. Three sessions run in parallel, so pick the one closest to your area of interest. It is worth staying for on a Friday evening.

Saturday 3/14

9:45 - 10:15 AM | Ballroom I-II, Level 400 GENEius Challenge Championship Round

There are some true geniuses in our field, and I think you will see some of them in action at this session! Participants are all geneticists or genetic counselors in training.

Track 2: Genomics and AI

The meeting has multiple sessions on AI and genomic technology that are scattered across the schedule. Trainees may be interested in what the future looks like, and I do think that genomics and AI are going to play an increasingly important role in the future of our field. Here are some sessions that stood out to me.

Wednesday 3/11

3:30 - 5:00 PM | Room 307-310, Level 300 Dilemmas of Omic Technologies for Molecular Diagnosis of Rare Disease

Exome, genome, transcriptome, metabolome, proteome -- the number of omic tools available for rare disease diagnosis keeps growing! I expect that this session will discuss when to consider sending each test, as well as the pros and cons of each. It is important to build realistic expectations about what these tools can and cannot deliver in clinic in order to use our resources effectively. As you attend this session, keep in mind the principle that there are false positives and false negatives with any diagnostic test.

Thursday 3/12

8:00 - 9:00 AM | Exhibit Hall AB, Level 100 Featured Platform Presentations (includes Demystifying Base Large Language Model Reproducibility and Accuracy in ACMG/AMP Variant Classification)

There is one key question that the field needs answered before LLMs get embedded in variant classification pipelines: can these models produce consistent, reproducible classifications according to standard ACMG/AMP criteria? This is coming, and the reproducibility of these tools will determine how fast. The authorship team lists individuals from both Mayo Clinic and Google, which highlights the growing intersection of information technology and genomics.

1:45 - 3:15 PM | Room 307-310, Level 300 Advances in Genomics With AI: From Patient Selection to Variant Analysis and Beyond

This session covers AI in variant classification (one of the most common use cases for AI in our field at present), electronic health record mining for identifying previously undiagnosed patients with rare disease (where there is a lot of potential), and facial analysis for recognition of rare disease (where the potential is more limited). The main question in our field over the next ten years is not how do we more accurately sequence a genome but rather what do we do with the mountains of data that come back. The trainees in this room will be the ones pioneering the adoption and integration of this technology into clinical workflows, and it is good to get exposure early.

4:00 - 5:30 PM | Ballroom IV, Level 400 Platform Session 4 -- Genomic Analysis Tools and Workforce (includes STELLAR-AIM for AI-based genetic differential diagnosis)

I want to highlight one abstract here: O24 (STELLAR-AIM), an AI-based differential diagnosis tool that integrates literature, metabolomic, genomic, and phenotypic data. Pulling multiple data types together like this is not yet a reality in most clinical genetics encounters. However, for the patient who has had non-diagnostic broad DNA sequencing and where there is a strong suspicion for an underlying monogenic disorder, this is the kind of system that could help find an answer.

Friday 3/13

1:30 - 3:00 PM | Ballroom I, Level 400 Platform Session 5 -- New Laboratory Techniques (Long-read, OGM, RNA, PRS)

This session is where the laboratory technology content peaks. O53 is the one I would not miss -- two years of clinical long-read sequencing data, and they are showing reimbursement outcomes. Reimbursement ultimately determines whether a technology actually makes it into routine practice or stays academic. O58 covers optical genome mapping in pediatric rare disease, and O35 tackles RNA sequencing for VUS reclassification. All three of these modalities will be increasingly available in genetics clinics in the next 3-5 years, but only if payers cover them. This session should help us understand how far along we are with these technologies.

Saturday 3/14

8:00 - 9:30 AM | Room 318-323, Level 300 Rewriting the Reference: Laboratory and Clinical Applications of the New Human Pangenome Reference

For years, clinical genomics has mapped everything against a single linear reference genome (hg19, hg38, or T2T). The idea behind the human pangenome reference is to incorporate genetic variation from diverse populations into the reference itself, which means fewer false positives and better variant calling when sending clinical genomic tests for patients whose backgrounds are underrepresented in genomic databases. This is the infrastructure layer underneath the field, and is a good way to end the week.

This is the 3rd post in our series on gastrointestinal genetics. This post focuses on Wilson disease, an important cause of liver disease that can present in childhood or adolescence and is one of the few hepatic conditions that is treatable if caught early.

We are also excited to announce that registration is now open for our ABMGG board review bootcamp, which will take place between March 17th - June 4th 2026. This bootcamp is for clinical and laboratory geneticists taking the ABMGG general exam in August 2026. We will cover topics from all 11 domains and 115 subdomains on the ABMGG content outline. Over 30 hours of live instruction plus access to a QBank (available starting May 1st) that simulates the exam environment will be provided. An early-bird discount is available through March 16th. For more information and to register, please visit our website.

If you would like to support our work, the best way to do so is to share this post with others who are preparing for genetics board exams.

Please feel free to reach out (daniel@studyrare.com) with any questions about the post, suggestions for future topics, or our upcoming courses. I hope you have a great week!

-Daniel

Questions

Question 102

A previously healthy 15-year-old boy is evaluated for progressive tremor, dysarthria, and declining school performance over the past 8 months. Physical examination shows hepatomegaly. Laboratory studies show elevated AST and ALT and low ceruloplasmin. Which of the following findings on liver biopsy would be most consistent with the suspected diagnosis?

Question 103

Genetic testing is performed for the patient in Question 102 and shows biallelic pathogenic variants in ATP7B. His 11-year-old asymptomatic sister undergoes genetic testing and is found to carry the same two variants. Which of the following is the most appropriate management for the sister?

Explanation

Question 102: Copper accumulation in hepatocytes

Question 103: Zinc therapy

The patient in Question 102 has Wilson disease, a disorder due to excess copper in the body. Wilson disease is caused by biallelic pathogenic variants in the ATP7B gene, which encodes a copper-transporting ATPase primarily expressed in the liver. This transporter has two main functions:

1. Excretion of copper into bile for elimination from the body

2. Incorporation of copper into ceruloplasmin (the main copper-carrying protein in blood)

When ATP7B is defective, copper cannot be excreted into bile and instead accumulates in hepatocytes (Question 102). This causes hepatomegaly and cirrhosis. Over time, copper spills into the bloodstream and deposits in other organs, particularly the brain (e.g., basal ganglia), cornea, and kidneys. Symptoms are progressive if the disease is untreated. This progressive deposition of copper in both liver and brain gave rise to the other name for this disease, “hepatolenticular degeneration” (hepato = liver, lenticular = lentiform nucleus, part of the basal ganglia).

Clinical Presentation

Wilson disease typically presents between ages 5 and 35 years. There are two main presentations, and the presentation depends on which organ is primarily affected:

1. Hepatic presentation (more common in children):

• Asymptomatic elevation of transaminases (AST, ALT)

• Acute hepatitis

• Chronic hepatitis progressing to cirrhosis

• Acute liver failure (can be the first presentation)

2. Neuropsychiatric presentation (more common in adolescents/young adults):

• Tremor (resting, intentional, or postural)

• Dysarthria and drooling

• Dystonia and rigidity

• Parkinsonian features

• Gait abnormalities

• Depression and anxiety

• Personality changes

• Declining academic/work performance

Other manifestations:

• Kayser-Fleischer rings (copper deposits in the cornea)

• Renal tubular dysfunction (Fanconi syndrome)

• Hemolytic anemia (Coombs-negative)

• Cardiomyopathy

• Arthropathy

Kayser-Fleischer (KF) rings are present in ~95% of patients with neurologic Wilson disease but only ~50% of those with the hepatic presentation. A slit-lamp examination by an ophthalmologist is required for detection, as the KF rings are often not visible to the naked eye.

Diagnosis

The diagnosis of Wilson disease is based on a combination of clinical findings and laboratory tests. Characteristic lab findings include low serum ceruloplasmin (this is because ATP7B helps add copper to ceruloplasmin, which would otherwise be degraded) and elevated 24-hour urine copper. Total serum copper is typically low because most of the copper in serum is bound to ceruloplasmin (which is low). However, the copper within tissues is high. Specifically, elevated hepatic copper content on liver biopsy is a highly specific test for Wilson disease. Genetic testing showing biallelic variants in ATP7B is confirmatory. The Leipzig scoring system combines clinical and laboratory findings to help establish the diagnosis, with a score ≥4 indicating a high likelihood of Wilson disease.

Management of Wilson Disease

The goals of treatment are to (1) remove excess copper from the body and (2) prevent re-accumulation of copper. Treatment is lifelong, as discontinuation leads to rapid copper re-accumulation and can precipitate acute liver failure.

Symptomatic patients should start with chelation therapy (penicillamine or trientine) to rapidly reduce copper load, then transition to zinc for maintenance therapy. Presymptomatic patients (like the sister in Question 103) should start with zinc therapy. Zinc helps prevent absorption of copper in the first place, and presymptomatic patients should remain asymptomatic as long as they continue with this therapy. Some patients with acute liver failure may require liver transplantation (which is curative for the hepatic form, as the donor liver has functional ATP7B). Patients should also avoid high-copper foods (shellfish, liver, chocolate, nuts, mushrooms), though dietary restriction alone is not sufficient.

Incorrect Answers

Question 102

Glycogen accumulation in hepatocytes (Choice A) is characteristic of the hepatic glycogen storage diseases (GSDs) such as GSD type I (von Gierke disease). GSD I present with hepatomegaly and hypoglycemia but does not cause neuropsychiatric symptoms or low ceruloplasmin. Iron deposition in hepatocytes (Choice B) describes hereditary hemochromatosis (HFE-related iron overload). Hemochromatosis typically presents in adults, is characterized by the accumulation of iron (not copper) in the liver, and does not cause the neuropsychiatric features seen in this patient. Reduction in the number of bile ducts (Choice D) is the classic histologic finding in Alagille syndrome, which presents in infancy with cholestasis and is associated with cardiac defects, butterfly vertebrae, and characteristic facies. The patient in this question was previously healthy without known congenital anomalies.

Question 103

Dietary copper supplementation (Choice A) is incorrect. Wilson disease is caused by copper excess, not deficiency. Copper supplementation would worsen the condition. Observation only (Choice C) is also incorrect. Presymptomatic treatment prevents organ damage (liver cirrhosis, brain injury) and is strongly recommended for all individuals with biallelic pathogenic variants, such as the sister mentioned in this question. Liver transplantation (Choice D) is reserved for acute liver failure or decompensated cirrhosis unresponsive to medical therapy. This intervention is not appropriate for an asymptomatic patient.

Learning objective

Wilson disease is an autosomal recessive disorder caused by biallelic pathogenic variants in ATP7B that results in excess accumulation of copper throughout the body. It typically presents in childhood or adolescence with liver disease, neuropsychiatric symptoms (tremor, dysarthria, behavioral changes), and Kayser-Fleischer rings. Diagnosis relies on low ceruloplasmin, elevated 24-hour urine copper, and elevated hepatic copper content on biopsy. Symptomatic patients are treated with copper chelation (helps remove copper from the body), while presymptomatic individuals receive zinc therapy (helps prevent copper absorption into the body). Early treatment prevents organ damage and is associated with a favorable prognosis.

2025 ABMGG General Exam Blueprint | V. Single gene inheritance → d) Single gene disorders → x) Other

2023 ABGC Exam Content Outline | Domain 1C. Genetic Conditions. (Wilson disease is one of the conditions listed on the ABGC self-study guide)

Additional resources

GeneReviews (Wilson disease)

Wilson disease (Nature Reviews Disease Primers)

Consider reviewing our previous post on Menkes disease (Questions 60-62), the other major disorder of copper metabolism.

This is the 2nd in a series of 3 posts related to gastrointestinal genetics. This month’s post will focus on a newborn with diarrhea.

We are also excited to announce that registration is open for the Winter ABGC board review bootcamp, which will take place between Dec 1, 2025 - Jan 22, 2026. This bootcamp is for genetic counselors preparing for the ABGC exam in February 2026. We will cover topics from all 5 domains on the ABGC content outline. An early-bird discount is available through Nov 30th, 2025. For more information and to register, please visit our website.

Please feel free to reach out to me (daniel@studyrare.com) with any questions about the bootcamp or the newsletter.

P.S. Happy Genetic Counselor Appreciation Day!

-Daniel

Questions

Question 100

A 10-day-old infant presents to the emergency department with severe watery diarrhea that began on day 2 of life. The parents switched from breast milk to soy-based formula on day 5 with no improvement. The infant appears severely dehydrated and has lost 20% of his birth weight. The infant is started on IV fluids, and the diarrhea persists despite stopping oral feeds. Which of the following processes is most likely impaired?

Question 101

Genetic sequencing is sent for the infant in Question 100, which confirms the diagnosis of congenital chloride diarrhea. Which of the following prenatal ultrasound findings is associated with this disorder?

Explanations

Question 100: Absorption of chloride ions

Question 101: Polyhydramnios

The infant discussed in these questions has classic features of congenital chloride diarrhea (CCD). CCD is an autosomal recessive condition caused by biallelic variants in SLC26A3, a gene that encodes an intestinal Cl⁻/HCO₃⁻ transporter. The mechanism of this disorder is illustrated and discussed in the image below.

Patients with CCD present with a combination of features that include:

• Watery, high-volume diarrhea from birth

• Diarrhea that persists even when patient does not take nutrition by mouth

• Severe dehydration and weight loss (this patient has lost 20% of his birth weight, which is significantly more than the expected 7-10% weight loss seen in healthy newborns during the first week of life)

• Excessive stool Cl⁻ loss leading to metabolic alkalosis (more about this mechanism here)

• Normal findings on small intestine biopsy (vs microvillus inclusion disease)

• Prenatal ultrasound may show dilated bowel loops and polyhydramnios (shown and discussed further below).

Management of CCD

The management of CCD is with lifelong oral chloride supplementation in the form of sodium chloride and potassium chloride. In addition to electrolyte replacement, patients require adequate hydration and monitoring of serum electrolytes, growth, and development. In contrast to certain other causes of congenital diarrhea (discussed below), there are no dietary restrictions in CCD, as this is not a food intolerance. If CCD is untreated, it can be fatal in the first few weeks of life. However, with appropriate management, the prognosis is overall favorable and patients can achieve normal growth and development.

