<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body text="#000000" bgcolor="#FFFFFF">
<div class="moz-cite-prefix">Dear Nicole,<br>
<br>
Thank you for reporting this.<br>
However you can see on the website that the phenotype "Hereditary
insensitivity to pain with anhidrosis" comes from dbSNP_ClinVar:<br>
<a
href="http://www.ensembl.org/Homo_sapiens/Variation/Phenotype?v=rs6339">http://www.ensembl.org/Homo_sapiens/Variation/Phenotype?v=rs6339</a><br>
<br>
You can see the corresponding page on ClinVar: <a
href="http://www.ncbi.nlm.nih.gov/clinvar/RCV000030667/">http://www.ncbi.nlm.nih.gov/clinvar/RCV000030667/</a><br>
<br>
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.<br>
<br>
Best regards,<br>
<pre class="moz-signature" cols="72">Laurent</pre>
On 19/08/2013 18:29, Nicole Washington wrote:<br>
</div>
<blockquote cite="mid:E6644C2C-107D-4EA2-8AC0-9CEF37A7E4C7@lbl.gov"
type="cite">Hi,
<div><br>
</div>
<div>i believe i have found an error in one of the phenotype
variant annotations.</div>
<div><br>
</div>
<div>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.</div>
<div><br>
</div>
<div>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:</div>
<div><br>
</div>
<div><a moz-do-not-send="true"
href="http://www.omim.org/entry/191315?search=rs6339&highlight=rs6339">http://www.omim.org/entry/191315?search=rs6339&highlight=rs6339</a></div>
<div><br>
</div>
<div>
<table class="entry-table" style="position: static; z-index:
auto; ">
<tbody>
<tr>
<td class="av-name text-font">
<div class=""><span class="av-number text-font"><span
text=".0005 INSENSITIVITY TO PAIN, CONGENITAL,
WITH ANHIDROSIS
NTRK1, GLN9TER, HIS598TYR, AND GLY607VAL
[dbSNP:rs6336] [dbSNP:rs6339] [dbSNP:rs80356673]
In an Italian patient with congenital
insensitivity to pain with anhidrosis (256800),
Mardy et al. (1999) 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) 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),
and are thus likely to be polymorphisms in this
population." style="margin: -20px 0px 0px 20px;
position: absolute; background:
url("/static/icons/tooltip-define.gif")
repeat scroll 0% 0% transparent; width: 46px;
height: 26px; cursor: pointer;" id="lookup"></span>.0005</span>
<span class="av-name text-font lookup">INSENSITIVITY
TO PAIN, CONGENITAL, WITH ANHIDROSIS</span> </div>
</td>
</tr>
<tr>
<td class="av-mutations text-font"> NTRK1, GLN9TER,
HIS598TYR, AND GLY607VAL [<a moz-do-not-send="true"
href="http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=rs6336;toggle_HGVS_names=open"
target="_blank">dbSNP:rs6336</a>] [<a
moz-do-not-send="true"
href="http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=rs6339;toggle_HGVS_names=open"
target="_blank">dbSNP:rs6339</a>] [<a
moz-do-not-send="true"
href="http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=rs80356673;toggle_HGVS_names=open"
target="_blank">dbSNP:rs80356673</a>] </td>
</tr>
<tr>
<td class="spacer"><br>
</td>
</tr>
<tr>
<td class="av-text text-font lookup">In an Italian patient
with<font class="Apple-style-span" color="#a21405">
congenital insensitivity to pain with anhidrosis</font>
(<a moz-do-not-send="true"
href="http://www.omim.org/entry/256800">256800</a>), <a
moz-do-not-send="true"
href="http://www.omim.org/entry/191315?search=rs6339&highlight=rs6339#reference30"
class="entry-reference" title="Mardy, S., Miura, Y.,
Endo, F., Matsuda, I., Sztriha, L., Frossard, P.,
Moosa, A., Ismail, E. A. R., Macaya, A., Andria, G.,
Toscano, E., Gibson, W., Graham, G. E., Indo, Y.
Congenital insensitivity to pain with anhidrosis:
novel mutations in the TRKA (NTRK1) gene encoding a
high-affinity receptor for nerve growth factor. Am. J.
