Identification of deleterious single nucleotide polymorphism (SNP)s on the humanTBX5gene & prediction of their structural & functional consequences: Anin silicoapproach

Abstract

T-box transcription factor 5 (TBX5) gene encodes the transcription factor TBX5 which plays a crucial role in the development of the heart and upper limbs. Alternative splicing resulting in several isoforms regulate the functions of this gene during the developmental process. Damaging single nucleotide variants in this gene alter the structure and disturb the functions of TBX5 and ultimately cause Holt-Oram Syndrome (HOS), an autosomal dominant disease where various congenital malformations of the heart (with or without conduction defects), upper limbs and shoulder girdles are observed. Besides HOS, TBX5 single nucleotide variants can also be associated with Dilated Cardiomyopathy, Atrial Fibrillation, and Tetralogy of Fallot without skeletal deformity. By exploiting available Single Nucleotide Polymorphism information in dbSNP, this study was designed to identify in silico the deleterious TBX5 SNPs, and predict their structural and functional consequences, and alteration of biochemical properties on the candidate protein. For this purpose, various reliable in silico analysis tools such as PROVEAN, SIFT, PolyPhen-2, MutPred2, PredictSNP1, PredictSNP2, MetaLR, MetaSVM, REVEL, ConSurf, NetsurfP-2.0, iStable 2.0, Missense3D, UTRdb, MirSNP, and Human Splicing Finder (HSF) have been used. 58 missense substitutions were found damaging by both sequence homology-based tools SIFT (Sorting Intolerant from Tolerant) and PROVEAN (Protein Variation Effect Analyzer), and structure homology-based tool PolyPhen-2 (Polymorphism Phenotyping-2). Among these 58 substitutions, 13 are already annotated as Pathogenic/Likely Pathogenic in ClinVar database, and so they were excluded. Then, the rest 45 high confidence substitutions were further scrutinized by various disease association predicting meta servers. Next, conservation profile of the native amino acid residues, their surface & solvent accessibility, and stability and structural integrity of the protein upon mutation were assessed. Analysis of 1 stop loss SNP, and 2 nonsense SNPs were done by PredictSNP2. Analysis of SNPs in the UTR region were done using UTRdb and MirSNP, and splice site SNPs were evaluated by Human Splicing Finder (HSF). This study provides a comprehensive list of most deleterious SNPs onTBX5 gene. The results from this study can help in early diagnosis of HOS and in relevant genetic counseling.

Whole-Exome Sequencing in a Cohort of High Myopia Patients in Northwest China

“…All mutations in these genes affect the function of the coding region according to the 3D structure model, and CSMD1, ADAMTSL1, and FNDC3B were absent in three examined databases (ExAC, 1000G, gnomAD). SIFT, PolyPhen-2-HDIV, PolyPhen-2-HVAR, Mutation Taster, LRT, Mutation Assessor, FATHMM, RadialSVM, and LR were employed to assess the mutation changes in protein function and mutation changes in protein spatial conformation, which further cause harmful changes in physiological functions (Mahfuz and Khan, 2020).…”

Impact of deleterious missense PRKCI variants on structural and functional dynamics of protein

“…SNPs were analyzed on 7 tools for sorting intolerant from tolerant (SIFT) 42 , Polymorphism Phenotyping v2 (PolyPhen-2) 43 , Protein variation effect Analyzer (PROVEAN) 44 , Mutation Accessor 45 , Rare exome variant ensemble learner (REVEL) 46 , meta LR 47 and Annotation dependent depletion (CADD) 48 . Through these tools, rigorous screening of deleterious SNPs was performed.…”