Cataloguing functionally relevant polymorphisms in gene DNA ligase I: a computational approach.

3 Biotech
Abhishek A SinghPallavi Somvanshi

Abstract

A computational approach for identifying functionally relevant SNPs in gene LIG1 has been proposed. LIG1 is a crucial gene which is involved in excision repair pathways and mutations in this gene may lead to increase sensitivity towards DNA damaging agents. A total of 792 SNPs were reported to be associated with gene LIG1 in dbSNP. Different web server namely SIFT, PolyPhen, CUPSAT, FASTSNP, MAPPER and dbSMR were used to identify potentially functional SNPs in gene LIG1. SIFT, PolyPhen and CUPSAT servers predicted eleven nsSNPs to be intolerant, thirteen nsSNP to be damaging and two nsSNPs have the potential to destabilize protein structure. The nsSNP rs11666150 was predicted to be damaging by all three servers and its mutant structure showed significant increase in overall energy. FASTSNP predicted twenty SNPs to be present in splicing modifier binding sites while rSNP module from MAPPER server predicted nine SNPs to influence the binding of transcription factors. The results from the study may provide vital clues in establishing affect of polymorphism on phenotype and in elucidating drug response.

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Citations

Sep 6, 2014·Journal of Genetics·Amit Kumar MitraSrikanta Kumar Rath
Apr 14, 2012·Critical Reviews in Microbiology·Baljinder SinghKashmir Singh

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Methods Mentioned

BETA
in silico methods

Software Mentioned

GROMACS
FAS
Visual Molecular Dynamics ( VMD )
rSNP
ESEfinder
FASTSNP
PDB Viewer
PolyPhen
CUPSAT Server
Swiss

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