Hi, in last period we used dbSNP database in NCBI for two variants rs2304365 and rs17315309 in ST18 gene According to the dsSNP database, about the variant rs2304365 the wild type allele is C and the variants are C or T, But according to the publications the risk alleles is A not C or T (Etesami, I., Seirafi, H., Ghandi, N., Salmani, H., Arabpour, M., Nasrollahzadeh, A., ... & Keramatipour, M. (2018). The association between ST 18 gene polymorphism and severe pemphigus disease among Iranian population. Experimental Dermatology, 27(12), 1395-1398.) Also specifically about rs17315309 the wild type is A and the variants are G or T , but in the references ( Vodo, D., Sarig, O., Geller, S., Ben-Asher, E., Olender, T., Bochner, R., ... & Sprecher, E. (2016). Identification of a functional risk variant for pemphigus vulgaris in the ST18 gene. PLoS genetics, 12(5), e1006008. ) ,
the article that cited in the database the variant risk allele is C, I don't understand why in the most of articles or specific articles that cited in the dsSNP database mention different SNPs with the dsSNP database .
I really want to understand this,
Thanks:)
Hi Yasmin
if you look at NCBI or even better at UCSC you'll see that the human ST gene is on the minus strand of DNA.
that means that the sequence of the variant rs2304365 is given on the + strand, and its impact given in the coding sequence strand, the-.
in consequence, the variant is a T on the genomic hand, and A when you look the impact on the RNA and proteins. the reverse complement is therefore to be applicator for minus strand coding genes.
you can zoom in, but look at the arrow:
https://genome-euro.ucsc.edu/cgi-bin/hgTracks?db=hg38&lastVirtModeType=default&lastVirtModeExtraState=&virtModeType=default&virtMode=0&nonVirtPosition=&position=chr8%3A52110838%2D52409756&hgsid=315803467_iX5fFm3Buo913xBvCaFJhK4CPhzO
all the best
fred