[ensembl-dev] OMIM numbers for genes

[Matthew Laird]

Hi Wolf,

If I'm understanding what you're describing, I'm assuming you're looking 
at GRCh37 Biomart for this inconsistency. While we maintain GRCh37 
archives, we no longer actively update xrefs for that assembly, they're 
all frozen as of Ensembl release 37. Looking up HYDIN in Ensembl 86, 
GRCh38 I see only 610812 is returned for this HGNC symbol, so whatever 
mis-mapping was occurring seems to be corrected.

If I'm misunderstanding the issue you're raising, please let us know. 
Thanks.

On 11/10/16 12:11, Wolf Beat wrote:
> Hi,
>
> i had an interesting issue with the OMIM number for a certain gene, HYDIN.
>
> When querying biomart, i get two OMIM numbers back for this gene:
>
> HYDROCEPHALUS-INDUCING, MOUSE, HOMOLOG OF, 2; HYDIN2	610813
> and
> HYDROCEPHALUS-INDUCING, MOUSE, HOMOLOG OF; HYDIN	610812
>
> The Problem, the first one is wrong. The first one is for the HYDIN2 gene, which is located on chromosome 1. HYDIN is on chromosome 16.
> Looking at the OMIM pages linked this is confirmed:
> HYDIN: http://omim.org/entry/610812
> HYDIN2: http://omim.org/entry/610813
>
> And here the ensembl pages:
> HYDIN:  http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000157423;r=16:70807378-71230722
> HYDIN2: http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000239475;r=1:146310555-146349531
>
> So my question is, is this an error on the part of ensembl (wrong annotation), some misunderstanding of my part and can i fix/detect this problem on my side?
>
> Thank you very much.
>
> Kind regards
>
> Beat Wolf
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