Expanding the Mutation Spectrum of USP53 and Evaluating the Functional Consequences of USP53 Missense Variants through Protein Modeling in Indian Patients with Progressive Familial Intrahepatic Cholestasis 7

Abstract Background: Progressive familial intrahepatic cholestasis (PFIC), is a rare genetic disorder characterized by impaired bile flow, leading to liver dysfunction. The USP53 gene has been recently associated with PFIC type 7, with or without hearing loss (OMIM # 619658), with limited variant characterization in literature. In this case series, we employed computational structural biology techniques, including homology modeling, to investigate missense variants detected in two unrelated Indian children as well as four missense variants previously reported to understand their pathogenicity. We also report other disease-causing variants in USP53 in a total of ten Indian patients. Materials and Methods: Phenotype-driven whole-exome sequencing was performed in all ten patients. Computational protein modeling was performed for the 2 missense variants detected in our study and four previously reported missense variants. Results: Sequencing revealed five novel variants, comprising three loss-of-function variants and two missense variants. We performed structural analysis of six missense variants, unraveling their damaging effects on the protein structure, thus supporting their classification as likely pathogenic. The final analysis revealed distinct patterns of molecular changes associated with each missense variant, highlighting their impact on protein stability, interactions, and local topology. Conclusions: Our study highlights the c.822+1delG variant as a common mutation in the Indian subcontinent, contributing to the growing knowledge of USP53 -related PFIC. These findings offer unprecedented insights into USP53 -related PFIC and underscore the significance of employing computational structural biology techniques for deciphering the molecular basis of genetic diseases. These results hold promising implications for genetic counseling and therapeutic interventions.