Structural and functional impact of SNPs in P-selectin gene: A comprehensive in silico analysis

Structural and functional impact of SNPs in P-selectin gene: A comprehensive in silico analysis AbstractP-selectin is an adhesion molecule which plays an important role in the development of inflammation. It is encoded by the SELP gene located on chromosome 1q21-q24. Various single nucleotide polymorphisms (SNPs) of SELP have been reported to be associated with various inflammatory disease conditions. The genetics behind these diseases could be better understood by knowing the structural and functional impact of various genetic determinants of SELP. So far, this is the first comprehensive and systematic in silico analysis of SNPs in SELP. A total of 2780 SNPs of SELP were retrieved from NCBI dbSNP. Only conserved and validated SNPs with minor allele frequency (MAF) ≥ 0.05 were subjected to further analysis. Based on these criteria, we selected 4 non-synonymous SNPs (nsSNPs) and 119 non-coding SNPs (ncSNPs). The nsSNPs were analyzed for deleterious effects using SIFT, Polyphen-2, nsSNPAnalyzer, SNP & Go, SNPs3, Mutperd and I-mutant web tools. The template prediction for variant structure modeling was performed using MUSTER and SWISS-MODEL. The functional impact of ncSNPs was analyzed by SNPinfo and RegulomeDB. The in silico analysis predicted 3 nsSNPs and 21 ncSNPs as potential candidates for future case-control association studies and functional analysis of SELP. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Open Life Sciences de Gruyter

Structural and functional impact of SNPs in P-selectin gene: A comprehensive in silico analysis

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Publisher
De Gruyter Open
Copyright
© 2017 Raminderjit Kaur et al.
ISSN
2391-5412
eISSN
2391-5412
D.O.I.
10.1515/biol-2017-0003
Publisher site
See Article on Publisher Site

Abstract

AbstractP-selectin is an adhesion molecule which plays an important role in the development of inflammation. It is encoded by the SELP gene located on chromosome 1q21-q24. Various single nucleotide polymorphisms (SNPs) of SELP have been reported to be associated with various inflammatory disease conditions. The genetics behind these diseases could be better understood by knowing the structural and functional impact of various genetic determinants of SELP. So far, this is the first comprehensive and systematic in silico analysis of SNPs in SELP. A total of 2780 SNPs of SELP were retrieved from NCBI dbSNP. Only conserved and validated SNPs with minor allele frequency (MAF) ≥ 0.05 were subjected to further analysis. Based on these criteria, we selected 4 non-synonymous SNPs (nsSNPs) and 119 non-coding SNPs (ncSNPs). The nsSNPs were analyzed for deleterious effects using SIFT, Polyphen-2, nsSNPAnalyzer, SNP & Go, SNPs3, Mutperd and I-mutant web tools. The template prediction for variant structure modeling was performed using MUSTER and SWISS-MODEL. The functional impact of ncSNPs was analyzed by SNPinfo and RegulomeDB. The in silico analysis predicted 3 nsSNPs and 21 ncSNPs as potential candidates for future case-control association studies and functional analysis of SELP.

Journal

Open Life Sciencesde Gruyter

Published: Feb 28, 2017

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