Bug #510
closed
More than one SNP in a codon not interpreted together
Description
In COL9A2 there are two neighboring SNPs resulting in three possible amino acids at position 326: rs2228564 (c.977A>G) is ancestral to this rs12077871 (c.976C>T), so there are three common triplets at this position: “CAG” codon = Gln/Q, “CGG” codon = Arg/R, and “TGG” codon = Trp/W.
The interpretation of rs12077871 when compared to reference in the absence of its neighboring polymorphism results it being misinterpreted as “Stop/X” (TAG). See: http://evidence.personalgenomes.org/COL9A2-Gln326Stop
Notably, the correct amino acid change (COL9A2-Q326W) is associated with a phenotype: susceptibility to intervertebral disc disease.
Updated by Ward Vandewege about 15 years ago
- Project changed from 19 to GET-Evidence
- Category deleted (
GET-Evidence)
Updated by Madeleine Ball about 15 years ago
- Status changed from New to Closed
This is "fixed" by the update which added interpretation of indels. b4141303
If the input data is good (with neighboring SNPs reported together in a single line), they will be interpreted together. The nonsynoymous interpretation now examines the predicted transcript as a whole for predicted coding changes rather than an individual codon.