In Silico Analysis of Single Nucleotide Polymorphism in Human Prothrombin Gene

Many SNPs in the Prothrombin gene were known to be of clinical significance and associated with variety of clinical states. Molecular composition of F2 gene variants could help in studying genotypic phenotypic relationship. We used computational methods to analyze F2 gene variants and predict the disease associated variants either due structural variation or expression dysregulation.F2 gene contain 2938 SNPs in Homo sapiens, 202 missense, 5 nonsynonymous, 118 synonymous, 21 in the 3'UTR and 10 in the 5'UTR. There were two SNPs In the 3'UTR with three different alleles two of them disrupts the miRNA binding site while the third one creates new miRNA binding sites. Of the missense SNPs 17.3% (35/202) were damaging by both SIFT and Polyphen-2. The SNPs then analyzed by I-Mutant 100% (35/35) of them found to be change protein stability, of which 65.7% (23/35) were disease related variants according to PHD-SNP. Damaging SNPs were then presented to Project HOPE for further functional analysis and Structural modeling. Our work proposes twelve most deleterious SNPs to be associated with Prothrombin gene disease affecting human health, SNP ID (rs121918484, rs147456134, rs150569436, rs121918482, rs139552841, rs121918478, rs377462682, rs202003146, rs121918480, rs142495261, rs201577861, rs188001809).