SNP Effect predictor

Exome sequenceなどで多くのvariantsが見つかるのだけど、それらがタンパク質に与える影響を知りたい時にどうするか? PolyPhenがよく用いられてるっぽいけど、UCSCのMLでEnsemblにもSNP Effect predictorというツールが加わったらしいのを知ったのでメモ代わりにコピペしとく。

Is there a tool or suggested method to determine how a particular SNP effects these residues?

Using the dbSNP track controls or the primary table itself,
Coding - Synonymous and Coding - Non-Synonymous
is an annotated for some of the data in this location:


You can also take any transcript (full or coding only),
swap in the variation, and use this tool to do a translation: -> Utilities (left blue navigation bar) -> DNA Duster

We have another table/file to suggest:

snp130CodingDbSnp -- it has more detailed functional annotations provided by dbSNP

Another option is the SNP consequence tool in Ensembl.

On an Ensembl Location page:

click on "Manage your data"

and select the SNP Effect predictor. This unsurprisingly works off
Ensembl Genes. The functionality is also available in the Ensembl API