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Background and objective: Genetic cholestatic liver diseases are increasingly stratified using NGS. The resulting information can guide treatment with novel drugs such as IBAT inhibitors, which have demonstrated efficacy in congenital liver disorders including Alagille syndrome and PFIC. We hypothesised that hypomorphic variants in NOTCH2 or JAG1 may predispose affected individuals to later-onset multifactorial cholestasis.

Method: We re-analysed NGS data from 128 patients with cholestatic liver disease of various aetiologies using a targeted sequencing panel comprising 36 candidate genes associated with hereditary cholestasis. Variants of interest were characterised by filtering allele frequencies in the gnomAD v4.1.0 database and evaluated for potential pathogenicity using bioinformatic tools including CADD, REVEL, and popEVE.

Result: Missense NOTCH2 variants were identified in twelve patients (age range 26–83 years; 10 women), whereas no pathogenic JAG1 variants were detected. None of the private or very rare NOTCH2 variants had previously been reported in paediatric patients with Alagille syndrome. Additional high-impact pro-cholestatic ABCB4 variants were found in three patients, lower-impact ABCB4 variants in another three, and one patient carried an ABCC2 variant associated with Dubin–Johnson syndrome. Low-impact single nucleotide polymorphisms predisposing to cholestatic conditions were identified in five patients. Among the twelve patients with NOTCH2 variants, three exhibited phenotypes consistent with co-inherited pathogenic ABCB4 variants (i.e., PFIC or LPAC syndrome). The filtered allele frequencies of five NOTCH2 variants identified in six patients ranged from 0.12% to 5.05%, suggesting they were unlikely to be associated with modestly or highly penetrant disease. In the remaining three patients, the predicted functional impact, low allele frequency, and absence of alternative explanatory variants support a plausible contribution of NOTCH2 variants to the pathogenesis of episodic intrahepatic cholestasis, consistent with their clinical presentation.

Summary: Our findings suggest that rare heterozygous NOTCH2 variants may predispose carriers to juvenile- or adult-onset recurrent intrahepatic cholestasis, potentially mediated through bile duct paucity.