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

[Matthew Astley]

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 product” 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 project”.

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not be published, because of this genomic sequence issue.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=HG-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