Question: Polyphen2 And Nonsense Codons
gravatar for Pierre Lindenbaum
5.1 years ago by
Pierre Lindenbaum77k wrote:

Does Polyphen2/batch ( ) skip the nonsense mutations ?

I tested it with (hg18) chr22:40053278 C/G the file pph2-snps.txt contained the nonsense mutation but the file pph2-full.txt was empty.

Am I wrong ?

codon prediction mutation snp • 1.4k views
ADD COMMENTlink modified 5.1 years ago by Lars Juhl Jensen9.0k • written 5.1 years ago by Pierre Lindenbaum77k

I think the Polyphen only considers the missense mutation in their prediction pipeline. In the dbSNP id based interface [ ] - no results are provided for other class of SNPs.

ADD REPLYlink written 5.1 years ago by Khader Shameer15k
gravatar for Lars Juhl Jensen
5.1 years ago by
Copenhagen, Denmark
Lars Juhl Jensen9.0k wrote:

Considering that the title of the latest PolyPhen paper is "A method and server for predicting damaging missense mutations", I think it is safe to say that it only predicts the effect of missense mutations and not of nonsense mutations.

ADD COMMENTlink written 5.1 years ago by Lars Juhl Jensen9.0k
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