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Please do not send identical questions in to Ensembl helpdesk and
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<div class="moz-cite-prefix">On 30/03/2016 16:04, <a class="moz-txt-link-abbreviated" href="mailto:ptashkir@mskcc.org">ptashkir@mskcc.org</a>
wrote:<br>
</div>
<blockquote cite="mid:D3216333.31DC%25ptashkir@mskcc.org"
type="cite">
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<div>
<div><font face="Consolas">Hi,</font></div>
<div><font face="Consolas"><br>
</font></div>
<div><font face="Consolas"><br>
</font></div>
<div><font face="Consolas">I'm looking for any insight into an
issue we are having with the annotation of missense
variants in MAP3K14. It appears that after exon 1, a
different reading frame is selected for different exons. </font></div>
<div><font face="Consolas"><br>
</font></div>
<div><font face="Consolas">Please see the test case below,
using the VEP web interface. We are interested in RefSeq
annotations, but even the ENSMBL annotations are also
confusing. Results are the same for our local install of
version 82. </font></div>
<div><font face="Consolas"><br>
</font></div>
<div><font face="Consolas">For the RefSeq annotation, how is
the reading frame selected? The variant is annotated
as (p.W406C) , why is it not G407S? After exon 1, it
looks like reading frame is not consistent from exon to
exon. Splicing mutations are properly annotated however. </font></div>
<div><font face="Consolas"><br>
</font></div>
<div><font face="Consolas">All ensmbl annotations are listed
as non-coding. You'll also notice on the provided IGV
screenshot that the MAP3K14-AS1 non-coding transcript is
well downstream of this exon6 mutation. Any insight is
greatly appreciated. Thanks!</font></div>
<div><font face="Consolas"><br>
</font></div>
<div><font face="Consolas"><br>
</font></div>
<div><font face="Consolas">Test case: <span
style="background-color: rgb(255, 255, 255); color:
rgb(85, 85, 85); line-height: 14.4px; widows: 1;">Ensembl
GRCh37 release 84 - March 2016</span></font></div>
<div><font face="Consolas">####################</font></div>
<div><font face="Consolas">INPUT:</font></div>
<div><font face="Consolas">####################</font></div>
<div><font face="Consolas">17 43362250 . C A . . .</font></div>
<div><font face="Consolas"><br>
</font></div>
<div><font face="Consolas"><br>
</font></div>
<div><font face="Consolas">######### VEP ANNOTATIONS RefSeq
and ENSMBL: ##################################</font></div>
<div><font face="Consolas"><br>
</font></div>
<div><font face="Consolas">NM_003954.3<span class="Apple-tab-span" style="white-space: pre;">
</span>protein_coding<span class="Apple-tab-span" style="white-space: pre;"> </span>
6/16<span class="Apple-tab-span" style="white-space: pre;"> </span>-<span class="Apple-tab-span" style="white-space: pre;">
</span>NM_003954.3:c.1218G>T NP_003945.2:p.Trp406Cys<span class="Apple-tab-span" style="white-space: pre;">
</span></font></div>
<div><font face="Consolas"><br>
</font></div>
<div><font face="Consolas">ENST00000376926<span class="Apple-tab-span" style="white-space: pre;">
</span>processed_transcript<span class="Apple-tab-span" style="white-space: pre;">
</span>4/8<span class="Apple-tab-span" style="white-space: pre;"> </span>-<span class="Apple-tab-span" style="white-space: pre;">
</span>ENST00000376926.4:n.568G>T<span class="Apple-tab-span" style="white-space: pre;">
</span>-</font></div>
<div><font face="Consolas"><br>
</font></div>
<div><font face="Consolas">ENST00000344686<span class="Apple-tab-span" style="white-space: pre;">
</span>processed_transcript<span class="Apple-tab-span" style="white-space: pre;">
</span>7/17<span class="Apple-tab-span" style="white-space: pre;"> </span>-<span class="Apple-tab-span" style="white-space: pre;">
</span>ENST00000344686.2:n.1325G>T<span class="Apple-tab-span" style="white-space: pre;">
</span>-</font></div>
<div><font face="Consolas"><br>
</font></div>
<div><font face="Consolas">ENST00000587332<span class="Apple-tab-span" style="white-space: pre;">
</span>processed_transcript<span class="Apple-tab-span" style="white-space: pre;">
</span>6/16<span class="Apple-tab-span" style="white-space: pre;"> </span>-<span class="Apple-tab-span" style="white-space: pre;">
</span>ENST00000587332.1:n.1319G>T<span class="Apple-tab-span" style="white-space: pre;">
</span>-</font></div>
</div>
</div>
<div><font face="Consolas"><br>
</font></div>
<div><font face="Consolas"><br>
</font></div>
<div><font face="Consolas"><br>
</font></div>
<div><font face="Consolas">Thanks, </font></div>
<div><font face="Consolas"><br>
</font></div>
<div>
<div><font face="Consolas">Ryan Ptashkin</font></div>
<div><font face="Consolas">Computational Biologist</font></div>
<div><font face="Consolas">Memorial Sloan Kettering Cancer
Center</font></div>
<div><a moz-do-not-send="true" href="mailto:ptashkir@mskcc.org"><font
face="Consolas">ptashkir@mskcc.org</font></a></div>
</div>
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<pre class="moz-signature" cols="72">--
Dr Emily Perry (Pritchard)
Ensembl Outreach Project Leader
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge
CB10 1SD
UK </pre>
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