Hum. Genet. 64: 1570-1579, 1999. [PubMed: <a
href="http://www.ncbi.nlm.nih.gov/pubmed/10330344"
target="_blank"
onclick="_gaq.push(['_trackEvent', 'Outbound',
'PubMed',
'ncbi.nlm.nih.gov'])">10330344</a>]
[Full Text: <a
href="http://linkinghub.elsevier.com/retrieve/pii/S0002-9297(07)63659-3"
target="_blank"
onclick="_gaq.push(['_trackEvent', 'Outbound',
'Publisher'])">Elsevier Science</a>]">Mardy
et al. (1999)</a> 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). <a
moz-do-not-send="true"
href="http://www.omim.org/entry/191315?search=rs6339&highlight=rs6339#reference30"
class="entry-reference" title="Mardy, S., Miura, Y.,
Endo, F., Matsuda, I., Sztriha, L., Frossard, P.,
Moosa, A., Ismail, E. A. R., Macaya, A., Andria, G.,
Toscano, E., Gibson, W., Graham, G. E., Indo, Y.
Congenital insensitivity to pain with anhidrosis:
novel mutations in the TRKA (NTRK1) gene encoding a
high-affinity receptor for nerve growth factor. Am. J.
Hum. Genet. 64: 1570-1579, 1999. [PubMed: <a
href="http://www.ncbi.nlm.nih.gov/pubmed/10330344"
target="_blank"
onclick="_gaq.push(['_trackEvent', 'Outbound',
'PubMed',
'ncbi.nlm.nih.gov'])">10330344</a>]
[Full Text: <a
href="http://linkinghub.elsevier.com/retrieve/pii/S0002-9297(07)63659-3"
target="_blank"
onclick="_gaq.push(['_trackEvent', 'Outbound',
'Publisher'])">Elsevier Science</a>]">Mardy
et al. (1999)</a> suggested that the gln9-to-ter
mutation was the most likely cause of CIPA in this
family. <font class="Apple-style-span" color="#a21405">The
missense mutations were later determined to have no
effect on autophosphorylation of NTRK1 (<a
moz-do-not-send="true"
href="http://www.omim.org/entry/191315?search=rs6339&highlight=rs6339#reference29"
class="entry-reference" title="Mardy, S., Miura, Y.,
Endo, F., Matsuda, I., Indo, Y. Congenital
insensitivity to pain with anhidrosis (CIPA): effect
of TRKA (NTRK1) missense mutations on
autophosphorylation of the receptor tyrosine kinase
for nerve growth factor. Hum. Molec. Genet. 10:
179-188, 2001. [PubMed: <a
href="http://www.ncbi.nlm.nih.gov/pubmed/11159935"
target="_blank"
onclick="_gaq.push(['_trackEvent', 'Outbound',
'PubMed',
'ncbi.nlm.nih.gov'])">11159935</a>]
[Full Text: <a
href="http://hmg.oxfordjournals.org/cgi/pmidlookup?view=long&pmid=11159935"
target="_blank"
onclick="_gaq.push(['_trackEvent', 'Outbound',
'Publisher'])">HighWire Press</a>]">Mardy
et al., 2001</a>), and are thus likely to be
polymorphisms in this population.</font></td>
</tr>
</tbody>
</table>
<div><br>
</div>
</div>
<div>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?</div>
<div><br>
</div>
<div>Thanks for your time,</div>
<div><br>
</div>
<div>Nicole</div>
<div><br>
</div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
<pre wrap="">_______________________________________________
Dev mailing list <a class="moz-txt-link-abbreviated" href="mailto:Dev@ensembl.org">Dev@ensembl.org</a>
Posting guidelines and subscribe/unsubscribe info: <a class="moz-txt-link-freetext" href="http://lists.ensembl.org/mailman/listinfo/dev">http://lists.ensembl.org/mailman/listinfo/dev</a>
Ensembl Blog: <a class="moz-txt-link-freetext" href="http://www.ensembl.info/">http://www.ensembl.info/</a>
</pre>
</blockquote>
<br>
</body>
</html>