A Comprehensive <i>in Silico</i> Analysis of the Functional and Structural Consequences of the Deleterious Missense Nonsynonymous SNPs in Human <i>GABRA6</i> Gene

Abstract

Epilepsy, a prevalent neurological disorder, affects more than 50 million individuals worldwide and is characterized by recurring seizures. Nonsynonymous single nucleotide polymorphisms (nsSNPs) found within coding regions of epilepsy-related genes are believed to have significant impacts on protein function. This is due to their tendency to cause mutations in the encoded amino acids, which can subsequently lead to pathogenic alterations in protein structure and function. Consequently, nsSNPs have the potential to serve as diagnostic markers for epilepsy and other neuropsychiatric conditions. The primary objective of this study is to evaluate the harmful effects of missense nsSNP mutations on the <em>GABRA6</em> gene. The <em>GABRA6</em> gene encodes the alpha-6 subunit of the GABA<sub>A</sub> receptor, and previous research showed one case substitution mutation in the GABRA6 gene is associated with childhood absence epilepsy (CAE) and atonic seizures. To achieve this, we employed various computational tools, including SIFT, PolyPhen-2, PROVEAN, Condel, SNPs & GO, PMut, SNAP2, MutPred2, and SNPeffect4.0, for predicting missense nsSNPs. Additionally, we used I-Mutant3.0 and MUpro to analyze protein stability, ConSurf to assess evolutionary conservation, FTSite and COACH to predict ligand binding sites, SOPMA and PSIPRED to analyze protein secondary structures, project HOPE to predict structural changes, and I-TASSER to model the 3D structure. Furthermore, structural validation was conducted using the PROCHECK and ERRAT servers. At the same time, molecular dynamics simulations were performed using GROMACS to gain a better understanding of the effects of mutations on protein structure. Among the 451 missense nsSNPs identified within the <em>GABRA6</em> gene, three were found to have pathogenic effects on the structure and function of the protein, potentially, there may be a contribution to the development of seizures or other neuropsychiatric disorders. Notably, two of these missense nsSNPs (<em>W87S</em> and <em>W112R</em>) were located within the ligand-binding domain, while the third (<em>C310R</em>) was situated in the transmembrane domain. It is crucial to acknowledge that despite their predicted pathogenicity, these variants are currently classified as of uncertain significance in clinical and genomic databases worldwide due to the lack of correlation with epilepsy in empirical studies. Without experimental data to validate these predictions, caution is warranted in interpreting the findings.