First Comprehensive In Silico Analysis of the Functional and Structural Consequences of SNPs in Human GalNAc-T1 Gene

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 comp...

Full description

Saved in:

Bibliographic Details
Published in:	Computational and mathematical methods in medicine Vol. 2014; no. 2014; pp. 1 - 15
Main 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, Bundajji, Nabil S., al-Aama, Jumana Yousuf
Format:	Journal Article
Language:	English
Published:	Cairo, Egypt Hindawi Puplishing Corporation 01-01-2014 Hindawi Publishing Corporation
Subjects:	Algorithms Amino Acid Sequence Bayes Theorem Binding Sites Computational Biology - methods Computer Simulation Conserved Sequence Data Mining - methods Disease Susceptibility Evolution, Molecular Humans Hydrogen Bonding Ligands Models, Molecular Molecular Conformation Molecular Sequence Data Mutation N-Acetylgalactosaminyltransferases - genetics Polymorphism, Single Nucleotide Polypeptide N-acetylgalactosaminyltransferase Protein Binding Protein Interaction Mapping Sequence Homology, Amino Acid Software Static Electricity
Online Access:	Get full text
Tags:	Add Tag No Tags, Be the first to tag this record!

Description
Summary:	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.
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 Academic Editor: Emil Alexov
ISSN:	1748-670X 1748-6718
DOI:	10.1155/2014/904052