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Patel SM, Koringa PG, Reddy BB, et al. In silico analysis of consequences of non-synonymous SNPs of Slc11a2 gene in Indian bovines. Genom Data. 2015;5:72-9doi: 10.1016/j.gdata.2015.05.015.
Patel, S. M., Koringa, P. G., Reddy, B. B., Nathani, N. M., & Joshi, C. G. (2015). In silico analysis of consequences of non-synonymous SNPs of Slc11a2 gene in Indian bovines. Genomics data, 572-9. https://doi.org/10.1016/j.gdata.2015.05.015
Patel, Shreya M, et al. "In silico analysis of consequences of non-synonymous SNPs of Slc11a2 gene in Indian bovines." Genomics data vol. 5 (2015): 72-9. doi: https://doi.org/10.1016/j.gdata.2015.05.015
Patel SM, Koringa PG, Reddy BB, Nathani NM, Joshi CG. In silico analysis of consequences of non-synonymous SNPs of Slc11a2 gene in Indian bovines. Genom Data. 2015 May 30;5:72-9. doi: 10.1016/j.gdata.2015.05.015. eCollection 2015 Sep. PMID: 26484229; PMCID: PMC4583633.
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Genom Data. 2015 May 30;5:72-9. doi: 10.1016/j.gdata.2015.05.015. eCollection 2015 Sep.

In silico analysis of consequences of non-synonymous SNPs of Slc11a2 gene in Indian bovines.

Genomics data

Shreya M Patel, Prakash G Koringa, Bhaskar B Reddy, Neelam M Nathani, Chaitanya G Joshi

Affiliations

  1. Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand,388001 Gujarat, India.

PMID: 26484229 PMCID: PMC4583633 DOI: 10.1016/j.gdata.2015.05.015

Abstract

The aim of our study was to analyze the consequences of non-synonymous SNPs in Slc11a2 gene using bioinformatic tools. There is a current need of efficient bioinformatic tools for in-depth analysis of data generated by the next generation sequencing technologies. SNPs are known to play an imperative role in understanding the genetic basis of many genetic diseases. Slc11a2 is one of the major metal transporter families in mammals and plays a critical role in host defenses. In this study, we performed a comprehensive analysis of the impact of all non-synonymous SNPs in this gene using multiple tools like SIFT, PROVEAN, I-Mutant and PANTHER. Among the total 124 SNPs obtained from amplicon sequencing of Slc11a2 gene by Ion Torrent PGM involving 10 individuals of Gir cattle and Murrah buffalo each, we found 22 non-synonymous. Comparing the prediction of these 4 methods, 5 nsSNPs (G369R, Y374C, A377V, Q385H and N492S) were identified as deleterious. In addition, while tested out for polar interactions with other amino acids in the protein, from above 5, Y374C, Q385H and N492S showed a change in interaction pattern and further confirmed by an increase in total energy after energy minimizations in case of mutant protein compared to the native.

Keywords: ATM, ataxia telangiectasia mutated; BRAF, B-Raf; CFTR, cystic fibrosis transmembrane conductance regulator; GATK, Genome Analysis Tool Kit; GalNAc-T1, N-acetylgalactosaminyltransferase 1; HBB, hemoglobin beta; HMM, Hidden Markov Model; IGF1R, insulin-like growth factor 1 receptor; Ion torrent PGM; NCBI, National Center for Biotechnology Information; Non-synonymous; PANTHER; PANTHER, Protein Analysis Through Evolutionary Relationships; PROVEAN, Protein Variation Effect Analyzer; PolyPhen, Polymorphism Phenotyping; Protein; RMSD, root-mean-square deviation; SIFT; SIFT, sorting intolerant from tolerant; SNP, single nucleotide polymorphism; Slc11a2, solute carrier family 11 member 2; TMDs, transmembrane domains; TYRP1, tyrosinase-related protein 1

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