[ensembl-dev] OMIM numbers for genes

[Wolf Beat]

This is correct.

I'm i correct in understanding, that no errors will be corrected in the GRCH37 version?
I also wanted to mention, that the HYDIN2 gene does not have any OMIM number associated in the GRCH37 archive.

With many tools and laboratories still being stuck with grch37, it would be good if at least the known errors are corrected in that database.

Thank you very much

Beat Wolf
________________________________________
From: dev-bounces at ensembl.org [dev-bounces at ensembl.org] on behalf of Matthew Laird [lairdm at ebi.ac.uk]
Sent: Tuesday, October 11, 2016 4:31 PM
To: Ensembl developers list
Subject: Re: [ensembl-dev] OMIM numbers for genes

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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