[ensembl-dev] FW: why is NEFL ENSG00000104725 ENST00000221169 annotated as "No protein product"?

Katherine Auger kaa at sanger.ac.uk
Tue May 8 14:41:06 BST 2012


Hi All

Human chromosome 8 is being curated at the Genome Institute at the
University of Washington (TGI). In the ticket that corresponds to this
region (HG-307), it is noted that the reference component in question,
AC107373.4, is clone CTD-2168K21. Source DNA is not available for this
library, therefore it is unclear whether the nucleotide in the reference
reflects a rare allele (based on the PCR results from a panel of 24 DNAs) or
an error in the clone sequence. Investigation of the 1000 genomes data also
suggests either an error or a rare allele. Investigations are ongoing to
fully determine the nature of this discrepancy and the subsequent action
that is required to resolve it. Updates to the ticket can be viewed here:

http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/issue_detail.cgi?id
=HG-307

Kind regards,

Kate

------ Forwarded Message
From: Kerstin Howe <kerstin at sanger.ac.uk>
Date: Tue, 8 May 2012 11:44:05 +0100
To: Katherine Auger <kaa at sanger.ac.uk>
Subject: Fwd: [ensembl-dev] why is NEFL ENSG00000104725 ENST00000221169
annotated as "No protein product"?

Hi Kate,

can you please have a look at this and comment if necessary?

Thanks

Kerstin

Begin forwarded message:

> From: Matthew Astley <mca at sanger.ac.uk>
> Date: 8 May 2012 10:55:05 GMT+01:00
> To: dev at ensembl.org
> Subject: Re: [ensembl-dev] why is NEFL ENSG00000104725 ENST00000221169
> annotated as "No protein product"?
> Reply-To: Ensembl developers list <dev at ensembl.org>
> 
> On Sun, May 06, 2012 at 12:30:27PM -0700, Michael Yourshaw wrote:
> 
>> This issue came up when the variant effect predictor failed
>> recognize a Charcot-Marie-Tooth disease variant in NEFL
>> (neurofilament, light polypeptide) as as a coding variant.
>> 
>> Gene ENSG00000104725 transcript ENST00000221169 is annotated as "No
>> protein product² by Ensembl.
> 
> In short, it seems likely there is a genomic sequencing error
> affecting the CDS.
> 
> 
>> On Ensembl the prediction method is given as "Manual annotation
>> (determined on a case-by-case basis) from the Havana project².
> 
> I asked an annotator about this (thanks Mark).
> 
> The GRC has a ticket[1] on this clone, which you can see by switching
> on the "GRC region NCBI_37" DAS track[2] in Ensembl.
> 
> 
>> The gene is annotated as protein coding by UniProt, RefSeq, and
>> UCSC. CCDS apparently recognizes the mouse flavor of the gene but
>> not the human.
> 
> There is another transcript in our database which is marked so it will
> not be published, because of this genomic sequence issue.
> 
> I will open a helpdesk ticket in your name with Havana, in case there
> is more to be said about it.
> 
> 
> hth,
> -- 
> Matthew
> 
> [1]
>   
> http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/issue_detail.cgi?id=H
> G-307
> 
> [2] this should enable it for you,
>   
> http://www.ensembl.org/Homo_sapiens/Location/View?db=core;g=ENSG00000104725;r=
> 8:24801089-24825012;t=ENST00000221169;contigviewbottom=das_DS_775=labels
> 
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--
Dr. Kerstin Howe
Senior Scientific Manager
Genome Reference Informatics (Team 135)
kerstin at sanger.ac.uk

Wellcome Trust Sanger Institute
Hinxton, Cambridge CB10 1SA, UK






------ End of Forwarded Message

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