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A Comprehensive in silico Analysis of Functional and Structural Impact SNPS in the MC1R Gene

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Author(s): Chuan-Sheng Zhang | Li-Ying Geng | Zheng-Zhu Liu | Zhi-Xin Fu | Yuan-Fang Gong | Min-Shan Feng | Chen Juan | Qing-Hui Jia | Qiu-Yue Wang | Xie-Rong Liu | Su-Min Pan

Journal: Journal of Animal and Veterinary Advances
ISSN 1680-5593

Volume: 10;
Issue: 7;
Start page: 928;
Date: 2011;
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Keywords: MC1R | MC1R | SIFT | PolyPhen | PolyPhen | PolyPhen

ABSTRACT
The aim of this study was to analyze the genetic variation that can alter the expression and the function of the MC1R gene using computational methods. Out of the total 222 SNPs, 22 were found to be non-synonymous (ns) SNPs, 9 were found in the 5' upstream and 7 were found in the 3'UTR. It was found that these 6 nsSNPs rs3212366, rs11547464, rs1805009, rs1805008 and rs1805007 were damaging by both the SIFT and the Poly Phen servers. We identified, a mutation from Phe to Leu at positions 196 (rs3212366) on the surface of the protein caused the greatest impact on stability. The rs3212362, rs3212379 and rs35025176 in the 5' upstream were suggested might change the MC1R gene expression levels by FastSNP. Based on the in silico search, the rs3212369 located in the putative Hsa-miR-421 target sequences might have some effect on MC1R gene expression.
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