Monogenic causes of congenital diarrhea

CCD is part of a family of congenital diarrheal disorders, which are inherited conditions that typically present in neonates and infants with severe diarrhea. These disorders often result from defects in the intestinal microvilli, which form the absorptive surface of the small intestine. The defects may affect the structure of the microvilli themselves (e.g., microvillus inclusion disease, which has a poor prognosis) or the function of enzymes and transporters found on the surface of the microvilli. The congenital diarrheal disorders that affect a single enzyme or transporter (rather than the entire structure of the microvilli) generally have a better prognosis and are in most cases treatable. The schematic below shows the architecture of intestinal villi and microvilli in more detail.

The table below compares CCD with other monogenic causes of congenital diarrhea. One important distinguishing feature of CCD is that the diarrhea persists despite stopping oral feeds and changing formulas.

Incorrect answer choices (Question 100)

(Choice A) Dietary disaccharides (disaccharide = two sugars linked together) such as lactose (the main sugar in breast milk), sucrose, and maltose must be broken down into monosaccharides (single sugars) before they can be absorbed by the intestines. If the disaccharides cannot be broken down due to a congenital enzyme deficiency, they remain in the intestinal lumen, attracting water and producing diarrhea. Typically, a dietary adjustment (e.g. removing the offending disaccharide) or stopping feeding will result in symptomatic improvement.

In the patient in question 100, the lack of improvement after switching to soy formula helps rule out congenital lactase deficiency, a disorder that presents in neonates after starting breast milk and that would be expected to improve with a lactose-free formula like soy. In addition, the lack of improvement of this patient after stopping oral feeds points away from congenital lactase deficiency.

(Choice C) Bile acids are an important component of bile, a substance that breaks down fats in the intestine. Patients with bile acid synthesis defects therefore have inadequate bile production and present with fat in the stool (steatorrhea), not watery diarrhea as was the case with our patient. Because bile is a breakdown product of bilirubin, patients who are unable to synthesize bile will also have hyperbilirubinemia and cholestatic jaundice (elevated conjugated bilirubin, hepatomegaly), and there was no mention of jaundice in this patient. Furthermore, the diarrhea in a bile acid synthesis defect would be expected to improve when dietary fat intake is eliminated, unlike in our patient.

(Choice D) The transport of dietary monosaccharides is disrupted in glucose-galactose malabsorption. This is a disorder caused by defects the sodium-glucose cotransporter (encoded by SLC5A1) that absorbs glucose and galactose from the intestinal lumen. Patients present in the neonatal period with severe watery diarrhea similar to CCD. However, unlike the patient in this question, patients improve after stopping oral feeds. Treatment is with a formula containing fructose, which uses a different transporter to enter the body.

Answer choices (Question 101)

Patients with CCD may have signs on prenatal ultrasound including dilated bowel loops (see image below) and polyhydramnios (Choice D). This is because in CCD, large volumes of fluid are secreted into the fetal intestinal lumen, which enlarges and produces a characteristic “honeycomb” pattern seen on ultrasound. The excess fluid in the intestinal lumen is then emptied into the amniotic cavity, causing polyhydramnios.

(Choice A) An absent stomach bubble is seen in esophageal atresia, not in CCD.

(Choice B) Increased nuchal translucency suggests chromosomal anomalies, especially aneuploidy (e.g., trisomy 21, Turner syndrome), and may be a sign of a lymphatic malformation. Increased nuchal translucency is not characteristic of congenital diarrheal syndromes.

(Choice C) Oligohydramnios is associated with renal agenesis or urinary tract obstruction. In contrast, CCD increases the fluid output into the amniotic space, causing polyhydramnios.

Learning objective

Congenital chloride diarrhea (CCD) is caused by the impaired absorption of chloride ions from the intestinal lumen into the body. Patients present with watery diarrhea in the neonatal period that persists despite stopping oral feeds and/or altering formula. Key diagnostic features include very high stool chloride (>90 mEq/L) and hypochloremic metabolic alkalosis. Prenatal ultrasound may show dilated bowel loops and polyhydramnios. Treatment requires lifelong electrolyte supplementation, and no dietary restriction is required.

2025 ABMGG General Exam Blueprint | V. Single gene inheritance → d) Single gene disorders → x) Other

2023 ABGC Exam Content Outline | Domain 1C. Genetic Conditions

Additional resources

The genetic architecture of congenital diarrhea and enteropathy (NEJM, 2025)

Honeycomb fetal abdomen: characteristic sign of congenital chloride diarrhea (2016)

This is the first in a series of three posts related to gastrointestinal system.

In this first post, we will be discussing a case of failure to pass meconium. This occurs when a newborn does not have a bowel movement in the first 24-48 hours of life.

If you would like to support our work, the best way to do so is to share this post with others who are interested in learning more about genetics.

Please feel free to reach out (daniel@studyrare.com) with any questions about the post or suggestions. I hope you have a great week!

-Daniel

Questions

Question 98

A 2-day-old boy is admitted to the hospital for bilious emesis and abdominal distension. He has not passed meconium. Physical exam shows a distended abdomen, and digital rectal exam produces explosive passage of stool. A rectal suction biopsy shows the absence of ganglion cells. This patient’s symptoms result from an abnormality in which embryologic process?

Question 99

The patient in question 98 is diagnosed with Hirschsprung disease. His birth weight and length are within normal limits, and no other abnormalities are noted on physical exam. A variant in which gene would be MOST consistent with the likely diagnosis?

Explanations

Question 98: Neural crest migration

Question 99: RET

Mechanism of Hirschsprung disease

Hirschsprung disease is a disorder that results from failed migration of neural crest cells (Question 98, Choice B) into the distal colon. Neural crest cells are an important embryonic tissue that gives rise to peripheral neurons, including those within the gastrointestinal system. The neurons in the colon are known as ganglion cells. Therefore, the hallmark finding in Hirschsprung is the absence of ganglion cells (aganglionosis) within the walls of the colon.

Without ganglion cells in the colon, coordinated peristalsis cannot occur and produces a functional obstruction. This in turn can cause a megacolon, or dilation of the colon (see image below). Hirschsprung disease is therefore also known as congenital aganglionic megacolon (congenital = present from birth; aganglionic = without ganglia; and megacolon = dilation of the colon).

Clinical features of Hirschsprung disease

Patients with Hirschsprung disease present as newborns with failure to pass meconium (differential diagnosis discussed further below). Classic findings in newborns include signs of intestinal obstruction (bilious vomiting, abdominal distension) and the “explosive” passage of stool following a rectal exam. Some patients who are more mildly affected can present in childhood with severe and chronic constipation.

The diagnosis of Hirschsprung is made with a rectal suction biopsy (as was the case in Question 98) that shows the absence of ganglion cells on microscopy. Definitive treatment involves surgical resection of the aganglionic segment, while supportive measures for constipation (e.g. laxatives, enema) can help manage milder cases.

Isolated vs syndromic Hirschsprung

In about 2/3 of cases, Hirschsprung disease is isolated, meaning that there are no other symptoms or systems that are affected aside from the colon. The remaining 1/3 of cases occur as part of an underlying multi-systemic disorder. This distinction helps guide genetic testing and risk counseling.

Isolated Hirschsprung

While most isolated cases of Hirschsprung are multifactorial (meaning no single pathogenic variant is identified), loss-of-function variants in RET are the most common monogenic cause of isolated Hirschsprung disease (Question 99, Choice C). These variants are inherited in an autosomal dominant manner with incomplete penetrance (some patients with a pathogenic variant are asymptomatic) and variable expressivity (two individuals with the same variant may have different severity of disease). Because of this inheritance pattern, consider asking patients about a family history of constipation. Hirschsprung is more common in males than females for unknown reasons, and more severe cases (e.g. longer aganglionic segment) are associated with a higher risk of recurrence.

Syndromic Hirschsprung

Hirschsprung disease may also occur as part of several multi-systemic disorders. Examples include:

• Waardenburg syndrome, type 4 (hypopigmentation + sensorineural hearing loss; due to variants in SOX10, EDNRB, or EDN3)

• Mowat-Wilson syndrome (intellectual disability, distinctive facial features; ZEB2)

• Trisomy 21 (short stature, characteristic facies, hypotonia)

Because of these associations, genetic testing is warranted in any patient with Hirschsprung disease, particularly if there are dysmorphic features or developmental concerns.

Genotype-phenotype correlation (RET)

As discussed above, loss-of-function variants in the RET proto-oncogene (Question 99, Choice C) are the most common monogenic cause of isolated Hirschsprung disease. In contrast, gain-of-function variants in this same gene cause multiple endocrine neoplasia type 2 (MEN2), a syndrome that increases the risk for a variety of cancers. However, this association is likely more complex. Some patients with Hirschsprung have later developed MEN2-related cancers (e.g. medullary thyroid carcinoma), and the exact relationship between RET variants and these phenotypes requires further study (see this article for additional details).

Differential diagnosis of failure to pass meconium

There are several potential mechanisms that could lead to the failure to pass meconium in a newborn, which was the clinical scenario in Question 98. Possible causes include structural malformations that block the passage of stool (e.g. imperforate anus), functional obstruction (due to impaired GI motility), and endocrine causes (hypothyroidism) that also impair GI motility. The table below lists some of these causes.

Incorrect answer choices (Question 98)

Many developmental GI anomalies can be traced back to the embryonic gut, which consists of 3 segments: foregut, midgut, and hindgut (see image). The foregut forms the trachea (windpipe), esophagus, stomach, and first part of the duodenum. Defects in division of the foregut (Choice D) can cause a tracheoesophageal fistula, which is an abnormal connection between the esophagus and the trachea. The midgut forms the structures from the duodenum to the distal 2/3 of the colon. Abnormalities in the rotation of the midgut (Choice C), a normal developmental process that is complete around 10-12 weeks of gestation, cause malrotation with volvulus, a condition that can present with bilious emesis. The hindgut forms the distal portion of the colon and rectum. Because the hindgut is the farthest distance from where neural crest cells originate, this segment is most vulnerable to incomplete migration and aganglionosis and is therefore most often affected in Hirschsprung disease. Impaired neural tube closure (Choice A) results in spina bifida or anencephaly. While some patients with neural tube defects may have impaired bowel function, this is secondary to spinal cord dysfunction rather than a primary GI abnormality.

Incorrect answer choices (Question 99)

Biallelic variants in CFTR (Choice A) are associated with cystic fibrosis, which can present with meconium ileus (intestinal obstruction due to thick, viscous stool) and bilious emesis. However, in a patient with cystic fibrosis, a rectal suction biopsy would show the presence of ganglion cells. Variants in PAX3 (Choice B) cause Waardenburg syndrome type 1 and type 3, which are characterized by sensorineural hearing loss and pigmentary abnormalities (e.g. white forelock). While some forms of Waardenburg syndrome are associated with Hirschsprung disease, these are typically caused by variants in SOX10, EDNRB, or EDN3 (Waardenburg syndrome type 4), not PAX3. Furthermore, the patient in Question 99 has isolated Hirschsprung without pigmentary or other anomalies. Variants in ZEB2 (Choice D) are associated with Mowat-Wilson syndrome, which includes Hirschsprung disease plus intellectual disability, microcephaly, distinctive facial features (pointed chin, wide-spaced eyes), and multiple congenital anomalies. The patient in Question 99 has isolated Hirschsprung with no dysmorphic features or other developmental anomalies.

Learning objective

Hirschsprung disease results from failure of neural crest cell migration into the distal colon. This leads to absence of ganglion cells (aganglionosis) and functional bowel obstruction. Patients present in the newborn period with failure to pass meconium, bilious vomiting, abdominal distension, and explosive passage of stool after rectal examination. The diagnosis is confirmed by rectal suction biopsy showing absence of ganglion cells. Loss-of-function variants in RET are the most common monogenic cause of isolated Hirschsprung disease.

2025 ABMGG General Exam Blueprint | V. Single gene inheritance → d) Single gene disorders → x) Other

2023 ABGC Exam Content Outline | Domain 1A, 1B & 1C → Clinical information, human development, and genetic conditions

Additional resources

Hirschsprung disease (5-minute video)

Case 718 - Genetic Testing in Hirschsprung (Univ of Pittsburg, Dept of Pathology)

Thompson & Thompson Genetics and Genomics in Medicine, 9th Edition (Chapter 9)

Molecular Genetic Anatomy and Risk Profile of Hirschsprung’s Disease (NEJM, 2019)

This is the third in a series of three posts related to prenatal genetics.

In the first post of this series, we discussed how maternal disorders can adversely impact fetal development (e.g. maternal PKU, maternal diabetes). This post focuses on the opposite: fetal genetic disorders that affect the mother’s health.

Also, we have extended our early-bird deadline for the 2025 ABGC board review bootcamp to Fri, June 6th, 2025. Please consider signing up before this date to take advantage of the discount. The bootcamp will take place between June 12th - July 24th, 2025 and is for genetic counselors taking the ABGC exam in August 2025. We also have a separate ongoing bootcamp for laboratory and clinical geneticists preparing for the ABMGG exam. For more information and to register, please visit our website.

Please feel free to reach out to me (daniel@studyrare.com) with any questions about the bootcamp or the newsletter. I hope you have a great week!

-Daniel

Questions

Question 96

A 28-year-old G2P1 woman presents at 24 weeks gestation for a prenatal visit. Over the last several weeks, she has developed facial hair, new-onset acne, and a deeper voice. She is otherwise generally healthy, and her first pregnancy was uneventful. Laboratory testing in the mother reveals elevated androgens and low estriol. An ultrasound of the fetus shows ambiguous genitalia, and an amniocentesis shows a 46,XX karyotype. Which of the following disorders affecting the fetus best explains the maternal and fetal findings?

Question 97

A 33-year-old G1P0 woman presents at 34 weeks gestation with new-onset right upper quadrant pain, nausea, vomiting, and fatigue. Her blood pressure is 140/90. Laboratory studies show elevated liver transaminases, low platelets, and hypoglycemia. A prenatal ultrasound shows a female fetus with no structural abnormalities. Which of the following fetal conditions is most likely responsible for the symptoms seen in the mother?

Explanations

Question 96: Aromatase deficiency

Question 97: LCHAD deficiency

Fetal genetic disorders that affect maternal health

Most genetic disorders that affect the fetus do not directly impact the pregnant mother’s health. However, there are a handful of fetal disorders that do. These generally fall into one of two categories: disorders of hormone metabolism and disorders of fatty acid metabolism. Hormones produced by the fetus or by the placenta (which is mostly fetal in origin) can enter the maternal circulation. These hormones, particularly estrogen, support fetal development and promote maternal adaptations to pregnancy (e.g. uterine growth, breast development). In addition, certain fetoplacental hormones serve as biomarkers of fetal health and form the basis of the quad screen in pregnancy (e.g. alpha-fetoprotein, hCG, estriol, and inhibin-A). Maternal symptoms that result from fetal genetic anomalies typically resolve after delivery.

