Leber's Optic Atrophy

Checking the mitochondrial DNA using the raw data provided by 23andme I noticed that there were a few Leber's Optic Atrophy variants tested for.  This disease does not always present if someone ends up inheriting the pathogenic allele (or alleles) but it is important to know if you're a carrier.  The following are a few variants tested for:

rs1599988, with C being the risk allele
i5000099 (aka rs199476112 from what I gather looking at the position) = A
i3001205 (aka rs200855215) = G
i4000834 (aka = rs199476104) = C

It may be possible that there are miscalls in the raw data that 23andme provides.  One way to check is to see how many people on OpenSNP have the risk allele.  If it seems like a lot compared to the MAF (frequency) reported on dbSNP, then the genotype may be miscalled by 23andme.  Sometimes that is not enough to know for sure, as 2% of the people on OpenSNP have a G for i3001205.  Is that a lot of people or are those genotypes correct?

Welcome to Genomic Explorer

Welcome to Genomic Explorer!  In 2014, I took the 23andme test to see if I had the MTHFR mutations and have been exploring my genome ever since.  No significant MTHFR mutation was discovered in my genome (as of yet!) but the search for other mutations ensued.  The purpose of this blog is to provide information about interesting SNPs (single nucleotide polymorphisms) in 23andme raw data.  Note that just because I mention it does not mean I have the mutation myself.

First things first, here's an interesting SNP...

rs2272783 is a mutation in the FECH (ferrochelatase) gene.  Being heterozygous for the minor allele reduces the expression of the gene.  Being heterozygous in this SNP and also having a loss of function mutation in the same gene can cause one to have a terrible genetic disease, erythropoietic protoporphyria!  Photosensitivity and sensitivity to some forms of artificial light is the result.  Thanks mom or dad!  Considering the rarity of other genetic mutations this particular mutation is rather common with the minor allele frequency (MAF) of 0.1374.