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:

snp130.func

http://genome.ucsc.edu/FAQ/FAQdownloads#download1
http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html

You can also take any transcript (full or coding only),
swap in the variation, and use this tool to do a translation:
http://genome.ucsc.edu/ -> Utilities (left blue navigation bar) -> DNA Duster
http://users.soe.ucsc.edu/~kent/dnaDust/dnadust.html

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:

http://www.ensembl.org/Homo_sapiens/Location/View?r=6:133017695-133161157

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