Identification of functional SNPs in human LGALS3 gene by in silico analyses

Abstract

Background: Galectin-3 protein, an S-type lectin, is encoded by LGALS3 gene. It consists of carbohydrate recognition domain (CRD), collagen like tandem repeats of nine amino acids and N-terminal 12-mer peptide. Its serum levels as well as some genetic variants were reported to be involved in various disease conditions like cancer, autoimmune diseases, heart diseases etc. Being viewed as an important molecule in biological responses and its association with various diseases, the present study was designed. This is the first in silico analyses of LGALS3.
Aim: To systematically explore the plausible effects of LGALS3 genetic variants on structure and functions of galectin-3.
Material and methods: Both sequence based and structure based approaches were adopted for analyses of non-synonymous single nucleotide polymorphisms (nsSNPs). Putative methylation and other post translational modifications were also analyzed using different tools. Muster and Swiss-PDB Viewer were used for modeling of predicted functional variants.
Results: Out of 1130 SNPs reported in dbSNP, only validated SNPs were chosen for analyses. A total of nine nsSNPs which included, 3 of N-terminal region and 6 of CRD encoding region, were found to have deleterious effect as predicted by various softwares. Analyses of regulatory SNPs predicted five functional SNPs in 30UTR having putative miRNA binding sites and 3 intronic SNPs in potential transcription factor binding sites.
Conclusion: Based on these analyses, the present study suggested that the reported functional SNPs may act as potential targets in genetic association studies.