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<p>Yes we are using GRCh37. So we looked at the Ensembl release 75 genes (just using biomart) and there are still a number of gene symbols that VEP is outputting that don't occur in the GRCh37 Ensembl database at all (as far as I can tell anyway).</p>
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<p>Namely:</p>
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<li>ARMCX5-GPRASP2<br>
</li><li>C7orf10<br>
</li><li>PCDHGB5<br>
</li><li>PHOSPHO2-KLHL23<br>
</li><li>THEG5<br>
</li><li>UQCRHL<br>
</li><li>ZSCAN26</li></ul>
<div style="">There are others (100-200 I believe?) but this is just a small sample.<font face="Calibri"></font></div>
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<div style="">Any ideas where these symbols are derived from?</div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> dev-bounces@ensembl.org <dev-bounces@ensembl.org> on behalf of Will McLaren <wm2@ebi.ac.uk><br>
<b>Sent:</b> Wednesday, 3 August 2016 10:46:02 PM<br>
<b>To:</b> Ensembl developers list<br>
<b>Subject:</b> Re: [ensembl-dev] VEP Cache Gene List</font>
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<div dir="ltr">Hi Michael,
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<div>I assume from this that you are using the GRCh37 assembly? Ensembl and therefore VEP annotations on GRCh37 were frozen at Ensembl release 75 as we have moved our main annotation pipelines to GRCh38.</div>
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<div>See the about box on the RH side of <a href="http://grch37.ensembl.org/index.html" target="_blank" id="LPlnk150775">http://grch37.ensembl.org/index.html</a></div>
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<div>Regards</div>
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<div>Will McLaren</div>
<div>Ensembl Variation</div>
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<div class="gmail_quote">On 3 August 2016 at 06:41, Michael Milton <span dir="ltr">
<<a href="mailto:michael.milton@unimelb.edu.au" target="_blank">michael.milton@unimelb.edu.au</a>></span> wrote:<br>
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<p>Hi, I'm using VEP with a downloaded cache, and it seems that VEP is annotating some non-hgnc gene symbols or at least outdated symbols. I need a gene list including all possible genes that VEP could output for a downstream application. Is there a definitive
list of genes that VEP could output? Otherwise, what source is used to build the VEP cache?</p>
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<p>Some of the superceded gene symbols it's outputting, using the Ensembl 83 refseq cache, are:</p>
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<li>GLTPD1<br>
</li><li>C1orf86<br>
</li><li>C7orf63<br>
</li><li>PCNXL3</li></ul>
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Thanks!
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