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In silico analysis of non-synonymous single nucleotide polymorphisms of human DEFB1 gene

Authors
  • Venkata Subbiah, Harini1
  • Ramesh Babu, Polani1
  • Subbiah, Usha1
  • 1 Bharath Institute of Higher Education and Research, Chennai, Tamil Nadu, India , Chennai (India)
Type
Published Article
Journal
Egyptian Journal of Medical Human Genetics
Publisher
Springer Berlin Heidelberg
Publication Date
Nov 29, 2020
Volume
21
Issue
1
Identifiers
DOI: 10.1186/s43042-020-00110-3
Source
Springer Nature
Keywords
License
Green

Abstract

BackgroundSingle nucleotide polymorphisms (SNPs) play a significant role in differences in individual’s susceptibility to diseases, and it is imperative to differentiate potentially harmful SNPs from neutral ones. Defensins are small cationic antimicrobial peptides that serve as antimicrobial and immunomodulatory molecules, and SNPs in β-defensin 1 (DEFB1 gene) have been associated with several diseases. In this study, we have determined deleterious SNPs of the DEFB1 gene that can affect the susceptibility to diseases by using different computational methods. Non-synonymous SNPs (nsSNPs) of the DEFB1 gene that have the ability to affect protein structure and functions were determined by several in silico tools—SIFT, PolyPhen v2, PROVEAN, SNAP, PhD-SNP, and SNPs&GO. Then, nsSNPs identified to be potentially deleterious were further analyzed by I-Mutant and ConSurf. Post-translational modifications mediated by nsSNPs were predicted by ModPred, and gene-gene interaction was studied by GeneMANIA. Finally, nsSNPs were submitted to Project HOPE analysis.ResultsTen nsSNPs of the DEFB1 gene were found to be potentially deleterious: rs1800968, rs55874920, rs56270143, rs140503947, rs145468425, rs146603349, rs199581284, rs201260899, rs371897938, rs376876621. I-Mutant server showed that nsSNPs rs140503947 and rs146603349 decreased stability of the protein, and ConSurf analysis revealed that SNPs were located in conserved regions. The physiochemical properties of the polymorphic amino acid residues and their effect on structure were determined by Project HOPE.ConclusionThis study has determined high-risk deleterious nsSNPs of β-defensin 1 and could increase the knowledge of nsSNPs towards the impact of mutations on structure and functions mediated by β-defensin 1 protein.

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