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mutalyzer / mutalyzer2

HGVS variant nomenclature checker
https://mutalyzer.nl
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getGeneName returns outdated symbol instead of TRAPPC11 #385

Closed jxchong closed 8 years ago

jxchong commented 8 years ago

It seems like getGeneName can retrieve outdated gene symbols. For example:

https://www.mutalyzer.nl/json/getGeneName?build=hg19&accno=NM_021942.5 returns C4orf41

https://www.mutalyzer.nl/json/runMutalyzer?variant=NM_021942.5:c.851A%3EC returns "transcriptDescriptions": ["NM_021942.5(TRAPPC11_v001):c.2938G>A"]

This gene has been named TRAPPC11 for quite a while (since at least before 2012)

martijnvermaat commented 8 years ago

Hi @jxchong thanks for reporting this!

You are correct. Actually, the Mutalyzer database has C4orf41 for NM_021942.4 and TRAPPC11 for NM_021942.5. This already points me to a problem, and that is that older transcript versions will never be updated (nor will any entry on hg19 actually), since the NCBI mapview files we use for this are no longer being updated for hg19.

However, the issue here is a different one, since as I said our database actually has the newer gene symbol for transcript version 5 which you queried. From a quick glance at the code it looks like the transcript version is ignored by this webservice call. This shouldn't be hard to fix, I might have a look tomorrow.

martijnvermaat commented 8 years ago

Hi @jxchong, the fix is now available:

https://www.mutalyzer.nl/json/getGeneName?build=hg19&accno=NM_021942.5

jxchong commented 8 years ago

awesome thanks for the quick response!