Placental aromatase converts androgens to estrogens

During pregnancy, the fetal adrenal glands produce large amounts of androgens. These androgens travel to the placenta, where they are converted into estrogens by the placental enzyme aromatase (aka estrogen synthase, encoded by CYP19A1). Most of the circulating estrogens in both the mother and the fetus (particularly in later trimesters) are generated by the synergy between the fetal adrenal glands and placental aromatase.

Aromatase deficiency results in excess androgens

When there is a deficiency of placental aromatase (e.g. due to biallelic variants in CYP19A1 in the fetus), androgens from the fetal adrenals are not converted to estrogen and instead enter the maternal circulation directly as androgens (e.g. testosterone). This causes the virilization (aka masculinization) seen in the mother in Question 96 that includes voice deepening, the development of facial hair, male-pattern baldness, and clitoromegaly. The excess androgens also remain in the fetal circulation, which can result in a 46,XX fetus with ambiguous genitalia. (Note that ultrasound in a 46,XY male fetus with aromatase deficiency is typically normal).

Laboratory studies in aromatase deficiency show elevated androgens and low estrogen levels in the maternal circulation (see diagram below). During the prenatal period, this condition may also present with low estriol as part of the second trimester maternal serum screen. The combination of elevated maternal androgens, low maternal estrogen, maternal virilization, and ambiguous genitalia in a 46,XX fetus all point toward aromatase deficiency.

💡 To remember the function of aromatase, look at the first and last letters. AromatasE: Androgen → Estrogen

Acute fatty liver of pregnancy (AFLP) and LCHAD deficiency

Question 97 presents a case of acute fatty liver of pregnancy (AFLP), a rare and serious complication that typically occurs in the third trimester. The mother’s symptoms (right upper quadrant pain, nausea, vomiting, fatigue, hypertension) combined with laboratory findings (elevated liver enzymes, low platelets, hypoglycemia) are classic for AFLP. These symptoms can be life-threatening for the mother (e.g. acute liver failure), and the treatment for AFLP is immediate delivery of the fetus.

About 20% of cases of AFLP are associated with fetal long-chain 3-hydroxyacyl-CoA dehydrogenase (LCHAD) deficiency. This condition impairs mitochondrial fatty acid β-oxidation, a process that converts fatty acids into acetyl-CoA, a versatile cellular energy precursor. LCHAD deficiency is caused by biallelic variants in the HADHA gene, which encodes the α-subunit of the mitochondrial trifunctional protein complex that is responsible for several steps in fatty acid β-oxidation.

Testing for LCHAD deficiency involves sending a maternal plasma acylcarnitine profile (which will show elevated long-chain 3-hydroxyacylcarnitine species) and an amniocentesis to obtain a sample for genetic testing of the fetus. In addition, newborn screening (which includes the equivalent of an acylcarnitine profile) after delivery will flag positive (see this video for more on the postnatal complications of LCHAD). Prenatal ultrasound in a fetus with LCHAD deficiency is typically normal.

While the exact mechanism by which LCHAD deficiency affects the mother is unclear, there are two leading hypotheses. First, excessive hydroxyacyl derivatives produced by the affected fetus may cross the placenta and cause direct hepatic toxicity. Second, maternal heterozygosity* for LCHAD deficiency may cause hepatic insufficiency that predisposes to AFLP.

💡 *When a child is found to have an autosomal recessive disorder like LCHAD deficiency, the parents are almost always heterozygous carriers for that disorder.

Incorrect answers

Question 96

Androgen insensitivity syndrome (Choice A) typically presents with external female genitalia in a patient with a 46,XY karyotype. This is due to the inability of the body to respond to androgens, which promote the development of male genitalia in utero. Patients with a 46,XX karyotype would not be expected to have ambiguous genitalia, and maternal virilization does not occur during pregnancy. Steroid sulfatase deficiency (X-linked ichthyosis) (Choice C) affects estrogen metabolism and can present with a low estriol on maternal serum screening. It does not cause maternal or fetal virilization. Smith-Lemli-Opitz syndrome (Choice D) is a cholesterol biosynthesis disorder that causes multiple congenital anomalies in the fetus. In some cases, a fetus with a 46,XY karyotype can present with female-appearing or ambiguous genitalia due to the deficiency of sex hormones, which are derived from cholesterol. While SLO can present with low estriol on maternal serum screening, this condition does not cause maternal virilization or ambiguous genitalia in a 46,XX fetus.

Question 97

Antley-Bixler syndrome (ABS) (Choice A) is a skeletal dysplasia that is associated with short, bowed femurs and ambiguous genitalia on fetal ultrasound. One of the causes of ABS is deficiency of cytochrome P450 oxidoreductase, which plays an important role in steroid metabolism. ABS does not cause AFLP, and the absence of major abnormalities on ultrasound in this question points away from this diagnosis. 21-hydroxylase deficiency (Choice B) is the most common cause of congenital adrenal hyperplasia and can cause ambiguous genitalia in 46,XX fetuses due to excess adrenal androgens. It can cause adrenal insufficiency with hypotension in a newborn but not AFLP in the mother. A partial hydatidiform mole (Choice C) can cause maternal hypertension due to excessive production of beta-HCG. However, ultrasound would show a cystic placenta and a growth-restricted fetus, and genetic testing of the fetus would show a triploid karyotype (with 69 chromosomes), not a diploid karyotype. In addition, molar pregnancies typically become symptomatic and are diagnosed in the first trimester, not the third trimester.

Learning objective

There are several disorders that, when present in the fetus, directly affect the pregnant mother’s health. Examples include aromatase deficiency, which should be considered when a pregnant woman develops virilization in the setting of a 46,XX fetus with ambiguous genitalia. The combination of elevated maternal androgens and low estrogens in this clinical context is diagnostic. Another example is fetal LCHAD deficiency, a fatty acid oxidation disorder associated with AFLP in the mother. In most cases, symptoms in the mother that are caused by a genetic disorder in the fetus resolve with delivery of the fetus and placenta.

2025 ABMGG General Exam Blueprint | V. Single gene inheritance → d) Single gene disorders → ix) Metabolic disease & VII. Reproductive Genetics

2023 ABGC Exam Content Outline | Domain 3C. Reproductive Risk Management → 3. Prenatal screening & Domain 1B. Human development → 1. Fetal development

Additional resources

LCHAD deficiency (GeneReviews)

LCHAD deficiency (video)

Aromatase deficiency

This is the 2nd in a series of 3 posts related to prenatal genetics. This month’s post will focus on prenatal ultrasound findings.

We are also excited to announce that registration is open for the 2025 ABGC board review bootcamp, which will take place between June 12th - July 24th, 2025. This bootcamp is for genetic counselors taking the ABGC exam in August 2025. We will cover topics from all 5 domains on the ABGC content outline. An early-bird discount is available through June 1, 2025. For more information and to register, please visit our website.

Please feel free to reach out to me (daniel@studyrare.com) with any questions about the bootcamp or the newsletter. I hope you have a great week!

-Daniel

Questions

Question 94

A woman at 10 weeks gestation presents for an evaluation. This is her first pregnancy, and her blood type is O positive. Ultrasound imaging of her fetus shows a large, multilocular, fluid-filled cavity behind the neck. Which of the following is the most appropriate next step in management?

Question 95

A woman at 20 weeks gestation presents for a second trimester ultrasound. Both she and her partner are known carriers of cystic fibrosis (CF). Which of the following findings on prenatal ultrasound would raise concern that the fetus has CF?

Explanations

Question 94: Offer chorionic villus sampling

Question 95: Echogenic bowel

Ultrasound is an imaging technique used throughout pregnancy to monitor fetal health and to detect fetal anomalies. An ultrasound is like a flashlight 🔦 that uses sound waves (instead of light waves) to illuminate the anatomy of internal structures. Denser structures (like bone) reflect more sound waves and appear brighter (more echogenic), while less dense structures (like fluid) appear darker (less echogenic). The fact that ultrasound is non-invasive, quick to perform, and does not involve radiation exposure makes it ideal for use in the prenatal setting. In addition to looking at the fetus, a prenatal ultrasonographer looks at the placenta, umbilical cord, amniotic fluid volume, uterus, uterine adnexa, and fetal membranes for any abnormalities. Here we will focus on ultrasound anomalies involving the fetus.

Ultrasound imaging of the fetus is divided into fetal biometry and the anatomy survey. Think of these like the vital signs and physical exam, respectively, for the fetus. Fetal biometry measures the length, head size, and estimated fetal weight, while the anatomy survey scans the organ systems of the fetus from head to toe. While major fetal anomalies can be seen in the first trimester, many minor anomalies become visible only as the fetus grows. This is why serial ultrasounds are performed throughout pregnancy.

There are two broad categories of fetal anomalies on prenatal ultrasound: major structural anomalies and “soft markers”. Major structural anomalies, like the large, multilocular, fluid-filled cavity mentioned in Question 94, are clear-cut findings that warrant additional diagnostic testing. This usually involves direct sampling of placental or fetal tissue (discussed further below). In contrast, “soft markers” are more subtle findings that may or may not be connected to an underlying disease process (and that may even self-resolve). In some cases, a “watch and wait” approach can be employed after a soft marker is identified (particularly if there are no other anomalies), though patients may also choose to proceed with diagnostic testing.

Cystic hygroma: An example of a major structural anomaly

The presence of a large, multilocular, fluid-filled cavity near the fetal neck is consistent with a cystic hygroma, which should raise concern for an underlying genetic disorder. Cystic hygromas are lymphatic malformations seen in genetic conditions such as Noonan and Turner syndrome that affect lymphatic development. They can also be seen in trisomies 13, 18, and 21. Given the gestational age of the patient in Question 94, the most appropriate next step is to offer chorionic villus sampling (CVS), a placental biopsy done at 10–13 weeks gestation to test for genetic causes of the cystic hygroma.

Isolated echogenic bowel: An example of a soft marker

Isolated echogenic bowel (Question 95) is an example of a soft marker seen in the 2nd trimester that is associated with a broad differential diagnosis. Echogenic bowel can be seen in trisomy 21, congenital infections like cytomegalovirus (CMV), and cystic fibrosis. Echogenic bowel may also represent swallowed intra-amniotic blood or dense meconium (fetal stool). In CF, the same chloride channel defect that causes thick, sticky mucus in the lungs also creates viscous intestinal secretions. This results in dense stools that appear bright on the prenatal ultrasound and that obstruct the intestines of newborns with CF (the latter is known as meconium ileus).

Chorionic villus sampling (CVS) versus amniocentesis

CVS and amniocentesis are procedures used to obtain tissue for diagnostic (not screening) purposes. In both cases, a needle is inserted into either the placenta (CVS) or the amniotic sac (amniocentesis) to obtain samples for cell culture and/or genetic testing. CVS can be performed earlier in pregnancy (late 1st trimester) than amniocentesis (early 2nd trimester), which can help if an earlier diagnosis is desired. Because the placenta is mostly derived from the fetus (and not the mother), it is a reliable proxy for genetic testing in the fetus in most cases. However, the placenta can sometimes have a different genetic makeup than the fetus. The term for a genetic abnormality restricted to the placenta is confined placental mosaicism, which can cause genetic test results to differ between the placenta and fetus. Note that NIPT (noninvasive prenatal testing), like CVS, is also a type of genetic testing performed on placental DNA.

💡 Remember that an amniocentesis samples the amniotic fluid (fluid that surrounds the baby), while chorionic villus sampling obtains tissue from the placenta, which contains microscopic projections called chorionic villi.

Incorrect answers (Question 94)

While scheduling a follow-up ultrasound (Choice A) is indicated for monitoring fetal health, the finding of a multilocular cystic hygroma increases the risk of an underlying monogenic disorder and warrants diagnostic testing now. Maternal serum screening for the presence of antibodies against Rh and other blood cell antigens (Choice B) is indicated in cases of suspected immune hydrops fetalis, which can present with increased nuchal translucency and fetal edema (but not a cystic hygroma). The fact that this is the mother’s first pregnancy, along with the mother’s Rh-positive status, also point away from a diagnosis of immune hydrops fetalis. Referral to pediatric surgery (Choice C) is premature without first establishing a diagnosis, as management decisions will depend on the underlying etiology of the findings.

Incorrect answers (Question 95)

The choroid plexus is a structure found within the ventricles of the brain that produces cerebrospinal fluid (CSF). Choroid plexus cysts (CPC, Choice A) form when pockets of CSF become trapped within the choroid plexus. CPC are common and usually benign when present in isolation, though can also be seen in trisomy 18, where they present alongside other findings. CPC are not associated with cystic fibrosis. Single umbilical artery (Choice B) is a soft marker associated with genitourinary defects and may be associated with aneuploidy or fetal growth restriction. A single umbilical artery is not associated with cystic fibrosis. Renal pyelectasis (Choice D), or dilation of the fetal renal pelvis, is often a transient finding and is considered a soft marker for trisomy 21. It is not associated with cystic fibrosis.

Learning objectives

Ultrasound is a technique used throughout pregnancy to monitor fetal well-being and detect fetal anomalies. Fetal anomalies on ultrasound include “soft markers” like echogenic bowel as well as major structural anomalies such as cystic hygromas. Diagnostic testing with chorionic villus sampling (CVS) or amniocentesis should be offered when major structural anomalies are identified on ultrasound in order to look for a genetic basis of the anomalies.

2025 ABMGG General Exam Blueprint | VII. Reproductive Genetics → b) Non-invasive prenatal screening → iii) Ultrasound & c) Invasive prenatal testing

2023 ABGC Exam Content Outline | Domain 3C. Reproductive Risk Management → 3. Prenatal screening & 4. Prenatal diagnostic procedures

Additional resources

A list of fetal anomalies by system (from the fetal medicine foundation)

A table showing examples of major structural anomalies and soft markers by system:

Today is Day 4 of the American College of Medical Genetics (ACMG) Annual Meeting in Los Angeles. In this podcast, I discuss a few sessions for today (Fri, March 21) that may be of interest to trainees.

