[ensembl-dev] human exome mutation database

Will McLaren wm2 at ebi.ac.uk
Thu Feb 23 10:41:18 GMT 2012

Hi Venu,

I'm afraid Ensembl doesn't carry this data.

We don't use RefSeq transcripts as our primary transcript type (although
they are available through our otherfeatures databases, and as mapped
identifiers to our Ensembl transcript identifiers).

We don't catalog all possible nucleotide changes either, although I am not
sure I see a reason for doing this?

Have you come across our Variant Effect Predictor software? You may find it
useful depending on what you want to do; it will map genomic variant
changes to transcript/protein changes and provides much more besides,
including SIFT and PolyPhen predictions. You can find full documentation


There is also a limited web interface if you just want to try it out:


Hope this helps

Will McLaren
Ensembl Variation

On 23 February 2012 01:32, Venugopal Valmeekam <vvalmeekam at yahoo.com> wrote:

> Hi,
> I am developing a human exome mutation database using the refseq
> transcript collection. This database maps the transcripts to the genome and
> for each of these genomic positions catalogs all the possible amino acid
> changes resulting from all possible nucleotides substitutions.  I was
> wondering if ensembl has this data.  I do not want to download this data
> for just few genomic positions but would like to get the complete dataset
> for the entire human exome.
> Thanks for your help.
> Venu
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