A novel computational and structural analysis of nsSNPs in CFTR geneReport as inadecuate

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Genomic Medicine

, Volume 2, Issue 1–2, pp 23–32

First Online: 14 May 2008Received: 15 February 2008Accepted: 25 April 2008DOI: 10.1007-s11568-008-9019-8

Cite this article as: George Priya Doss, C., Rajasekaran, R., Sudandiradoss, C. et al. HUGO J 2008 2: 23. doi:10.1007-s11568-008-9019-8


Single Nucleotide Polymorphisms SNPs are being intensively studied to understand the biological basis of complex traits and diseases. The Genetics of human phenotype variation could be understood by knowing the functions of SNPs. In this study using computational methods, we analyzed the genetic variations that can alter the expression and function of the CFTR gene responsible candidate for causing cystic fibrosis. We applied an evolutionary perspective to screen the SNPs using a sequence homology-based SIFT tool, which suggested that 17 nsSNPs 44% were found to be deleterious. The structure-based approach PolyPhen server suggested that 26 nsSNPS 66% may disrupt protein function and structure. The PupaSuite tool predicted the phenotypic effect of SNPs on the structure and function of the affected protein. Structure analysis was carried out with the major mutation that occurred in the native protein coded by CFTR gene, and which is at amino acid position F508C for nsSNP with id rs1800093. The amino acid residues in the native and mutant modeled protein were further analyzed for solvent accessibility, secondary structure and stabilizing residues to check the stability of the proteins. The SNPs were further subjected to iHAP analysis to identify htSNPs, and we report potential candidates for future studies on CFTR mutations.

KeywordsCFTR gene SIFT PolyPhen UTR Modeled structure Haplotype  Download fulltext PDF

Author: C. George Priya Doss - R. Rajasekaran - C. Sudandiradoss - K. Ramanathan - R. Purohit - R. Sethumadhavan

Source: https://link.springer.com/

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