1. The first session is "How to Get Your Content Published" (10:30 AM). This session is led by a representative from Elsevier, a large publisher. While publishing is an important way to get credit for your academic work, the process can be time-consuming and frustrating. Reasons for this include navigating complex submission systems, coordinating with busy co-authors, and balancing writing with other responsibilities. Hopefully, this session will offer some insight into making the publication process more efficient.

2. At 1:30 PM, there is a session titled “2025 Student Workshop: Pathways to Careers within Medical Genetics and Genomics.” This session is aimed at students and early-career professionals exploring career options in genetics. Speakers include Dr. Miriam Blitzer, the immediate past CEO of ABMGG, as well as representatives from clinical genetics, laboratory genetics, and genetic counseling. This seems like a great opportunity for undifferentiated students to connect with experts across a variety of career paths in genetics.

3. Also at 1:30 PM, there is a session titled “N-of-1 ASO Therapies: The How-Tos of Implementation.” ASO stands for “Antisense Oligonucleotides,” which are short strands of nucleotides that degrade specific mRNA transcripts or promote exon skipping. N-of-1 refers to a clinical trial that involves a single patient rather than a large study population. N-of-1 trials involving an ASO are appropriate for patients with a pathogenic variant causing an extremely rare and progressively fatal disorder with no other treatment options. But why ASOs specifically? ASOs target the molecular mechanism of disease, which offers the potential for a precise therapeutic intervention. The design and synthesis of ASOs is also more straightforward relative to other targeted genetic therapies. In addition, the FDA has guidance on using custom ASOs in N-of-1 settings, which provides a regulatory pathway for these therapies to help treat rare monogenic disorders.

4. At 3:30 PM, there’s a session titled “Current Practice and Future Prospects for Autologous Ex Vivo Gene Treatment and HSCT in Lysosomal Storage Disease.” Ex vivo gene therapy involves removing the patient’s bone marrow cells, modifying them with a genetic therapy (in this case, with the intent to replace the missing enzyme), and then reinfusing the cells back into the patient. This approach is used for treating certain lysosomal storage disorders, as the patient’s own genetically-modified stem cells can now produce functional enzymes to correct the underlying metabolic defect. An example of this therapy is atidarsagene autotemcel (Lenmeldy), an FDA-approved therapy used to treat metachromatic leukodystrophy. For those interested in gene therapy and hematopoietic stem cell transplantation (HSCT), this session will be valuable.

5. Finally, at 5:30 PM, there are several concurrent “Diagnostic Challenge” sessions. These sessions are split into different categories: pediatric & prenatal, laboratory genetics, and adult & cancer genetics. Each session features a panel of experts who will discuss particularly challenging or unsolved cases. These sessions will offer an opportunity to hear how experts approach and think through complex diagnoses.

Please feel free to share your thoughts, and see you in the next episode!

Daniel

Today is Day 3 of the American College of Medical Genetics (ACMG) Annual Meeting.

In this podcast, I discuss a few sessions for today (Thurs, March 20) that may be of interest to trainees. Of note, there are several sessions in the late morning that are specifically geared towards mentoring and networking.

1. The first session is called “Speed Mentoring” (10:15 am). The people you meet at this conference—especially those at a similar training stage—will likely be your colleagues for the next several decades, so it is a good idea to start building connections now. This event is a structured way to start making those connections.

2. The next session is called “Cracking the Codes: How CPT Codes and RVUs Affect Reimbursement and Credit for the Work You Do” (10:30 am). This topic is not often covered in training but it is important for folks working in a clinical setting. This is because both geneticists and genetic counselors face pay gaps relative to other medical specialties. In order to advocate for fair compensation, we need to have a solid understanding of how we are paid.

3. At 11:45 AM, there’s the “Early Career Genetic Mentor Luncheon.” This session will feature professionals across different specialties—clinical genetics, prenatal genetics, cancer genetics, biochemical genetics, and laboratory genetics. If you are considering different career options or want to see different ways in which you can apply your genetics expertise, this is a good session to attend.

4. In the early afternoon (1:30 PM) there will be a session on the forthcoming ACMG standard for variant classification (version 4.0). Variant interpretation is central to what many of us do, and staying up to date on the variant classification guidelines and how they evolve is beneficial.

5. In the late afternoon (5:10pm) there is a session titled “Fetal Fentanyl Syndrome: A Teratogen-Induced Embryopathy Masquerading as a Metabolic Disease.” Fentanyl, among other opioids, inhibits the enzyme 7-dehydrocholesterol reductase, which is the same enzyme that is deficient in Smith-Lemli-Opitz syndrome (SLO). Patients exposed to fentanyl overlap phenotypically (e.g. 2-3 toe syndactyly, genitourinary abnormalities, cleft palate) and also biochemically (elevated 7-dehydrocholesterol) with SLO. With opioid being use so prevalent in the U.S., this is an important diagnosis to keep on your radar.

Feel free to share your thoughts, and see you in the next post!

Daniel

Today is Day 2 of the American College of Medical Genetics (ACMG) Annual Meeting in Los Angeles. In this podcast, I discuss a few sessions for today (Wed, March 19) that may be of interest to trainees:

1. The “Early Genetics Trainee and Faculty Forum (Clinical Genetics) - Where Are We Headed?” (8:00 am) will feature Dr. Mira Irons, president of ACMG, and Dr. Sean McCandless, section head of genetics at Colorado Children’s Hospital, among others. They will be discussing the future role of clinical geneticists, especially as genetic testing becomes more accessible. How might our specialty evolve beyond ordering and interpreting genetic tests?

2. The “Foundation Awards & Presidential Plenary Session” (10:00 AM) is the one session today where everyone at the conference will be gathered. The theme this year is “Genetics in the Media” and will covering how genetics is portrayed in film and social media. Speakers include Dr. Susan Klugman, immediate past president of ACMG.

3. Over lunch, there are a number of sponsored sessions to consider. One session titled “Getting the Most Out of Your Genome” (sponsored by Illumina) may be of interest. Illumina, a leader in short-read sequencing technology, will discuss the role of clinical RNA sequencing. One example of when clinical RNA sequencing can be useful is when dealing with a variant of uncertain significance (VUS) that is suspected to impact splicing. If you are interested in laboratory genetics or variant interpretation, this session is worth checking out.

4. In the early afternoon (1:30 pm), there is a session titled “Evolution of Cytogenomic Technology – Optical Genome Mapping”. Optical genome mapping (OGM) is a technique that detects structural variants (e.g. insertions, deletions, inversions, and translocations) across the genome at high resolution (kilobases). I think of this technology of being like an ultra-detailed karyotype plus microarray in one. Because of this, OGM could be used by cytogenetics laboratories in undiagnosed patients with suspected Mendelian disorders as well as for detecting structural variants in somatic cancers.

5. In the mid-afternoon (3:30pm), there is a session titled "Diagnostic Dilemmas from the Undiagnosed Diseases Network (UDN)." The UDN is a group of researchers across multiple academic medical centers that help find diagnoses for patients with suspected monogenic disorders. To do this, they apply technologies like RNA sequencing, metabolomics, proteomics, and model organism studies on a research basis to patient samples. Patients have to apply to the UDN (not all are accepted due to limited resources), and a letter from a physician is required. If you have patients where you suspect they have a monogenic disorder despite negative exome sequencing, this is a good resource to keep in mind.

6. In the late afternoon, there will be time to browse the exhibit hall, and the first round of the Geneius challenge (6 pm) will begin. The Geneius challenge involves trainees who are competing for a prize based on how quickly they can respond to questions about genetics.

Feel free to share your thoughts, and see you in the next post!

Daniel

Welcome. My name is Daniel Piqué. I am a clinical geneticist and I write the StudyRare newsletter, which contains practice questions for genetics board exams.

StudyRare is starting a podcast with the goal of hosting an audio version of the newsletter posts as well as sharing additional educational content relevant for genetics and genetic counseling trainees.

The StudyRare Podcast is now available on Spotify and Apple podcasts. You can also find our podcast’s homepage by going to studyrare.substack.com and clicking on the “StudyRare Podcast” tab at the top.

This week, I am at American College of Medical Genetics (ACMG) meeting in Los Angeles. I wanted to use this opportunity to highlight a few talks for those who aren’t able to make it or who are still planning their schedule.

In this podcast, I discuss 3 sessions that I think are interesting for trainees on the first day of the conference (Tue, Mar 18). These talks include:

1. The “Genomic Explorations” workshop, which is divided into 2 parts: cytogenetics (10am-1pm) and molecular genetics (2pm-5pm). While the workshop is intended for laboratory geneticists, it seems to be a great opportunity for anyone looking to brush up on their knowledge of laboratory techniques. The workshop will be led by over a dozen faculty trained in laboratory genetics including the newly-appointed CEO of ABMGG, Dr. Azra Ligon.

2. A session titled “Back to Basics: The Physical Exam is the Cornerstone of Precision Medicine.” This session will cover the fundamentals of the genetics physical exam, an important part of the genetics evaluation. A thorough physical exam can help narrow your differential diagnosis, guide what testing you should send, and help with variant interpretation. In some cases (e.g. tuberous sclerosis, NF1), a diagnosis can even be confirmed based on the history and physical exam alone. The panel session features 4 geneticists who will each cover one topic: nose/philtrum, trunk/limbs, hands, and pigmented lesions.

3. A session titled “Challenging No More: Simultaneously Tackling CMRGs and Methylation,” sponsored by Oxford Nanopore, will explore approaches to sequencing Challenging Medically Relevant Genes (CMRGs). These genes are difficult to analyze with traditional short-read sequencing methods due to repetitive sequences or the presence of pseudogenes (e.g., SMN1/SMN2 in spinal muscular atrophy). Oxford Nanopore is one of 2 main companies (PacBio being the other) that develop long-read sequencing technology (for reference, Illumina is the main company that develops short-read sequencing technology). Long-read sequencing has the potential to consolidate many of the assays that we send separately (e.g. DNA sequence analysis, structural variant analysis, and DNA methylation) into a single test.

Even if you are not attending, you can still view the full program here.

If you see me at the conference, please feel free to say hello. It would be great to connect in person!

Daniel

-Daniel

https://studyrare.substack.com/p/20221024-questions-1-2

This is the 1st in a series of 3 posts related to prenatal genetics. This month’s post will focus on teratogens.

While it is tempting to study teratogens as a long list, there are a few principles that we discuss in this post that can help structure your learning on this topic. We also uploaded a video to YouTube to complement the written post (“Top 30 teratogens for board exams”) .

We are also excited to announce that registration is open for our new ABMGG board review bootcamp, which will take place between March 25 - June 19, 2025. This bootcamp is for clinical and laboratory geneticists taking the ABMGG general exam in August 2025. We will cover topics from all 11 domains and 115 subdomains on the ABMGG content outline. An early-bird discount is available through March 24, 2025. For more information and to register, please visit our website.

Note that we will share information about the schedule for our summer ABGC board review bootcamp for genetic counselors in an upcoming newsletter post.

If you would like to support our work, please forward this newsletter to folks in your network who might be interested in learning more about genetics and rare disease, and consider following our page on LinkedIn.

I hope you have a great week!

-Daniel

Questions

Question 92

A pregnant woman at 8 weeks gestation presents for her first prenatal visit. She is taking lisinopril for hypertension and is otherwise healthy with no medical conditions. If she remains on this medication throughout pregnancy, her fetus would be at risk for which of the following complications?

Question 93

A pregnant woman at 20 weeks gestation presents for prenatal care. She has a history of Graves disease and has been taking methimazole for hyperthyroidism throughout her pregnancy. Her fetus is at increased risk for which complication?

Explanations

Question 92: Pulmonary hypoplasia

Question 93: Areas of missing skin (aplasia cutis)

Teratogens are environmental factors that can disrupt normal fetal development. In order to understand their effects on the fetus, there are three important principles to keep in mind:

1. Timing: The first trimester is particularly vulnerable to teratogenic effects, as this is when vital organs like the heart and neural tube form. Exposure during this period typically results in the most severe developmental complications.

2. Dose-response relationships: The severity of teratogenic effects generally correlates with both the dose and duration of exposure. Higher doses or longer exposure periods typically increase the risk of fetal complications.

3. Individual genetic susceptibility: There is significant variation in how different pregnancies respond to teratogenic exposure. Two pregnancies exposed to the same dose of the same teratogen may have completely different outcomes. This may be due in part to underlying genetic factors in both the mother and fetus that are not well understood in most cases.

[Note: These 3 principles were derived for clinical relevance and brevity from Wilson’s original 6 principles of teratology, which was first published in 1959.]

Teratogen classification and safety databases

For many years, the FDA categorized the risk of drugs to a fetus using a five-letter system (A, B, C, D, and X). Each letter indicated the teratogenic potential of a drug based on available safety data, with “X” being clearly teratogenic. This 5-letter system has since been replaced with the Pregnancy and Lactation Labeling Rule (PLLR), which includes a description on the safety of drug in pregnancy, lactation, and in people of reproductive age. Safety information for FDA-approved medications can be found on the drug labels at the Drugs@FDA website. Subscription databases like Reprotox and TERIS also contain information on teratogens, and Mother-to-baby is a reliable resource on teratogens for patients.

Classification of teratogens

For board exams, think about teratogens as belonging into one of 4 categories: medications, recreational substances, maternal infections, and maternal illness.

1. Medications

There are multiple classes of medications that have well-documented teratogenic effects. During pregnancy, teratogenic medications should be discontinued or substituted for an alternative, when available. When this is not possible, the benefits of the mother taking a teratogenic medication should be weighed against the risk that their fetus would be affected by the medication. Below are a few examples:

• Angiotensin-converting enzyme (ACE) inhibitors (e.g. lisinopril) can cause fetal renal failure, which leads to oligohydramnios. This is because fetal urine forms the amniotic fluid, especially in the 2nd half of pregnancy. Fetal lung development requires the presence of amniotic fluid, and so pulmonary hypoplasia (underdevelopment of the lungs; Question 92) can result if amniotic fluid levels are low.

• Methimazole, an antithyroid medication, can cause aplasia cutis (Question 93) and micrognathia.

• Warfarin, an anticoagulant, can cause nasal hypoplasia and skeletal anomalies (e.g. short limbs and digits).

• Valproate is an antiepileptic that can cause neural tube defects and cardiac defects.

• Isotretinoin, a vitamin A derivative used to treat severe acne, affects the development of cranial neural crest cells, which causes craniofacial, cardiac, and thymic malformations.

