Exploring a SNP in mouse
Madsen et al in the paper ‘Altered metabolic signature in pre-diabetic NOD mice’ (PloS One. 2012; 7(4): e35445) have described several regulatory and coding SNPs, some of them in genes residing within the previously defined insulin dependent diabetes (IDD) regions. The authors describe that one of the identified SNPs in the murine Xdh gene (rs29522348) would lead to an amino acid substitution and could be damaging as predicted as by SIFT (http://sift.jcvi.org/).
(a) Where is the SNP located (chromosome and coordinates)?
(b) What is the HGVS recommendation nomenclature for this SNP?
(c) Why does Ensembl put the C allele first (C/T)?
(d) Are there differences between the genotypes reported in NOD/LTJ and BALB/cByJ, according to the PERLGEN panel?
(a) Go to www.ensembl.org, type rs29522348 in the search box. Click on rs29522348 (Mouse Variation).
SNP rs29522348 is located on 17:74231988. In Ensembl, its alleles are provided as in the forward strand.
(b) Click on HGVS names to reveal information about HGVS nomenclature.
This SNP has got five HGVS names, one at the genomic DNA level (17:g.74231988C>T), three at the transcript level (ENSMUST00000024866.4:c.721G>A, ENSMUST00000233162.1:n.738G>A and ENSMUST00000233621.1:c.*284G>A) and one at the protein level (ENSMUSP00000024866.4:p.Val241Ile).
(c) In Ensembl, the allele that is present in the reference genome assembly is always put first (C is the allele for the reference mouse genome, strain C57BL/6J).
(d) Click on Sample genotypes is the left hand side menu. In the summary of genotypes by population, click on Show for PERLEGEN:MM_PANEL2, or search for the two strain names. There are indeed differences between the genotypes reported in those two different strains. The genotype reported in NOD/LTJ is T|T whereas in BALB/cByJ the genotype is C|C.