In-silico analysis of phylogenetic relationship and potentially damaging nsSNPs in human SLC2A2 gene

Abstract

Transport of glucose across the eukaryotic cell membranes is carried out by members of the glucose transporter (GLUT) family which is mainly divided into three classes (I, II and III) on the basis of phylogenetic relationship. In humans, one member of Class I called GLUT2 is encoded by solute carrier family 2, facilitated glucose transporter member 2 (SLC2A2) gene located on third chromosome. Protein mediated glucose movement across cell membranes is made possible through GLUT2 that is a trans-membrane carrier protein. It regulates the entry of glucose and secretion of insulin in the pancreatic cell. It has three isoforms and the longest isoform consists of 524 amino acid. There are 13 extracellular, 12 transmembrane and 5 cytoplasmic domains in human GLUT2. The risk of Fanconi-Bickel syndrome (FBS), diabetes, breast cancer (BC) and Alzheimer disease (AD) is associated with improper functioning of GLUT2. The most frequent form of genetic changes is single nucleotide polymorphism (SNPs). Non synonymous SNPs (nsSNPs) can result in alterations of amino acids and subsequent changes in phenotype. In this study, in-silico analysis was done to find phylogenetic relationship of human GLUT2 protein and possible deleterious effect of nsSNPs of its coding region. Clustal Omega was used to make phylogenetic tree. SIFT, PolyPhen, PROVEAN and SNPeffect were used to predict deleterious or tolerated SNPs. 167 nsSNPs were predicted to be damaging by SIFT, 65 to be possibly damaging and 77 to be probably damaging by PolyPhen. PROVEAN predicted 162 nsSNPs to be neutral and 138 to be deleterious. 101 SNPs were found to be damaging by three algorithms; SIFT, PolyPhen and PROVEAN.

Keywords

• GLUT2
• SLC2A2 gene
• In silico analysis
• nsSNP
• Phylogenetic analysis