Identification of Damaging and Deleterious Non-Synonymous Single Nucleotide Polymorphisms (nsSNPs) in the Orang Asli, Jakun

Abstract

The study of genetics and its relation to different disorders has recently been getting remarkable attention worldwide. Non-synonymous single-nucleotide polymorphisms (nsSNPs) are coding variants that introduce amino acid alterations to proteins. Since nsSNPs have various effects on protein structure and function, these changes can significantly impact human health. The primary purpose of this research is to examine the relationship between diseases and Jakun nsSNP mutations. A total of 10 samples with 24,604 nsSNPs were used in the study. Several in silico bioinformatics tools were used to classify the high-risk nsSNPs that might affect the structure and function of proteins in the Jakun tribe. The in silico tools PROVEAN, SIFT and PolyPhen2 identified 1395 high-risk nsSNPs. Further analysis with the DAVID annotation tool revealed that these related genes are associated with cardiovascular diseases, myocardial infarction, Alzheimer's and obesity. Other bioinformatics tools were then used to infer the protein structures of these high-risk nsSNPs. From SNP&GO and PhD-SNPs, the results conclude that there are four damaging nsSNPs in the Jakun tribe. The damaging nsSNPs and the mutation positions are MTHFR (A222V), ESR2 (G445S), ACSM3 (G460R) and UGT3A1 with two mutation sites, C121G and C67G. This study using in silico tools can be the basis for increasing medical discoveries, reducing lab costs and helping with clinical trials for further studies by providing genetically related information.