I am currently designing a SNP genotyping assay for CYP2D6 and I am confused about the alternate loci that keep appearing in my blast searches. What is an alternate locus? Does every gene have an alternate locus? How do they change the translation of that gene? I tried googling the term but the definitions I found did not answer my questions.
It seems like this gene is located near two cytochrome P450 pseudogenes on chromosome 22q13.1. The pseudogenes might not be expressed but can have a high sequence identity to the region you want to assay. Is it a coding variant? This gene is known to be highly polymorphic and thus may have other SNPs close too your target SNP and this has to be taking into account when you perform the design of the genotyping assay for it to work. I haven´t looked into the details of this gene but you might cosider to do Sanger sequencing to assay the SNP if not the sample set is too large.
This definition can be found via the following link, hope this helps you understand the meaning of this alternate locus:
http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/info/definitions.shtml
My (limited) understanding is that some people could have multiple copies of this gene (up to 10).
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