First Comprehensive In Silico Analysis of the Functional and Structural Consequences of SNPs in Human GalNAc-T1 Gene. (4th March 2014)

• Record Type: Journal Article
• Authors: Ali Mohamoud, Hussein Sheikh; Manwar Hussain, Muhammad Ramzan; El-Harouni, Ashraf A.; Shaik, Noor Ahmad; Qasmi, Zaheer Ulhaq; Merican, Amir Feisal; Baig, Mukhtiar; Anwar, Yasir; Asfour, Hani; Bondagji, Nabeel; Al-Aama, Jumana Yousuf
• Other Names: Alexov Emil Academic Editor.
• Is Part Of: Computational and mathematical methods in medicine. Volume 2014(2014)
• Publication Date: 2014-03-04
• Subjects: Medicine -- Computer simulation -- Periodicals; Medicine -- Mathematical models -- Periodicals; 610.11
• DOI: 10.1155/2014/904052
• Languages: English
• ISSNs: 1748-670X

Abstract

Abstract : GalNAc-T1, a key candidate of GalNac-transferases genes family that is involved in mucin-type O -linked glycosylation pathway, is expressed in most biological tissues and cell types. Despite the reported association of GalNAc-T1 gene mutations with human disease susceptibility, the comprehensive computational analysis of coding, noncoding and regulatory SNPs, and their functional impacts on protein level, still remains unknown. Therefore, sequence- and structure-based computational tools were employed to screen the entire listed coding SNPs of GalNAc-T1 gene in order to identify and characterize them. Our concordant in silico analysis by SIFT, PolyPhen-2, PANTHER-cSNP, and SNPeffect tools, identified the potential nsSNPs (S143P, G258V, and Y414D variants) from 18 nsSNPs of GalNAc-T1 . Additionally, 2 regulatory SNPs (rs72964406 and #x26; rs34304568) were also identified in GalNAc-T1 by using FastSNP tool. Using multiple computational approaches, we have systematically classified the functional mutations in regulatory and coding regions that can modify expression and function of GalNAc-T1 enzyme. These genetic variants can further assist in better understanding the wide range of disease susceptibility associated with the mucin-based cell signalling and pathogenic binding, and may help to develop novel therapeutic elements for associated diseases.