Document Type

Article

Publication Date

10-11-2026

Identifier

DOI: 10.3390/genes17101259; PMCID: PMC13704217

Abstract

Background/Objectives: Interpretation of NOTCH2 variants of uncertain significance (VUSs) remains challenging in pediatric cholestasis and suspected Alagille syndrome (ALGS) due to incomplete penetrance, phenotypic variability, and extensive genetic variation. Although disease-specific variant classification criteria have identified pathogenic hotspots within epidermal growth factor (EGF)-like repeats 8-12 and ankyrin repeat domains 3-6, characterizing these VUSs requires a robust framework. Methods: We reviewed aggregate deidentified data from 519 multigene cholestasis panel entries and evaluated genotype-phenotype data from a consortium cohort of 7 pediatric patients with heterozygous NOTCH2 VUSs using a clinical-genomic prioritization framework informed by disease-specific ACMG criteria and domain location. Results: Across the 519 entries, 365 unique NOTCH2 VUSs were identified, none of which overlapped with 69 previously reported ALGS-associated variants or localized to established hotspots, with over 60% occurring outside recognized functional domains. Among the 7 consortium cases, one patient carrying a cysteine-altering variant (p.Cys593Arg) in EGF-like domain 15 demonstrated a strong ALGS-compatible phenotype, while alternative diagnoses in other cases included trisomy 21 and congenital hepatic fibrosis with polycystic kidney disease. Conclusions: 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. However, 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 for further evaluation.

Journal Title

Genes (Basel)

Volume

17

Issue

10

MeSH Keywords

Humans; Receptor, Notch2; Cholestasis; Alagille Syndrome; Female; Child; Genetic Association Studies; Male; Phenotype; Child, Preschool; Genetic Variation; Infant; Mutation

PubMed ID

42938375

Keywords

Alagille syndrome; cholestasis; domain mapping; genetic testing; precision medicine; variant interpretation; variant of uncertain significance

Comments

Grants and funding

This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license.

Publisher's Link: https://www.mdpi.com/2073-4425/17/10/1259

Download

Share

COinS