[ensembl-dev] where to report annotation errors?

Laurent Gil lgil at ebi.ac.uk
Tue Aug 20 08:44:07 BST 2013

Dear Nicole,

Thank you for reporting this.
However you can see on the website that the phenotype "Hereditary 
insensitivity to pain with anhidrosis" comes from dbSNP_ClinVar:

You can see the corresponding page on ClinVar: 

The variation set "ph_omim" lists all the variations which have at least 
one entry in OMIM, that's why you had access to this variation rs6339 
and then all its associated phenotypes in Ensembl Variation.

Best regards,


On 19/08/2013 18:29, Nicole Washington wrote:
> Hi,
> i believe i have found an error in one of the phenotype variant 
> annotations.
> the variation rs6339 is listed as having the phenotype "Hereditary 
> insensitivity to pain with anhidrosis", as sourced from the ph_omim 
> set.  However, when I have tried to identify the omim listing from 
> which this is derived, I cannot find it.
> In fact, I believe it might have been mis-curated to be "hereditary", 
> when is should be congenital (or in fact, probably neither, it is just 
> a variation with no phenotype and just a polymorphism), as summarized 
> here:
> http://www.omim.org/entry/191315?search=rs6339&highlight=rs6339
> NTRK1, GLN9TER, HIS598TYR, AND GLY607VAL [dbSNP:rs6336 
> <http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=rs6336;toggle_HGVS_names=open>] 
> [dbSNP:rs6339 
> <http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=rs6339;toggle_HGVS_names=open>] 
> [dbSNP:rs80356673 
> <http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=rs80356673;toggle_HGVS_names=open>] 
> In an Italian patient withcongenital insensitivity to pain with 
> anhidrosis (256800 <http://www.omim.org/entry/256800>), Mardy et al. 
> (1999) 
> <http://www.omim.org/entry/191315?search=rs6339&highlight=rs6339#reference30> 
> found homozygosity for a triple mutation in exons 1 and 15 in the 
> NTRK1 gene, leading to 1 nonsense mutation (gln9 to ter) and 2 
> missense mutations (his598 to tyr; gly607 to val). Mardy et al. (1999) 
> <http://www.omim.org/entry/191315?search=rs6339&highlight=rs6339#reference30> 
> suggested that the gln9-to-ter mutation was the most likely cause of 
> CIPA in this family. The missense mutations were later determined to 
> have no effect on autophosphorylation of NTRK1 (Mardy et al., 2001 
> <http://www.omim.org/entry/191315?search=rs6339&highlight=rs6339#reference29>), 
> and are thus likely to be polymorphisms in this population.
> I am unclear if you fetch this annotation from a remote source, or if 
> your team curated this, but I think it needs to be corrected.  Do I 
> need to report this elsewhere?
> Thanks for your time,
> Nicole
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