Identification of deleterious single nucleotide polymorphism (SNP)s in the human
TBX5 gene & prediction of their structural & functional consequences: An
in silico approach.
Biochem Biophys Rep 2021;
28:101179. [PMID:
34917776 PMCID:
PMC8646135 DOI:
10.1016/j.bbrep.2021.101179]
[Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 11/23/2021] [Accepted: 11/25/2021] [Indexed: 12/29/2022] Open
Abstract
T-box transcription factor 5 gene (TBX5) encodes the transcription factor TBX5, which plays a crucial role in the development of heart and upper limbs. Damaging single nucleotide variants in this gene alter the protein structure, disturb the functions of TBX5, and ultimately cause Holt-Oram Syndrome (HOS). By analyzing the available single nucleotide polymorphism information in the dbSNP database, this study was designed to identify the most deleterious TBX5 SNPs through insilico approaches and predict their structural and functional consequences.
Fifty-eight missense substitutions were found damaging by sequence homology-based tools: SIFT and PROVEAN, and structure homology-based tool PolyPhen-2. Various disease association meta-predictors further scrutinized these SNPs. Additionally, conservation profile of the amino acid residues, their surface accessibility, stability, and structural integrity of the native protein upon mutations were assessed. From these analyses, finally 5 SNPs were detected as the most damaging ones: [rs1565941579 (P85S), rs1269970792 (W121R), rs772248871 (V153D), rs769113870 (E208D), and rs1318021626 (I222N)]. Analyses of stop-lost, nonsense, UTR, and splice site SNPs were also conducted.
Through integrative bioinformatics analyses, this study has identified the SNPs that are deleterious to the TBX5 protein structure and have the potential to cause HOS. Further wet-lab experiments can validate these findings.
Deleterious SNPs in the human TBX5 gene responsible for Holt-Oram Syndrome have been identified.
58 missense and 2 nonsense SNPs were identified as deleterious.
86 3′ UTR SNPs were predicted to be located on miRNA target sites.
Possible effects of missense SNPs on the TBX5 protein structure have been studied.
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