Sequencing of FIC1, BSEP and MDR3 in a large cohort of patients with cholestasis revealed a high number of different genetic variants

BACKGROUND&AIMS: The bile salt export pump (BSEP, ABCB11), multidrug resistance protein 3 (MDR3, ABCB4) and the ATPase familial intrahepatic cholestasis 1 (FIC1, ATP8B1) mediate bile formation. Mutations in these genes underlie cholestatic liver diseases ranging from intrahepatic cholestasis of pregnancy, benign recurrent intrahepatic cholestasis or low phospholipid-associated cholelithiasis to progressive familial intrahepatic cholestasis.

METHODS: Coding exons with flanking intron regions of ATP8B1, ABCB11, and ABCB4 were sequenced in cholestatic patients with assumed genetic cause. Effects of new variants were evaluated by bioinformatics tools and 3D protein modelling.

RESULTS: In 427 patients with suspected inherited cholestasis 149 patients carried at least one disease-causing mutation in FIC1, BSEP or MDR3, respectively. Overall, 154 different mutations were identified comprising 25 novel ones. All 13 novel missense mutations were disease-causing according to bioinformatics analyses and homology modelling. 82% of patients with at least one disease-causing mutation in either of the three genes were children. One or more common polymorphisms were found in FIC1 in 35.3%, BSEP in 64.3% and MDR3 in 72.6% of patients without disease-causing mutation in the respective gene. Minor allele frequencies of common polymorphisms in BSEP and MDR3 varied in our cohort compared to the general population as described by gnomAD. However, differences in ethnic background may contribute to this effect.

CONCLUSIONS: In a large cohort of patients, 154 different variants were detected in FIC1, BSEP, and MDR3, 25 of which were novel. In our cohort, frequencies for risk alleles of BSEP (p.V444A) and MDR3 (p.I237I) polymorphisms were significantly overrepresented in patients without disease-causing mutation in the respective gene, underscoring that these common variants can contribute to a cholestatic phenotype.

LAY SUMMARY: FIC1, BSEP, and MDR3 represent hepatobiliary transport proteins essential for bile formation. Genetic variants in these transporters underlie a broad spectrum of cholestatic liver diseases. To confirm a genetic contribution to the patients' phenotypes, gene sequencing of these three major cholestasis-related genes was performed in 427 patients and revealed 154 different variants of which 25 have not been reported in a database yet. In patients without disease-causing mutation, common genetic variants were detected in a high number of cases, indicating that these common variants may contribute to cholestasis development.