Genomic structure of SLC2A4, substitutions found, inferred haplotypes and their frequencies.
2010-03-23T02:15:24Z (GMT) by
<p>Substitutions are represented by arrows and when no dbSNP name is available, named as in the SNP500Cancer database. A total of 29 polymorphisms (25 SNPs and 4 INDELs) were detected in the 204 worldwide re-sequenced chromosomes. Forty five percent of the substitutions were singletons and only 8 reached a MAF>0.05 in at least one studied population. Comparison with the homologous chimpanzee sequence suggests that for all SNPs the ancestral allele is modal in humans. In the human genome, there is a 27 bp fixed deletion 348 bp upstream of the transcription initiation site. Three non-coding SNPs are in evolutionarily conserved positions (UCSC Genome Browser, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0009827#pone.0009827-Sabeti1" target="_blank"></a>): rs5415 (conservation score: 0.96), within the promoter region, as well as rs222847 and rs222849, both with conservation score of 0.99 and within the first intron. Only one of the 4 coding-SNPs is non-synonymous (rs8192702, Ala358Val, a conservative substitution in exon 9, in the ninth trans-membrane domain), observed in a European. Haplotypes are inferred using only the 8 common SNPs.</p>