In Silico Functional Assessment of COL4A3, COL4A4, and COL4A5 SNPs in Alport Syndrome
TL;DR
A substantial number of deleterious variants involved glycine substitutions, which are likely to affect protein flexibility, folding, and intermolecular interactions, potentially impairing the structural integrity of the glomerular basement membrane.
Abstract
Aim: Alport syndrome is a rare genetic disorder characterized by hematuria, proteinuria, progressive renal failure, and, in some cases, hearing and visual impairment. This study aims to identify and prioritize deleterious missense single-nucleotide polymorphisms (SNPs) in the COL4A3, COL4A4, and COL4A5 genes associated with Alport syndrome and to evaluate their effects on protein stability and three-dimensional structure using an integrated multi-tool in silico approach.Method: SNP data and protein amino acid sequences were obtained from the NCBI dbSNP and UniProt databases; these data were used as input in in silico analyses performed using various bioinformatics tools, including SIFT, PolyPhen-2, SNPs&GO, PANTHER, PROVEAN, SNAP2, Mutation Assessor, I-Mutant 2.0, MUpro, and Project HOPE, to evaluate the potential structural and functional effects on COL4A3, COL4A4, and COL4A5 proteins. Only variants predicted as deleterious by all applied tools were selected for further analysis.Results: A large number of SNPs were initially identified for COL4A3, COL4A4, and COL4A5 genes; however, multi-tool consensus analysis identified 12, 14, and 146 deleterious missense variants in COL4A3, COL4A4, and COL4A5, respectively. Protein stability analyses produced divergent results: I-Mutant 2.0 predicted increased stability for 160 of 172 variants, whereas MUpro predicted decreased stability for 147 variants. In addition, a substantial number of deleterious variants involved glycine substitutions, which are likely to affect protein flexibility, folding, and intermolecular interactions, potentially impairing the structural integrity of the glomerular basement membrane.Conclusion: This study represents a comprehensive consensus-based in silico evaluation of deleterious missense SNPs in COL4A3, COL4A4, and COL4A5 genes. The findings highlight the potential role of glycine substitutions in disease pathogenesis and provide an important basis for future experimental studies.