• Lithium is a mood stabilizer used to treat bipolar disorder that can cause congenital heart defects (e.g. Ebstein anomaly, which presents with a malformed tricuspid valve, a large right atrium, and a small right ventricle).

2. Recreational substances

The use of recreational substances is relatively common nationwide among both pregnant and non-pregnant individuals. However, recreational substance use is particularly discouraged during pregnancy due to the risks to the fetus.

• Alcohol use causes fetal alcohol spectrum disorder (FASD), which can present with “FAS”: Facial differences (short palpebral fissures, epicanthal folds, thin upper lip, smooth philtrum), Altered CNS development (DD/ID, behavior), and Small size (body and head). FASD is the most common preventable cause of intellectual disability.

  • Note that FASD presents similarly to Down syndrome (epicanthal folds, short stature, DD/ID).

  • There are no safe levels of alcohol during pregnancy.

• Smoking cigarettes increases the risk of preterm birth, fetal growth restriction, cleft lip and palate, and jejunoilial atresia (like cocaine).

• Cocaine is a vasoconstrictor and is associated with vascular accidents (e.g. jejunoileal atresia) in the fetus.

  • Duodenal (not jejunoileal) atresia is more commonly associated with Down syndrome.

3. Maternal infections

Maternal infections can also impair fetal development. Primary infections (i.e., the mother’s first infection) typically carry the greatest risk for fetal teratogenesis (as the mother lacks protective antibodies that form after the first infection). In some cases, an infection may cause minimal or no symptoms in the mother. Medications that treat the maternal infection are available in some cases, though treatment may not necessarily prevent symptoms in the fetus. Skin rashes, hepatomegaly, or lymphadenopathy in a newborn should raise concern for a congenital infection. The main teratogenic infections can be remembered with the mnemonic "TORCHES":

• Toxoplasmosis, which is caused by a parasite acquired from cat feces, can cause intracranial calcifications and chorioretinitis in the fetus.

• “Other” reminds us that there are other infections (e.g. Zika, varicella) that can cause congenital birth defects.

• Congenital Rubella presents with a classic triad of deafness, cataracts, and cardiac defects.

• CMV (cytomegalovirus) can cause microcephaly, periventricular calcifications (CMV = “Calcify My Ventricles“), cataracts, chorioretinitis (think “Sight”omegalovirus), and hearing loss.

• Herpes simplex virus is typically acquired upon passage through birth canal. Babies may present within a few days after birth with a vesicular rash and temporal lobe hemorrhage (herpes encephalitis).

• Syphilis is a bacteria that can cause rhinorrhea (“syphilitic snuffles”), anemia, thrombocytopenia, hepatomegaly, skin rash, and skeletal anomalies.

4. Maternal illness

Certain non-infectious maternal illness can affect fetal development. Below are a few examples:

• Maternal diabetes, both pre-gestational and gestational, can impact the development of a fetus. This topic was also discussed in a prior post.

  • Pre-gestational diabetes (type 1 or 2) is associated with an increased risk of congenital heart disease, lower extremity anomalies (e.g. caudal regression syndrome), and holoprosencephaly. The risk of a major fetal anomaly or stillbirth correlates with maternal glucose control.

  • Gestational diabetes (defined as diabetes that develops after 20 weeks gestation) can present with macrosomia and neonatal hypoglycemia after delivery. There is a lower risk of major congenital anomalies compared to pre-gestational diabetes.

• Maternal phenylketonuria is due to high levels of phenylalanine and can cause cardiac defects, fetal growth restriction, and microcephaly.

• Obesity increases the risk of CHiN (Cleft lip/palate, Heart defect, and Neural tube defects) in the fetus.

• Hyperthermia (e.g. maternal fever) increases the risk for neural tube defects if this happens early in the first trimester (recall that the neural tube closes at 6 weeks gestation).

Disclaimer: This overview provides examples of teratogens that may be tested on exams and represents only a subset of all known teratogens. Our understanding of teratogens and the risks they pose continues to evolve as new research emerges.

Learning objectives

Teratogens can be classified into four main categories: medications, recreational substances, maternal illnesses, and maternal infections. In most cases, the risk of severe congenital anomalies is highest during critical periods of organogenesis in early pregnancy. Remember the 3 key factors that determine the effects of teratogens on the fetus: timing of exposure, dose-response relationships, and individual susceptibility due to polygenic factors.

2025 ABMGG General Exam Blueprint | VI. Gene environment interactions → c) Teratology

2023 ABGC Exam Content Outline | Domain 1A. Clinical information → 2. Teratogens, exposure, and other non-genetic risk factors

References

Teratogenesis (2017, Vargesson and Fraga)

Handbook of Teratology: General Principles and Etiology (Wilson, 1977)

Drugs@FDA search engine

Mother-to-baby website

This is the final post in our series on imprinting disorders. This series of posts has been written together with Sofia Dallarda, a genetic counseling student at UCSF. Sofia also recorded an excellent video on this topic, so please have a look!

Do you have an idea for a newsletter post, YouTube video, or other content? If so, share it with us using this form. It would really help us as we plan our content for this year.

Thank you for all of your support with this newsletter over this past year. Wishing you all the best for 2025!

-Daniel

🎁 P.S. Be sure to read until the end of this post! There is a bonus table and figure that provide more insights into the clinical and molecular features of Beckwith-Wiedemann.

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Questions

Question 90

A 2-year-old girl presents for a well-child visit. She has a history of hypoglycemia and feeding difficulties in infancy. Physical exam shows a large tongue and a 3 cm leg length discrepancy. A microarray sent for the child shows a duplication of chromosome 11p15.5 and a deletion of chromosome 5p15.3. A follow-up karyotype shows 46,XX,der(5)t(5;11)(p15.3;p15.5). A pedigree is obtained and is displayed below. To help determine the recurrence risk within the family, which individual should be tested FIRST?

Question 91

Additional genetic testing shows that the father is a balanced translocation carrier 46,XY,t(5;11)(p15.3;p15.5). The father should be counseled that his daughter is at risk for having a child affected by which disorder?

Explanation

Question 90: A (the child’s father)

Question 91: Russell-Silver syndrome

Beckwith-Wiedemann syndrome (BWS) overview

The child in Question 90 has features consistent with Beckwith-Wiedemann syndrome (BWS), an overgrowth disorder caused by molecular alterations at chromosome 11p15.5. In the newborn period, patients classically present with overgrowth-related symptoms including macroglossia👅, macrosomia (large body size), hyperinsulinism (from pancreatic hyperplasia) with associated hypoglycemia, and hemihyperplasia (lateralized overgrowth). BWS is also linked to early childhood embryonal tumors like Wilms tumor and hepatoblastoma, which are also manifestations of the excessive cell growth seen in overgrowth disorders. In addition, patients may present with structural kidney anomalies and anterior earlobe creases, among other features. In some cases, the diagnosis of BWS can be suspected prenatally, with the fetus presenting with omphalocele, organomegaly, macrosomia, and polyhydramnios. Based on these features, clinical diagnostic criteria for BWS are available. However, BWS is a spectrum, and most affected individuals will only have a subset of the classic features.

Diagnostic testing for suspected cases of BWS typically starts with DNA methylation analysis (just as with Russell-Silver syndrome) at the 11p15.5 locus. If this testing is negative and the diagnosis is still suspected clinically, consider DNA methylation testing using tissue from an affected site (to look for mosaic BWS) and/or CDKN1C sequencing. A more comprehensive testing algorithm is available here, and the molecular mechanisms of BWS are discussed further below.

Knowing the molecular subtype of BWS is important because it guides management. For example, consensus guidelines (see table 4 in this paper) state that patients with BWS due to loss of methylation at the maternal ICR2 (the most common molecular alteration in BWS) do not require tumor screening in childhood due to the low absolute risk of cancer. In contrast, patient with BWS due to gain of methylation at the maternal ICR1 region have a high risk of Wilms tumor (~25% of cases) and do require routine abdominal ultrasounds during childhood.

Familial BWS

While BWS is usually sporadic, certain molecular alterations can lead to familial or recurrent cases of BWS. Familial cases of BWS involve alterations to the DNA sequence. These include point mutations, copy number variations, or structural rearrangements. In contrast, BWS caused by altered DNA methylation without changes in the DNA sequence is not usually heritable.

The main molecular variants that lead to familial BWS include:

1. Maternally-inherited loss-of-function variant in CDKN1C. This is the most common cause of familial BWS. If this is the case, test the proband’s mother for the CDKN1C variant (as she may be an asymptomatic carrier).

2. Paternally-inherited copy number gain at 11p15. This can happen in 2 ways:

   1. If the father carries a balanced translocation that includes chromosome 11p15.5, then his child could have an unbalanced translocation that includes an extra copy of 11p15.5 (see diagram below). This was the case in Question 90.

   2. If the father has an 11p15.5 duplication (e.g. because he himself is affected with BWS), then his children could inherit that same 11p15.5 duplication and would be affected with BWS (50% recurrence risk).

   3. In contrast, mothers who have an 11p15.5 duplication (or a balanced translocation that includes 11p15.5) can have children affected with Russell-Silver syndrome (Question 91; also see Thompson & Thompson, 9th ed., Fig. 8.5 and our last post on Russell-Silver).

   4. Therefore, if the proband has BWS due to a copy number gain at 11p15.5, test the proband’s father to look for the presence of a balanced translocation or copy number gain involving 11p15.5.

Knowing the molecular alteration can help determine which relative to test first and also helps determine recurrence risk. In this case, since the child has a copy number gain at 11p15.5 secondary to a derivative chromosome (der(5)), her father should be tested for the presence of a balanced translocation (Question 90). Some unbalanced translocations arise de novo, in which case the recurrence risk in subsequent pregnancies is low (<1%). Otherwise, if the father is a balanced translocation carrier, the recurrence risk for BWS is higher.

Molecular genetics of BWS

Beckwith-Wiedemann syndrome (an overgrowth disorder) is caused by molecular changes at chromosome 11p15.5. Our previous post on Russell-Silver syndrome (an undergrowth disorder) discussed how the 11p15.5 region contains genes with opposing functions that regulate growth. To recap, the most important genes in this region are insulin-like growth factor 2, or IGF2 (a pro-growth factor 🟢), and cyclin dependent kinase inhibitor 1C, or CDKN1C (a growth and tumor suppressor 🛑). Healthy individuals with normal growth have balanced expression of IGF2 from the paternal allele and CDKN1C from the maternal allele.

In BWS, several molecular changes result in more pro-growth (IGF2) signals 🟢 relative to anti-growth (CDKN1C) 🛑 signals, resulting in an overgrowth phenotype. This is the opposite of what is seen in RSS (more anti-growth than pro-growth signals).

There are 5 main ways that BWS can happen:

➊ First, there could be loss of CDKN1C expression from the maternal allele due to loss of methylation at the maternal imprinting control region 2 (ICR2) on chromosome 11p15.5. This is the #1 cause of BWS.

➋ Second, there could be a loss-of-function variant present in CDKN1C on the maternal allele. This is similar to the first scenario, although instead of loss of CDKN1C expression, there is a DNA sequence variant causing loss of CDKN1C function.

➌ Third, there could be paternal uniparental disomy (UPD) of chromosome 11p15.5, which results in both excess IGF2 and loss of CDKN1C expression. In some cases, this presents as segmental mosaic UPD, a process that results from mitotic recombination.

➍ Fourth, there could be a paternally-derived duplication or copy number gain of 11p15.5 that gives rise to excess IGF2. This was the case in questions 90-91.

❺ Fifth, there could be a gain of IGF2 expression from the maternal allele due to increased methylation at ICR1.

In all cases, the excess of IGF2 relative to CDKN1C is what results in overgrowth.

A closer look at the relationship between methylation & gene expression at 11p15.5

The 11p15.5 locus contains two Imprinting Control Regions (ICR), ICR1 and ICR2, that regulate the expression of growth-related genes. The schematic below illustrates the relationship between DNA methylation and gene expression at 11p15.5 in an unaffected individual. In reality, there are multiple genes (not only IGF2 and CDKN1C) whose expression is associated with methylation differences at ICR1 and ICR2.

Incorrect answers

Question 90

Testing the mother (choice B) would be less helpful, as a copy number gain at 11p15.5 associated with BWS typically originates from the paternal chromosome. In contrast, a maternally-inherited copy number gain at 11p15.5 could result in a child with Russell-Silver syndrome. Testing the unaffected sibling (choice C) or the maternal uncle (choice D) would not help determine recurrence risk though could be considered if they were symptomatic.

Question 91

Females who have a 11p15.5 duplication or who carry a balanced translocation involving 11p15.5 are at increased risk for having a child with Russell-Silver syndrome. On the other hand, males who transmit an extra copy of 11p15.5 are at risk of having a child with BWS (choice A). WAGR syndrome (Wilms tumor, aniridia, genitourinary anomalies, and intellectual disability; Choice C) is associated with deletion of WT1, a gene found at chromosome 11p13. The 11p13 locus is adjacent to but distinct from 11p15.5.

Learning objective

BWS is an overgrowth disorder caused by molecular alterations at chromosome 11p15.5. Classically, patients present with macroglossia, hemihyperplasia, omphalocele, and an increased risk for certain childhood cancers. DNA methylation testing confirms the diagnosis in most cases. While most cases of BWS are sporadic, familial BWS may be due to paternally-inherited copy number gains at 11p15.5 or maternally-inherited loss-of-function variants in CDKN1C. Management varies on the molecular subtype and clinical symptoms and may include tumor surveillance, surgery for limb-length discrepancy or reduction of tongue size, and pharmacotherapy or partial pancreatectomy for hyperinsulinism.

2023 ABGC Exam Content Outline | Domain 1C. Genetic conditions → 1. Clinical features, 6. Diagnostic processes including clinical criteria and testing strategy, 7. Mode of inheritance, and 8. Etiology

2025 ABMGG Exam Content Outline | V. Single gene inheritance → c) Atypical inheritance → ii) Parent of origin effects on inheritance (genomic imprinting)

Bonus table:

Beckwith-Wiedemann Syndrome (BWS) and Russell-Silver Syndrome (RSS): Opposite Ends of the Growth Spectrum

Bonus figure:

Visualizing the mechanisms of Beckwith-Wiedemann in the context of ICR1 and ICR2 methylation.

References

Beckwith-Wiedemann Syndrome - GeneReviews

Slavotinek et al. (1997) Paternally inherited duplications of 11p15.5 and Beckwith-Wiedemann syndrome.

