Bork Group
Sunyaev Lab
PolyPhen: prediction of functional effect
of human nsSNPs
PolyPhen (=Polymorphism Phenotyping) is a tool which predicts possible impact of an amino acid substitution on the structure and function of a human protein using straightforward physical and comparative considerations
Fri Apr 6 17:30 EDT 2012:
Dear PolyPhen users! Please be aware that this service has been discontinued and replaced with PolyPhen-2.
(Click on the link above if you are not transferred automatically after 10 seconds.)
Wed Mar 31 07:30 EDT 2010:
New version of the PolyPhen web server has been released. PolyPhen-2 includes numerous improvements, as well as a simple and efficient batch query web interface. Also available as a standalone software for Linux / Mac OS X. We would appreciate your feedback.
Links Query data
PolyPhen description

SNP data collection
Precomputed data for human nsSNPs from dbSNP database

Papers on the method

A tool to map human DNA variation onto proteins. Please use it if you start with DNA sequences and are not sure whether your SNP is non-synonymous

dbSNP Database
Single Nucleotide Polymorphism Database at NCBI

Examples of PolyPhen output

Database statistics
Statistics on databases used by PolyPhen

E-mail us

Protein identifier (accession or name) from the UniProt database

Amino acid sequence in FASTA format

Position   Substitution  AA1   AA2 


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Query options
Structural database   PQS PDB
Sort hits by   Identity E-value
Map to mismatch   No Yes
Calculate structural parameters   For first hit only For all hits
Calculate contacts   For first hit only For all hits
Minimal alignment length    
Minimal identity in alignment    
Maximal gap length in alignment    
Threshold for contacts     Å