Whole exome sequencing in pediatric hyperammonemia: significant diagnostic yield and identification of three novel variants.

backgroundHyperammonemia, not a disorder, but an outcome of a disorder marked by elevated ammonia levels in the blood, is a serious medical condition that makes accurate diagnosis based on clinical and laboratory findings challenging. In this scenario, employing advanced genetic tests like whole exome sequencing can provide crucial insights that help clinicians better manage the disease. Also, identifying disease-causing variants provides conditions for genetic counseling and subsequent preventive measures, including prenatal diagnosis.

methodsThis study was conducted at the Comprehensive Genetic Services Center (CGSC) of Shahid Beheshti University of Medical Sciences (SBMU), Iran, from 2020 to 2024, involving 20 pediatric patients with clinically suspected hyperammonemia due to inborn errors of metabolism (IEMs). All patients underwent biochemical testing, including plasma amino acid (PAA). Whole-exome sequencing (WES) was performed for molecular diagnosis, and identified variants were interpreted according to ACMG/AMP guidelines. The identified variants were confirmed by Sanger sequencing in all the probands. No additional in vitro functional assays were performed.

resultsAmong the twelve genetically confirmed cases, pathogenic or likely pathogenic variants were identified in genes related to urea cycle disorders (CPS1, OTC, ASS1), organic acidemias (MMUT, PCCB, HMGCL), amino acid transport defects (SLC7A7), and mitochondrial disorders (PDHA1). Patients with CPS1 variants (P2 and P3) presented with hyperammonemia, seizures, and developmental delay, with distinct biochemical profiles reflecting different degrees of enzyme deficiency. The patient with MMUT variant (P10) showed marked metabolic acidosis, consistent with methylmalonic aciduria. Variants in OTC (P4, P5) and ASS1 (P6) were associated with urea cycle dysfunction with hyperammonemia, but the elevated plasma citrulline level was a significant biochemical finding in the patient (P6). Patients with HMGCL (P7), SLC7A7 (P8), and PCCB (P11) variants exhibited organic aciduria patterns compatible with their respective enzymatic defects. In addition, a hemizygous variant in PDHA1 (P12) was identified in a male patient with increased lactate and microcephaly. Detailed clinical, biochemical, and molecular features of all confirmed cases are summarized in Table 3.

conclusionThis study highlights the efficacy of whole exome sequencing in diagnosing genetically heterogeneous conditions like hyperammonemia, with implications for treatment optimization and genetic counseling. The identification of novel variants enhances understanding of the genetic landscape in populations with high rates of consanguinity. Future research should focus on expanding genetic databases and exploring the functional impacts of newly discovered variants.