Computational Analysis of Single Nucleotide Polymorphism (Snps) In Human MYC Gene - Abstract
Background: The proto-oncogene c-MYC encodes a transcription factor that regulates cell proliferation, growth, apoptosis microRNAs expression. Dysregulated expression or function of c-Myc is one of the most common abnormalities in human malignancy. The c-myc gene comprises three exons. Exon 1 contains two promoters and is non coding. Exons 2 and 3 encode the Myc protein with translation initiation at nucleotide 16 of exon. In this paper we focused on predicting the effects that can be imposed by single nucleotide polymorphisms that have been reported in MYC gene using Insilico approaches.
Material and Methods: MYC gene was investigated in NCBI database (http://www.ncbi.nlm.nih.gov/) and SNPs were analyzed by computational softwares. SNPs in the coding region (exonal SNPs) that are non-synonymous (nsSNP) were analyzed by (sift, polyphen, Imutant and PHD-snp) softwares, and SNPs at un-translated region at 3’ends (3’UTR) were analyzed to predict the effect on miRNA binding on these regions that may greatly associated with tumor progression [25]. The SNPs at un-traslated region at 5’ ends (5UTR) were analyzed too by SNPs Function prediction software
Result: We analyzed 5954 SNPs from NCBI ,647 of them found in Homo sapiens, 156 SNPs in coding non synonymous regions (missense), 101 synonymous, 42 3UTR and 47 5UTR. Only SNPs are present on coding region, 3UTR and 5UTR selected to analysis.
Conclusion: Four SNPs had high score with PSIC SD range (1-099) and TOLERANCE INDEX equal (0 - 0.009); rs200431478, rs114570780, rs150308400, rs137906262. There were predicted to change the protein stability but only rs150308400 was predicted to be disease related. in 3UTR there were only 11 functional SNPs predicted, rs185650723 and rs4645970 contain D allele which is derived allele that disrupts a conserved miRNA sit while rs35524866 SNP contain (C) allele which is can create a new microRNA site.