Brown et al. (1994) Paternal origin of 11p15 duplications in the Beckwith-Wiedemann syndrome. A new case and review of the literature

Slatter et al. (1994) Mosaic uniparental disomy in Beckwith-Wiedemann syndrome

Thompson & Thompson Genetics and Genomics in Medicine 9th Edition (Chapter 8 and Case 6)

This is the third in a series of 4 posts related to imprinting disorders. This series of posts on imprinting has been written together with Sofia Dallarda, a genetic counseling student at UCSF.

We are running an ABGC board prep bootcamp from Dec 2, 2024 - Jan 23, 2025 to help GCs prepare for the February 2025 ABGC exam. Our early-bird registration ($100 discount) is available through Friday, Nov 22. Register here.

Also, for anyone taking the ABGC exam, there is an updated (and smaller!) set of exam references (see this LinkedIn post for more details). And for folks taking the 2025 ABMGG exam, the 2025 content outlines have been posted.

Please feel free to let me know if you have any comments or suggestions. I hope you are having a great week!

-Daniel

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Questions

Question 88

A 6-year-old boy presents with short stature. He started 1st grade this year and is in a regular classroom. Physical exam shows frontal bossing, relative macrocephaly, and triangular facies. His height is <1st percentile. Family history is non-contributory. He meets the diagnostic criteria for Russell-Silver syndrome (RSS). What is the best INITIAL test to establish a molecular diagnosis of RSS?

* SNP = Single nucleotide polymorphism

* MLPA = Multiplex ligation-dependent probe amplification

Question 89

Methylation-specific MLPA is sent for the patient in question 88 and shows hypomethylation at the imprinting control region 1 (ICR1) on chromosome 11p15.5. A referral to which of the following specialists is most important at this time?

Explanation

Question 88: Methylation-specific MLPA

Question 89: Endocrinology

Russell-Silver Syndrome Overview

Russell-Silver syndrome (RSS) is an imprinting disorder characterized by undergrowth. Patients are typically born small for their gestational age and experience difficulty growing in the postnatal period. Relative macrocephaly with a prominent forehead, a small chin, triangular facies (see description below), body asymmetry (due to undergrowth of one side of the body), and feeding difficulties are also characteristic. Short stature may be the chief concern for some patients (as was the case in Question 88). Patients with RSS can expect to live a normal lifespan.

Regarding specialist referrals, evaluation by an endocrinologist (Question 89) is important to assess for growth hormone deficiency as a cause of short stature and to monitor for precocious puberty. Some patients may need an orthopedic evaluation to address limb length discrepancies. A gastroenterologist or nutritionist can help optimize caloric intake in patients with feeding difficulties. Patients with developmental delays would benefit from developmental pediatrics or supportive therapies, though most patients have normal neurocognitive development. A genetics evaluation can help the family clarify that RSS usually occurs sporadically and that the recurrence risk for siblings in most cases is low.

The diagnosis of RSS should be suspected based on the presence of characteristic clinical features. The NH-CSS diagnostic criteria is a 6-point clinical scoring system used as part of a decision tree (see image below) for whether to send genetic testing for RSS. The NH-CSS score includes symptoms related to undergrowth, relative macrocephaly, and feeding difficulties. Patients who meet 4 of the 6 NH-CSS diagnostic criteria should undergo genetic testing with methylation-specific MLPA (see algorithm below) (Question 88). This test flags positive in the presence of DNA methylation changes or copy number variants in the assayed regions (chromosome 11p15 and chromosome 7).

Molecular genetics

Russell-Silver syndrome is usually caused by molecular changes at chromosome 11p15.5. This region contains genes with opposing functions that regulate growth. The most important genes in this region are insulin-like growth factor 2, or IGF2 (a pro-growth factor 🟢), and cyclin dependent kinase inhibitor 1C, or CDKN1C (a growth and tumor suppressor 🛑). Healthy individuals with normal growth have balanced expression of IGF2 from the paternal allele and CDKN1C from the maternal allele.

In RSS, several molecular changes result in more anti-growth (CDKN1C) 🛑 relative to pro-growth (IGF2) signals 🟢, resulting in an undergrowth phenotype. There are 4 main ways that this can occur:

➊ First, there could be loss of IGF2 expression from the paternal allele due to loss of methylation at the paternal imprinting control center 1 (ICR1) on chromosome 11p15.5. This is the #1 cause of RSS.

➋ Second, there could be a loss-of-function variant present in IGF2 on the paternal allele. This is similar to the first scenario, although instead of loss of IGF2 expression, there is a DNA sequence variant causing loss of IGF2 function.

➌ Third, there could be maternal uniparental disomy (UPD) of chromosome 11p15.5, which results in both excess CDKN1C and loss of IGF2 expression.

➍ Fourth, there could be a duplication or copy number gain at 11p15.5 on the maternal allele that gives rise to excess CDKN1C.

In all cases, the excess of CDKN1C relative to IGF2 is what results in undergrowth.

💡Remember this: fathers are taller than mothers (usually). So it follows that the paternal allele expresses the “pro-growth” IGF2, while the maternal allele expresses the “anti-growth” CDKN1C.

While the above provides a simplified schematic for understanding the molecular mechanisms of RSS, the reality is more complex. For example, there are other molecular causes of RSS including maternal UPD of chromosome 7 (~7% of cases) that do not fit neatly into this framework. In addition, 30-40% of patients with a clinical diagnosis of RSS have negative molecular testing, which suggests the presence of as-yet unidentified molecular mechanisms of disease. And the expression of IGF2 and CDKN1C is governed by imprinting control regions (ICRs), ICR1 and ICR2, respectively, that undergo DNA methylation and establish parent-of-origin gene expression.

To illustrate this last point, we have included a closer look at the imprinting control region 1 (ICR1), where IGF2 is expressed:

Detecting DNA methylation at ICRs using MS-MLPA

An Imprinting Control Region (ICR) is a DNA locus whose methylation status is associated with gene expression. Methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) (Question 88) is used to detect the methylation status of ICRs and other known DNA loci. There are three main steps in MS-MLPA:

1. Denaturation and hybridization: The double-stranded DNA is heated to separate it into single strands (denaturation). Then, pairs of oligonucleotide probes are added to the reaction. Each probe consists of two separate oligonucleotides—a left probe and a right probe—that hybridize to complementary target sequences on the single-stranded DNA (see figure below). The left and right probes bind immediately next to each other on the target DNA sequence 👥. This precise binding is crucial for the next step, as only immediately adjacent probes can be ligated by DNA ligase.

2. Ligation and digestion: The adjacent probes are then joined together (ligated) by a DNA ligase, forming a single, continuous probe for each target sequence. After ligation, a methylation-sensitive endonuclease is added to the reaction to digest the DNA-probe complexes at specific unmethylated DNA sites. As a result, the unmethylated alleles are cut by the endonuclease and are not amplified by PCR.

3. PCR amplification: Only the ligated probes associated with methylated alleles remain intact after digestion. During PCR amplification, these intact probes are amplified, resulting in DNA fragments that represent the methylated regions. The PCR products vary in length, allowing multiple target sequences to be analyzed simultaneously (this is the “multiplex” in MLPA) through capillary electrophoresis.

This reaction is performed alongside an undigested control, which omits the digestion step. In the undigested control, all target sequences are amplified regardless of methylation status because they haven't been cut by the methylation-sensitive endonuclease. The proportion of methylated alleles in the sample can be estimated by comparing the outputs of the digested and undigested reactions.

Incorrect answers

Question 88

SNP-based microarray (Choice A) can detect copy number variations (CNVs) and uniparental isodisomy (e.g. maternal UPD7), which is a known cause of RSS in some cases. However, it does not detect the most common cause of RSS, which is hypomethylation of ICR1 on chromosome 11p15.5. Gene panel testing (Choice B) identifies single nucleotide variants, which can cause RSS in rare cases (e.g. loss-of-function variant in IGF2). While most cases of RSS are not caused by DNA sequence variants, panel-based testing may be considered as a second-line test in cases with negative methylation results and a strong clinical suspicion for RSS. Fluorescence in situ hybridization (FISH) (Choice D) is limited to detecting large structural changes and does not assess methylation or smaller CNVs effectively.

Question 89

A referral to pulmonology (Choice A) would be indicated for patients with a diagnosis of cystic fibrosis or primary ciliary dyskinesia. RSS is not associated with significant respiratory issues. Referral to cardiology (Choice C) would be indicated in patients with Noonan or Turner syndrome. Congenital heart disease and other cardiac manifestations are not associated with RSS. Evaluation by a nephrologist (Choice D) may be warranted in Beckwith-Wiedemann syndrome, an overgrowth disorder associated with nephromegaly, nephrocalcinosis, and kidney cancer.

Learning Objective

Russell-Silver syndrome is an undergrowth disorder characterized by short stature that is most often caused by hypomethylation of the imprinting control region 1 (ICR1) at 11p15.5. In most cases, the undergrowth seen in RSS is due to an excess of CDKN1C (anti-growth signal) relative to IGF2 (pro-growth signal). The diagnosis can be made with DNA methylation testing (MS-MLPA). Patients should be evaluated by an endocrinologist because of the risk of growth hormone deficiency and early puberty. The recurrence risk is low, and management is supportive.

2023 ABGC Exam Content Outline | Domain 3B. Testing Options → 1. Diagnostic | Domain 1A. Clinical Information → 4. Appropriateness and urgency of referral

2025 ABMGG Exam Content Outline | V. Single gene inheritance → c) Atypical inheritance → ii) Parent of origin effects on inheritance (genomic imprinting)

References

Silver-Russell syndrome (GeneReviews)

Russell-Silver syndrome (GeNotes)

Diagnosis and management of Silver–Russell syndrome: first international consensus statement

Overview of MS-MLPA

Bonus figure

Visualizing the mechanisms of Russell-Silver syndrome in the context of ICR1 and ICR2 methylation

This is the second in a series of 4 posts related to imprinting disorders. This series of posts has been written together with Sofia Dallarda, a genetic counseling student who worked with us over the summer.

I am also excited to announce our winter bootcamp for anyone preparing for the Feb 2025 ABGC board exam! The course will run from Dec 2, 2024 - Jan 23, 2025. Early-bird registration at a discounted rate is available through November 22nd. Register here.

Please feel free to let me know if you have any comments or suggestions related to this post. I hope you have a great week!

-Daniel

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Questions

Question 86

A 12-month-old girl presents to the clinic for an evaluation. She has global developmental delay and difficulty feeding. She is at the 5th percentile for weight and height and at the 2nd percentile for head circumference. She meets the clinical diagnostic criteria for Angelman syndrome. DNA methylation analysis at 15q11-q13 is sent and is non-diagnostic. Which of the following is the next best step in diagnosis?

Question 87

Genetic testing is sent for the patient in Question 86 and is positive for a pathogenic loss-of-function variant in UBE3A. Which of the following pieces of anticipatory guidance is most appropriate to share with the family in this scenario?

Explanation

Question 86: UBE3A gene sequencing

Question 87: "She is at risk for seizures."

Angelman syndrome is an imprinting disorder characterized by multiple neurologic features that include developmental delays, minimal speech, gait ataxia, acquired microcephaly, and seizures (Question 87). Angelman usually presents as gross motor or speech delays in the first 6-12 months of life, and there are typically no signs of Angelman at birth. Seizures affect many patients with Angelman syndrome and typically start within the first few years of life. Behaviorally, children with Angelman may laugh and smile frequently and may seem easily excitable. Skin hypopigmentation can be seen with patients who have a deletion at 15q11.2-q13 that includes the melanin-related protein OCA2 (discussed further below). Children with Angelman syndrome most often have a structurally normal brain and will usually reach a typical adult height.

💡 Think of Angelman as a disease of the brain 🧠. Most of the major symptoms of Angelman (e.g. seizures, intellectual disability, ataxia) can be linked back to the brain in some way.

Molecular basis of Angelman syndrome

Angelman syndrome results from the loss of ubiquitin protein ligase E3A (UBE3A) expression, which plays a crucial role in the formation of neuronal synapses. In the brain 🧠, UBE3A is expressed only from the maternally-inherited allele (and not from the paternally-inherited allele). Angelman syndrome results when the maternally-inherited copy of UBE3A is altered or missing, which leaves the brain with no functional copies of UBE3A.

Molecular alterations of UBE3A most commonly result from a de novo 5-6 megabase deletion at 15q11.2-q13. While deletion of this region on the maternally-inherited chromosome results in Angelman syndrome, deletion of this same imprinted region on the paternally-inherited chromosome causes Prader-Willi syndrome (see our previous post). Many deletions at 15q11.2-q13 include OCA2, a non-imprinted gene involved in melanin production. Loss of OCA2 results in hypopigmentation, which is observed in patients with both Angelman and Prader-Willi syndromes when the deletion involves this gene.

Recurrent deletions and duplications at 15q11.2-q13

Recurrent deletions and duplications with similar breakpoints occur at the 15q11.2-q13 region in unrelated individuals. But why does this happen? This is because this region is flanked by segmental duplications (aka low copy repeats, or LCRs), which are highly similar repetitive sequences (see image below). The presence of these LCRs can result in non-allelic homologous recombination (NAHR), which happens when the LCRs misalign in meiosis and cause unequal crossing over between homologous chromosomes. This can cause a deletion and duplication of the genetic material between the LCRs (see this paper for an illustration). NAHR at 15q11.2-q13 is thus the mechanism behind the deletions seen in Prader-Willi and Angelman and the interstitial duplications seen in Dup15q syndrome.

Diagnosing Angelman syndrome

The definitive diagnosis of Angelman is based on molecular testing. The three most common molecular changes that lead to Angelman include:

• Deletions of 15q11.2-q13 (~70% of cases)

• Paternal uniparental disomy (UPD) of chromosome 15 (~5% of cases)

• UBE3A pathogenic variants (~10% of cases)

Molecular testing identifies a genetic etiology in about 90% of people with Angelman syndrome. The first step in molecular testing for Angelman syndrome is DNA methylation analysis, which would flag positive in the presence of a deletion or paternal UPD. If the methylation analysis returns normal, UBE3A gene sequencing should be sent next (Question 86). Of note, pathogenic UBE3A variants that are inherited from an unaffected mother can result in children with Angelman syndrome (50% recurrence risk). A diagnostic flowchart is available through the Angelman syndrome foundation, and an illustration of the 3 molecular mechanisms is shown below.

