Polyphen2 And Nonsense Codons
Does Polyphen2/batch ( http://genetics.bwh.harvard.edu/pph2/bgi.shtml ) 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 ?
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Lars Juhl Jensen
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Pierre Lindenbaum
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Pierre Lindenbaum
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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.
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I think the Polyphen only considers the missense mutation in their prediction pipeline. In the dbSNP id based interface [http://genetics.bwh.harvard.edu/pph2/dbsearch.shtml ] - no results are provided for other class of SNPs.