Among 365 unique NOTCH2 VUSs identified through pediatric cholestasis panel testing, none overlapped with previously reported ALGS-associated variants or localized to established pathogenic hotspots, but a cysteine-altering variant outside canonical hotspots occurred in a patient with a strong ALGS-compatible phenotype, highlighting the importance of integrating variant characteristics, domain location, detailed phenotyping, and alternative diagnoses when prioritizing NOTCH2 VUSs.
Review of 519 multigene cholestasis panel entries identified 365 unique NOTCH2 variants of uncertain significance (VUSs).
None of the 365 NOTCH2 VUSs overlapped with the 69 previously reported ALGS-associated variants.
None of the 365 NOTCH2 VUSs localized to established pathogenic hotspots (EGF-like repeats 8-12 and ankyrin repeat domains 3-6).
More than 60% of the NOTCH2 VUSs occurred outside recognized functional domains.
Among 7 consortium patients with heterozygous NOTCH2 VUSs, one patient with a cysteine-altering variant (p.Cys593Arg) in EGF-like domain 15 had a strong ALGS-compatible phenotype.
Alternative diagnoses were identified in other consortium cases, including trisomy 21 and congenital hepatic fibrosis with polycystic kidney disease.
Prioritizing NOTCH2 VUSs requires integrating variant characteristics, domain location, detailed phenotyping, and alternative diagnoses.
Alagille syndrome is a genetic liver condition that can cause cholestasis (impaired bile flow) in children, and it is sometimes linked to changes in the NOTCH2 gene. Genetic testing often finds NOTCH2 changes whose meaning is unclear, called variants of uncertain significance (VUSs). This makes it hard for doctors and families to know whether a change explains a child's illness. The researchers reviewed data from 519 cholestasis gene panel entries and found 365 different NOTCH2 VUSs. None matched previously reported Alagille-associated variants or fell in the gene regions known to be disease-causing hotspots, and over 60% were outside recognized functional regions. They also examined 7 children with such variants. One child had a change that alters a cysteine amino acid (p.Cys593Arg) in a region outside the usual hotspots, and that child had features strongly consistent with Alagille syndrome. Other children had different explanations for their liver disease, including trisomy 21 and congenital hepatic fibrosis with polycystic kidney disease. This research suggests that most NOTCH2 VUSs found on cholestasis panels are unlikely to match known Alagille-causing patterns, but some variants outside hotspots may still matter. It supports evaluating the type of variant, its location in the protein, the child's detailed clinical features, and other possible diagnoses together. The study is small in terms of clinical cases (7 patients), so the findings are best viewed as a framework for prioritizing variants for further study rather than as definitive conclusions.
Hoskins B, Pramparo T, Vandriel S, Jarasvaraparn C, Wilsey M, Slowik V, et al.. (2026). NOTCH2 VUS Interpretation in Pediatric Cholestasis: A 365-Variant Landscape and Genotype-Phenotype Analysis of 7 Cases.. Genes. https://doi.org/10.3390/genes17101259