Characterization of Novel Truncated Variants Identified From Indian Autosomal Dominant Polycystic Kidney Disease Cases

Abstract

Background: Autosomal dominant polycystic kidney disease (ADPKD) is the most common, late-onset and genetically heterogenous disorder. Altered genetic background is the prime cause of ADPKD. Most of the cases showed mutations in PKD1, PKD2, GANAB and DNAJB11. Previous mutation screening studies reported that PKD1 and PKD2 are the major contributors to the disease. Among all types of DNA sequence variants, majority of the variants are protein truncating in nature. Loss of normal polycystin 1 (PC1) and polycystin 2 (PC2) proteins, encoded by PKD1 and PKD2 respectively, leads to the disease manifestation.

Methods: Three cases and 100 controls were selected for mutational screening of PKD1 and PKD2 gene using Sanger sequencing. To characterize the variants, in silico (mutation taster, Align-Grantham Variation Grantham Deviation (Align-GVGD), Polymorphism Phenotyping v2 (PolyPhen2), Protein Variation Effect Analyzer (PROVEAN), Sorting Intolerant From Tolerant (SIFT), Polycystic Kidney Disease Mutation Database (PKDB), ProtScale and protein Basic Local Alignment Search Tool (BLAST-p)) as well as in vitro (Western blot) studies were performed.

Results: We have identified a total of 14 variants (three truncating, three nonsynonymous, seven synonymous and one intronic). Three deletions (PKD1: c.445_445delC, PKD2: c.854_854delG and PKD2: c.1050_1050delC) were confirmed as rare, private and novel mutations in Indian ADPKD cases. Rest 11 variants were previously reported and likely neutral in nature. Loss of conservation of amino acid, decreased hydrophobicity and decreased coil forming ability of truncated proteins were supposed to affect the protein functions. Immunoblotting verified the expression of truncated proteins in cell.

Conclusions: We can conclude that identified deletion variants were truncating in nature and hence they were pathogenic mutations responsible for disease manifestation.




World J Nephrol Urol. 2020;9(1):15-24
doi: https://doi.org/10.14740/wjnu392