Genotype-phenotype relationship

In Angelman syndrome, patients with large megabase-sized deletions at 15q11.2-q13 are often the most severely affected, while patients with paternal uniparental disomy (UPD) have fewer and more mild symptoms (e.g. no microcephaly, fewer seizures). Patients with imprinting defects and UBE3A variants may fall somewhere in the middle of this spectrum. Note that there is a high degree of clinical variability even among patients with the same underlying disease mechanism.

Management

Management of Angelman syndrome is supportive and requires a multidisciplinary team of clinicians including neurology (for seizures, motor delays, and ataxia), physical therapy, speech therapy, nutrition, and ophthalmology (if strabismus is present), among other specialists. A table listing management guidelines by age is available in this paper (Table 1). Clinical trials involving antisense oligonucleotide therapy that activates the paternal copy of UBE3A are in progress (see full list here), though no targeted therapeutics are currently available.

Incorrect answers

Question 86

Microsatellite studies (choice A) are used to assess parental origin in the setting of uniparental disomy (UPD). Once the DNA methylation analysis is negative (as was the case for this patient), UPD is virtually excluded as a cause of Angelman syndrome. Therefore, microsatellite studies would not provide further diagnostic clarity in this case. Fluorescence in situ hybridization (FISH) (choice C) is used to detect chromosomal deletions, duplications, or rearrangements. Since the DNA methylation analysis (which flags positive with most chromosomal deletions) was negative, FISH is unlikely to uncover additional findings and is not the most appropriate next step. While DNA methylation testing of the mother (choice D) would be normal and would not provide additional information in this scenario, testing her for the presence of a UBE3A variant could be considered once a variant is identified in the proband. Alterations such as DNA methylation that do not permanently change the DNA sequence are not typically heritable.

Question 87

Cardiac arrhythmias (choice A) are not characteristic of Angelman syndrome (AS) though are a feature of long QT syndrome and Brugada syndrome, among others. Progressive hearing loss (choice B) and progressive vision loss (choice D) are not features of AS though can be seen in Usher syndrome and mitochondrial disorders such as progressive external ophthalmoplegia (PEO). While speech delays can be secondary to hearing loss, the speech delay in AS is not due to hearing loss but rather due to differences in how the brain functions. Some patients with AS may have strabismus or refractive errors that affect vision, though this would not result in progressive vision loss.

Learning objective

Angelman syndrome is an imprinting disorder characterized primarily by neurologic symptoms including seizures, intellectual disability, ataxia, and gross motor delays. On a molecular level, loss of UBE3A expression from the maternally-inherited allele results in Angelman syndrome. UBE3A plays an important role in neurons and synapse formation, which explains the primarily neurologic features of this disorder. The diagnosis of Angelman is typically made with DNA methylation testing or UBE3A sequencing. Management is supportive, and clinical trials involving targeted therapeutics to increase UBE3A expression are ongoing.

2023 ABGC Exam Content Outline | Domain 1. Clinical Information, Human Development, and Genetic Conditions → C. Genetic Conditions → 8. Etiology | Domain 3. Testing Interpretation, Testing Options, and Reproductive Risk Management → B. Testing Options → 1. Diagnostic

2025 ABMGG General Exam Blueprint | V. Single gene inheritance → c. Atypical inheritance → ii) Parent of origin effects on inheritance (genomic imprinting)

References

GeneReviews (Angelman Syndrome)

A multidisciplinary approach and consensus statement to establish standards of care for Angelman syndrome (Duis et al, 2022)

Educational resources from the Angelman Syndrome Foundation

This is the first in a series of 4 posts related to imprinting disorders. Imprinting disorders are important to consider clinically as part of your differential diagnoses and are high-yield for board exams. An audio version of this post is also available.

This series of posts was co-authored with Sofia Dallarda, a talented genetic counseling student from UCSF who interned with us over the summer. Sofia took the lead in drafting the text for this series, created several high-quality illustrations, and produced 2 videos on this topic (the video related to this post is linked here). I am very grateful for her dedication and hard work. Thank you, Sofia!

If you would like to support our work, please forward this newsletter to anyone in your network who might be interested.

Please feel free to let me know if you have any comments or suggestions. I hope you are having a great week!

-Daniel

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Questions

Question 84

A 4-year-old boy presents to the clinic for a well-child visit. The family remarks that when he was an infant, he had trouble feeding. They report that he is now “constantly hungry.” He has a 20-word vocabulary and speaks in 1-word phrases. Physical exam shows almond-shaped eyes and small hands. His weight is > 99th percentile and height is at the 10th percentile. Which diagnostic test should be sent FIRST to confirm the diagnosis of Prader-Willi syndrome?

Question 85

DNA methylation studies are sent for the patient in Question 84 and show hypermethylation at the 5’ end of the SNRPN gene. A chromosomal microarray is also sent and is normal. Which of the following molecular mechanisms would be most consistent with these results?

Explanation

Question 84: DNA methylation analysis

Question 85: Maternal uniparental disomy, chr 15

Prader-Willi syndrome (PWS) is a multi-systemic disorder that affects the endocrine (hypogonadism and dysregulated eating) and neurological systems (developmental delays and mild intellectual disability). One unique characteristic of PWS are the two distinct nutritional phases, which range from hypotonia and poor feeding at birth (Phase 1) to an insatiable appetite in childhood and adolescence (Phase 2). Patients who are in nutritional phase 2 of PWS may exhibit tantrums, rigidity, and manipulative behaviors, particularly around food. PWS also presents with features that mimic growth hormone (GH) deficiency, including short stature, increased body fat, and low muscle mass, and GH therapy is FDA-approved for patients with PWS. Management of PWS is supportive and includes measures to prevent excessive weight gain, such as restricting unsupervised access to food (e.g., placing locks on fridges). Most cases of PWS are de novo though may be paternally inherited in rare cases.

Diagnosing Prader-Willi syndrome

While clinical diagnostic criteria exist for PWS, the definitive diagnosis of PWS is based on molecular testing. There are three major molecular changes that can lead to PWS:

1. Deletion of the paternally-inherited 15q11.2-q13 region [60-70% of PWS cases]

2. Maternal uniparental disomy involving chromosome 15 [29-39% of PWS cases]

3. An imprinting defect of the paternal chromosome 15q11.2-q13 region either due to an imprinting center deletion or epimutation [2-4% of PWS cases]

DNA methylation analysis (Question 84) is the only technique that flags positive regardless of the type of molecular alteration that is causing PWS. There are two main types of DNA methylation analysis, methylation-specific PCR (MSP) and methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA). While MSP detects only the DNA methylation status at the PWS imprinting center, which is located at the 5’ end of the SNURF-SNRPN gene (discussed further below), MS-MLPA detects both DNA methylation and copy number status throughout the broader 15q11.2-q13 region. MS-MLPA is the preferred method used today to diagnose PWS.

Imprinting Disorders

Imprinting disorders such as Prader-Willi syndrome arise from alterations in genomic regions where gene expression differs based on the parental origin of the chromosome*. At an imprinted locus, such as the 15q11-q13 region, some genes are expressed only from the paternally-inherited allele, while others are expressed only from the maternally-inherited allele. These differences in gene expression are governed by different patterns of DNA methylation on each allele that are established during gametogenesis and maintained throughout development.

*At non-imprinted loci, gene expression is thought to be more or less equal from the maternally-inherited and paternally-inherited alleles.

Imprinting Control Regions Regulate Gene Expression

In healthy people without disease (see image below), gene expression at 15q11-q13 differs between the paternal and maternal alleles. But how does this happen? This is the job of imprinting control regions (ICRs), which act as molecular “hubs” that help regulate gene expression and that are often differentially methylated with respect to the maternal and paternal alleles. Within the ICR at 15q11-q13, there are two smaller imprinting centers (IC), the Prader-Willi syndrome IC (PWS-IC) and the Angelman syndrome IC (AS-IC). On the paternal allele, the PWS-IC (shown in blue in image below) is unmethylated, while the PWS-IC on the maternal allele is methylated. The PWS-IC is about 4 kilobases in size and is located at the 5’ end of the SNURF-SNRPN gene (labeled below as “SNRPN”). In this case, the lack of DNA methylation at the PWS-IC on the paternal allele permits gene expression.

The ICR at 15q11-q13 is located within the larger Prader-Willi Critical Region (PWCR), a 5-6 megabase region that spans chromosome 15q11-q13. This region includes multiple genes that are expressed in a parent-of-origin-specific manner. The most common molecular mechanism that causes PWS is a deletion of the PWCR (usually as a result of non-allelic homologous recombination) on the paternally-inherited chromosome, while the second most common mechanism is maternal uniparental disomy (Question 85). Both mechanisms (see illustration below) disrupt the normal balance of methylation at the PWS-IC and thus the normal patterns of gene expression within the broader PWCR. In general, any molecular change that results in a (relative or absolute) excess of DNA methylation at the PWS-IC can cause PWS.

UPD Refresher

Uniparental disomy (UPD) is one important way by which imprinting disorders arise. There are 3 main mechanisms by which UPD arises:

1. Trisomy rescue (resulting in heterodisomy or isodisomy)

2. Monosomy rescue (resulting in isodisomy)

3. Mitotic crossing over (resulting in segmental isodisomy)

💡The term “uniparental disomy” can be broken down to derive its meaning. “Uni-parental” means “one parent”. And “di-somy” means “two bodies” (“bodies” refers to chromosomes here). Therefore, “uniparental disomy” literally means “two chromosomes coming from one parent.”

UPD may arise from nondisjunction in meiosis I or II, which results in missing or extra chromosomes that segregate to the gametes. Broadly, there are 2 types of UPD:

1. Heterodisomy occurs when a cell receives both copies of the maternal or paternal chromosomes from one parent. This typically results from nondisjunction during meiosis I.

2. Isodisomy occurs when an embryo contains two identical copies of a chromosome from one parent. This may result from nondisjunction during meiosis II.

💡 Use the prefix of each word to remember the difference between isodisomy and heterodisomy. “iso-” means identical, and “hetero-” means different. Because patients with isodisomy have 2 copies of the exact same chromosome (see panel 2 in the image below), they are at increased risk for autosomal recessive disorders (vs heterodisomy, where there is no increased risk for autosomal recessive disorders).

While either type of UPD may result in PWS, the most common form is segmental isodisomy, which accounts for ~20% of all cases of PWS. Segmental isodisomy occurs when a cell contains two identical copies of a segment of a chromosome from one parent and typically results from mitotic (not meiotic) recombination during an early embryonic division. Note that PWS due to segmental heterodisomy has been reported though is rare.

Incorrect answers

Question 84

Both FISH and karyotype can detect large deletions that result in PWS. However, neither technique would detect smaller deletions or DNA methylation abnormalities that can cause PWS. Gene panel testing can detect single nucleotide variants and in some cases deletion and duplications for genes present on the panel, though cannot detect DNA methylation abnormalities. In contrast to many other genetic disorders, PWS is not due to single nucleotide variants in a gene.

Question 85

Paternal uniparental disomy of chromosome 15 and a loss of function variant in UBE3A would both result in Angelman syndrome, an imprinting disorder that is also due to molecular alterations at 15q11-q13. Most deletions involving 15q11-q13 would have been detected by chromosomal microarray (Choice D), which the question stem stated was normal.

Learning objective

Prader-Willi syndrome (PWS) is an imprinting disorder that affects the neurologic (developmental delays, intellectual disability) and endocrine (obesity, hypogonadism) systems. Paternal deletion of 15q11-q13 and maternal uniparental disomy of chromosome 15 each lead to an unbalanced excess of DNA methylation at the PWS imprinting center and result in PWS. DNA methylation analysis through MS-MLPA can be used to establish the diagnosis of PWS. Management involves growth hormone therapy starting in infancy and is otherwise supportive.

2023 ABGC Exam Content Outline | Domain 1. Clinical Information, Human Development, and Genetic Conditions | C. Genetic Conditions → 8. Etiology | Domain 3. Testing Interpretation, Testing Options, and Reproductive Risk Management | A. Testing and Interpretation → 3. Clinical Context

2025 ABMGG General Exam Blueprint | V. Single gene inheritance → c. Atypical inheritance → ii) Parent of origin effects on inheritance (genomic imprinting)

References

Prader-Willi syndrome (GeneReviews)

Thompson & Thompson Genetics and Genomics in Medicine, 9th Edition (Case #38)

ACMG statement on diagnostic testing for uniparental disomy

This is the 3rd in a series of 3 posts related to cardiovascular genetics. We will discuss the case of an infant with congenital heart disease. There is also a video on congenital heart disease that is now available on the StudyRare YouTube channel.

We are also proud to announce Sonia Nessari, a genetic counselor and graduate of the GC program at Boise State, as the recipient of the StudyRare scholarship. This award will cover her ABGC board exam registration fee and enrollment in our ongoing board review course. We recorded an interview with Sonia here. Congratulations, Sonia — we are proud to be able to support you!

Please let me know if you have any feedback on this post or suggestions for future posts. I hope you are having a great week!

-Daniel

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Questions

Question 82

A newborn girl is admitted to the NICU due to respiratory distress. She was born large for her age and her skin has a bluish discoloration. An echocardiogram shows truncus arteriosus. Genetic testing is sent for the newborn and is pending. Her mother does not receive routine medical care. Which of the following studies would be most useful in determining the likely cause of the baby’s symptoms?

Question 83

A hemoglobin A1c level is checked on the mother of the newborn in Question 82 and is 9.0% (normal < 5.7%). Which of the following genetic disorders is associated with truncus arteriosus and should also be tested for in this newborn?

Explanations

Question 82: Maternal hemoglobin A1c

Question 83: DiGeorge syndrome

The patient in question 82 has truncus arteriosus (TA), a congenital heart defect that occurs when the aorta and pulmonary artery fail to separate properly during fetal development. This results in a single large vessel, or "trunk," exiting the heart. When deoxygenated blood from the pulmonary artery mixes with oxygenated blood from the aorta, as is the case with TA, circulating oxygen levels decrease and can cause cyanosis (bluish skin). Complications of TA include pulmonary hypertension, which results from too much blood going to the lungs, congestive heart failure, and poor growth. Management of TA is with surgical repair within the first few days to weeks of life.

Classification of congenital heart disease

Broadly speaking, congenital heart disease (CHD) can be subdivided into cyanotic and acyanotic lesions, based on whether or not the lesion lowers systemic oxygen levels. A list of some of the more common forms of congenital heart disease within each of these categories is listed below.

