Thursday, February 1, 2018

Chromosome 4: Rare and Uncommon SNPs

I found a few SNPs in Chromosome 4 that are interesting.  

rs358231 in the GBA3 gene.  Some people have the allele that results in a premature stop codon.  Premature stop codons result in a truncated protein.  As far as I know truncated proteins do not "do their job".  MAF (minor allele frequency),T, is 0.1084 so it is not very rare.

rs1799895.  This is a pathogenic missense allele in the SOD3 gene where mutations can increases the risk of cerebral infarction in women, emphysema, and several other conditions according to GeneCards.  Fortunately, it is not the most common variant with a MAF, G, of 0.024.  This missense results in a codon that codes for the protein glycine instead of arginine.  It's rather unfortunate that my maternal grandmother died at the age of 43 of a cerebral infarction and I'm a recipient of the pathogenic allele.  My mother is alive and well in her late 50s.  Then again, there's my father that almost died of a brain hemorrhage, but he made it and is in his 60s. 

rs2231142.  This a missense mutation in the ABCG2 gene.  According to dbSNP, it is a "drug response allele" and also associated with gout.  The MAF, T, is 0.1194 so it is not very rare, but being homozygous reduces uric acid excretion by about 50%!  I have gout and am homozygous for this SNP and was not the most likely candidate for gout otherwise.

rs72552713.  This is the SNP that results in a premature stop codon in the ABCG2 protein.  MAF, T, is 0.0012.  Good thing I do not also have one of these SNPs!

rs2231134 with MAF, G =0.0124.  Upstream variant of the ABCG2 gene.  I'm not sure of the significance, but since I have gout, I'm watching out for more research on this and on rs2728125 (MAF, G = 0.099).  SNPs upstream of genes could potentially affect gene expression.  I'm heterozygous for the former and homozygous for the latter.
rs1281138 in SH3TC1 with MAF, A= 0.007.  I'm not sure of the function of this gene, but since it is a missense, I'm reporting on it.

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