Risk factors for truncus arteriosus

There are several risk factors (both environmental and genetic) for truncus arteriosus (TA). First, pregestational diabetes (discussed further below) is a well-established risk factor for conotruncal anomalies like TA, which is why checking a maternal hemoglobin A1c level (Question 82) is important in this scenario. Genetic associations with TA can be divided into syndromic and non-syndromic causes. DiGeorge syndrome (22q11.2 deletion syndrome) is an example of a syndromic cause of TA and is also associated with cleft palate, immunodeficiency, hearing loss, and learning difficulties. Up to 1 in 3 cases of TA have been associated with DiGeorge syndrome. Non-syndromic causes of TA include variants in genes such as NKX2-6 and GATA6.

Even in the presence of a clear environmental risk factor like pregestational diabetes, genetic testing for babies with congenital heart disease should still be considered. This is because not all IDM will develop congenital heart disease (CHD), and patients may have multiple factors (both environmental and genetic) that contribute to their CHD. If an underlying monogenic disorder were identified, this can inform recurrence risk and also guide management, as in the case of DiGeorge syndrome. However, many cases of CHD (including truncus arteriosus) occur sporadically and without an identifiable environmental or genetic cause.

Infants of diabetic mothers

Babies born to mothers with diabetes are known as infants of diabetic mothers (IDM). There are two types of diabetes in pregnancy, both of which can cause complications in the fetus:

• Pregestational diabetes is present before pregnancy. Persistently elevated maternal glucose levels can act as a teratogen during the first trimester, which is a critical period for organ development. This increases the risk of congenital anomalies affecting the heart (e.g., conotruncal defects like truncus arteriosus), gastrointestinal tract (small left colon syndrome), lower limbs (caudal regression syndrome), and spine (spina bifida). The risk for congenital heart disease (CHD) and other anomalies is correlated with the control of maternal blood glucose levels. Pregestational diabetes is typically diagnosed with an elevated hemoglobin A1c level prior to pregnancy.

• Gestational diabetes develops during the second or third trimester of pregnancy. It is not associated with an increased risk of congenital malformations because it occurs after the critical period of organogenesis. However, both pregestational and gestational diabetes can result in an infant who is large for gestational age, which may cause delivery complications like shoulder dystocia, as well as metabolic and hematologic issues including hypoglycemia, polycythemia, and hyperbilirubinemia that present shortly after birth. Gestational diabetes is diagnosed with an oral glucose tolerance test in the late second or third trimester and usually resolves after delivery.

💡 Hemoglobin A1c is not used to diagnose gestational diabetes, as it can underestimate the glucose intolerance due to lower maternal hemoglobin levels in pregnancy.

Incorrect answers

Question 82

Maternal phenylalanine levels (choice A) should be checked in patients with phenylketonuria. Elevated phenylalanine levels in mothers with PKU are teratogenic and can cause maternal PKU, which is characterized by multiple fetal anomalies including congenital heart disease (though not typically truncus arteriosus), microcephaly, and intrauterine growth restriction (vs the infant in this question, who was large for their age). A maternal folate level (Choice C) could be considered if the newborn had been diagnosed with a neural tube defect, which is linked to maternal folate deficiency. Congenital heart disease, however, is not linked to folate deficiency. A maternal karyotype (Choice D) could be considered if there were a history of recurrent miscarriage or infertility. However, most patients with congenital heart disease (and their parents) will have a normal karyotype, which lacks the resolution to detect copy number variants that are seen in some patients with congenital heart disease.

Question 83

While Down syndrome (Choice A) is associated with congenital heart defects, truncus arteriosus is not typically seen in these patients. Common cardiac anomalies in Down syndrome include atrioventricular septal defects (AVSD), also known as endocardial cushion defects. Specific defects include ventricular septal defects (VSD), atrial septal defects (ASD), and malformed tricuspid and mitral valves. Williams syndrome (7q11.23 deletion syndrome, Choice C) is often associated with supravalvular aortic stenosis but not with truncus arteriosus. Noonan syndrome (Choice D) can present with various cardiac anomalies including pulmonary valve stenosis and hypertrophic cardiomyopathy, though truncus arteriosus is not typically associated with this condition.

Learning objective

Truncus arteriosus is a cyanotic congenital heart defect where the aorta and pulmonary artery do not properly separate. The risk for truncus arteriosus, among other congenital anomalies, is increased in the offspring of mothers with pregestational diabetes but not gestational diabetes. Genetic testing for DiGeorge syndrome should be considered in patients with TA, as ~1/3 of patients with truncus arteriosus have DiGeorge syndrome.

2023 ABMGG General Exam Blueprint | V. Single gene inheritance → d. Single gene disorders → iii) Cardiac disorders

2023 ABGC Exam Content Outline | Domain 1C. Genetic Conditions → 1. Clinical features, 5. Management options, and 8. Etiology

References

Frequency of 22q11 deletions in patients with conotruncal defects

Truncus arterious (Mott Children’s hospital)

Infant of a diabetic mother: clinical presentation, diagnosis and treatment

This is the 2nd in a series of 3 posts related to cardiovascular genetics. I will discuss the case of a girl affected by a RASopathy, a class of disorders that are associated with cardiomyopathy and other structural heart differences. An audio version of this post is also available.

Update (Aug 2026): Our summer intern, Michelle Murphy, made a video on the different causes of cardiomyopathy. Check it out here!

Also, we have 2 exciting announcements 📢:

1. Signups for the 30-hour ABGC Board Review Bootcamp in preparation for the August 2024 exam are now open! The course will take place June 13th - July 25th, 2024. Lynsey Rodriguez, MS, LCGC and I are excited to work with you. The signup page and the flyer below have more information about the course, and testimonials from our recent courses are available on our website. A discount is available for folks who sign up before June 1st. Please reach out with any questions (daniel@studyrare.com).

2. We are excited to announce the StudyRare ABGC board exam scholarship for GC students in need who are taking the August 2024 board exam. This scholarship covers the cost of the ABGC exam registration and the bootcamp this summer. Apply by May 24th. Please share this with anyone in your network who might be eligible.

I hope you have a great week!

-Daniel

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Questions

Question 79

An 11-year-old girl with mild intellectual disability presents to the cardiology clinic for a follow-up visit. She was diagnosed with hypertrophic cardiomyopathy as an infant. Physical exam shows short stature and several scattered facial papillomas. Genetic testing is performed and shows a variant in HRAS, consistent with the diagnosis of Costello syndrome. Her parents should be advised about the risk of which of the following?

Question 80

Which of the following types of HRAS variants is most likely to be seen in a patient with Costello syndrome?

Question 81

The girl returns to the cardiology clinic 2 years later. The girl’s mother, Sally, is currently 10 weeks pregnant and has a new partner, Tim, who she has been with for the past year and who is not the girl’s biological father. Both Sally and Tim are healthy and have no known medical conditions. Neither parent has had genetic testing. Sally asks about the risk that her current pregnancy is affected with Costello syndrome. Which statement would be the MOST appropriate answer to share with the patient?

Explanations

Question 79: Bladder cancer

Question 80: p.G12S (missense)

Question 81: “The recurrence risk is 1-2%.”

Costello syndrome is a multi-systemic disorder that is associated with the “7 C’s”: Cardiac involvement🫀, ↑ Cancer risk🎗️, Craniofacial & skeletal differences💀🦴, Cerebrum (intellectual disability) & Cerebellum (Chiari I malformation) 🧠, Cutaneous manifestations (skin findings), and Cryptorchidism (in males). The most common cardiac findings in Costello syndrome include hypertrophic cardiomyopathy (HCM), which this patient has, and pulmonic stenosis. HCM can be progressive over time and requires routine follow up with cardiology. Cancer risks include neuroblastoma and rhabdomyosarcoma in young children, as well as bladder carcinoma (Question 79) in adolescents and young adults. Craniofacial and skeletal differences in patients with Costello include short stature, joint laxity, and scoliosis. Patients may have developmental delays and mild to moderate intellectual disability and are at risk for developing a Chiari I malformation. Skin findings may include hyperkeratosis and calluses, loose skin, and papillomas of the face or perianal region starting in childhood. Cryptorchidism, or undescended testes, are a common finding in males with Costello syndrome.

💡Note that many of these “7 C’s” are also common to other RASopathies, which are disorders due to variants in genes that encode proteins within the RAS/MAPK pathway (picture below). For example, the more common types of cardiac involvement seen in Costello syndrome (e.g., pulmonic stenosis, hypertrophic cardiomyopathy) are also highly prevalent in Noonan syndrome and cardio-facio-cutaneous syndrome.

Molecular genetics of Costello syndrome

Costello syndrome is most often caused by de novo missense variants in the gene HRAS, a GTPase protein that, when active, promotes cell growth. Most of these missense variants (~95%) affect amino acids 12 or 13 of the HRAS gene (Question 80) and are therefore examples of “hotspot” mutations, whereby a recurrent genetic change in the same position in the same gene results in the same disease. Variants like p.Gly12Ser disrupt GTPase function and impair the protein's ability to deactivate downstream protein signaling (kind of like a light switch💡 that is stuck in the “on” position). Consequently, there is continuous activation of the RAS/MAPK pathway, leading to uncontrolled cell proliferation. This persistent cell growth contributes to several characteristics seen in Costello syndrome, including an increased risk for certain cancers (e.g., rhabdomyosarcoma, neuroblastoma, and bladder), the development of benign papillomas on the face and perianal region, overgrowth of the cerebellum (resulting in Chiari I malformation), and overgrowth of heart muscle (leading to hypertrophic cardiomyopathy).

Inheritance of Costello syndrome

The vast majority of cases of Costello syndrome are due to de novo variants in HRAS. Therefore, the recurrence risk for siblings is low, but not zero. This is due to the risk of germline mosaicism, typically quoted at 1-2% (Question 81), which results in only the germ cells (egg or sperm) harboring the HRAS variant. While germline mosaicism cannot be directly tested for, it is presumed to be present if there are multiple siblings with the same genetic condition in a family where both parents have tested negative for the variant in blood or saliva. There is increasing evidence that most de novo variants resulting in Costello and other RASopathies are due to variants in sperm and therefore arise from the paternal lineage. Some cases of Costello also may arise from somatic mosaicism, where a genetic mutation in HRAS arises post-zygotically.

Screening and management recommendations for Costello syndrome

Due to the increased risk of benign and malignant tumors, including rhabdomyosarcoma and bladder cancer (Question 79), individuals with Costello syndrome require regular screening and monitoring for cancer and heart disease. Cancer screening may include periodic abdominal and pelvic ultrasound to screen for rhabdomyosarcoma and neuroblastoma until the age of 10 years (after which the risk for these cancers decreases). In addition, an annual urinalysis to check for hematuria, a sign of bladder cancer, can be performed starting at age ten years. Routine cardiac follow up even in patients without known cardiac disease is also important due to the risk of hypertrophic cardiomyopathy, which can be progressive and life-threatening. For patients with severe cardiomyopathy, treatment with trametinib, an inhibitor of the RAS/MAPK pathway, may reduce the degree of cardiomyopathy. More broadly, there are efforts to repurpose approved anti-cancer therapeutics that inhibit RAS/MAPK signaling to help treat some of the complications of the RASopathies.

Incorrect answers

Question 79

Spontaneous pneumothorax (Choice A) can be seen in Marfan syndrome, a connective tissue disorder affecting the skeleton, eye, and aorta. The risk for pneumothorax is not increased in Costello syndrome. Progressive neurological decline (Choice C) is not typically associated with Costello syndrome, which is instead characterized by developmental delays and non-progressive intellectual disability. Progressive neurological decline can be observed in lysosomal storage disorders such as Tay-Sachs disease, which is characterized by the progressive buildup of toxic metabolites within neurons. Early menopause (choice D) can be seen in Turner syndrome, a condition affecting females that is also associated with short stature and cardiac anomalies, and is not a feature of Costello syndrome.

Question 80

Frameshift variants (p.Leu69HisfsTer10, Choice A) often result in stop-gain variants that truncate the protein prematurely and result in haploinsufficiency. While many genetic disorders can be due to haploinsufficiency (loss of 50% of the normal amount of protein expressed; think “half”-loinsufficiency), Costello syndrome is due to gain-of-function rather than haploinsufficiency. In-frame deletions, which result in the loss of 1 or more amino acids, are not well-established causes of Costello syndrome. The in-frame deletion (p.Tyr157del) in Choice B results in the loss of 1 amino acid and is seen in the general population. Splice site variants that do not occur at canonical splice donor or acceptor site (e.g., c.451-9C>T, Choice D) are more difficult to interpret in terms of their clinical significance and are often not clearly pathogenic. Splice site variants are not well-established causes of Costello syndrome.

Question 81

A recurrence risk of 50% (Choice A) is seen with disorders inherited in an autosomal dominant manner. Costello syndrome is usually not inherited and typically occurs de novo in a child. While transmission of Costello from an affected parent to child is technically possible, the likelihood that either parent carries the HRAS variant is quite low in this case given their lack of symptoms and the fact that Costello syndrome has near-complete penetrance (~100%). If germline mosaicism for an HRAS variant were present (~1-2% of cases), then the recurrence risk for each pregnancy would be 50%. Testing Tim (Choice B), the new partner of the mother, would be needed to assess risk if the disorder in question were inherited in an autosomal recessive manner. Costello syndrome is not sex-linked and affects males and females equally (Choice D).

Learning objective

Costello syndrome, characterized by the "7 C’s," is a multi-systemic disorder caused by de novo, gain-of-function variants in the HRAS gene. These variants activate the RAS/MAPK signaling pathway and promote uncontrolled cell growth. This excessive cell growth underlies several clinically-important features seen in Costello syndrome, including a predisposition to cancer, skin papillomas, hypertrophic cardiomyopathy, and Chiari I malformation. Routine surveillance for certain cancers and cardiac complications such as hypertrophic cardiomyopathy is recommended. Costello syndrome shares clinical overlap with other RASopathies (e.g. Noonan, cardio-facio-cutaneous syndrome), which are disorders characterized by constitutional variants that activate the RAS/MAPK signaling pathway.

2023 ABMGG General Exam Blueprint | V. Single gene inheritance → d. Single gene disorders → iii) Cardiac disorders

2023 ABGC Exam Content Outline | Domain 1C. Genetic Conditions → 1. Clinical features, 5. Management options, and 8. Etiology

References

Costello syndrome (GeneReviews)

RASopathies and cardiac manifestations (2023 review article)

RASopathies network (patient advocacy group)