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Protocols

PolyPhen specifications

Information


Unique identifier OMICS_00136
Name PolyPhen
Alternative names Polymorphism Phenotyping, PolyPhen-2
Interface Web user interface
Restrictions to use Academic or non-commercial use
Input data A protein sequence
Input format FASTA
Output data A prediction of probably damaging, possibly damaging, or benign, along with a numerical score ranging from 0.0 (benign) to 1.0 (damaging).
Computer skills Basic
Version 2.2.2
Stability Stable
Source code URL http://genetics.bwh.harvard.edu/pph2/dokuwiki/_media/polyphen-2.2.2r405c.tar.gz
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

Documentation


Maintainer


  • person_outline Shamil R Sunyaev

Information


Unique identifier OMICS_00136
Name PolyPhen
Alternative names Polymorphism Phenotyping, PolyPhen-2
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use Academic or non-commercial use
Input data A protein sequence
Input format FASTA
Output data A prediction of probably damaging, possibly damaging, or benign, along with a numerical score ranging from 0.0 (benign) to 1.0 (damaging).
Operating system Unix/Linux, Mac OS
Computer skills Advanced
Version 2.2.2
Stability Stable
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

Download


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Versioning


No version available

Documentation


Maintainer


  • person_outline Shamil R Sunyaev

Publications for Polymorphism Phenotyping

PolyPhen citations

 (2784)
library_books

Mutations in six nephrosis genes delineate a pathogenic pathway amenable to treatment

2018
Nat Commun
PMCID: 5958119
PMID: 29773874
DOI: 10.1038/s41467-018-04193-w

[…] ntified mutations in the Exome Aggregation Consortium (ExaC) and the genome aggregation database (GnomAD) along with their prediction scores using Mutation Taster (http://www.mutationtaster.org/) and Polyphen 2 (http://genetics.bwh.harvard.edu/pph2/) in silico tools. As a negative control, we performed screening for all variants that we detected in the pTSNS patients in an in-house cohort of exome […]

call_split

Systematic pan cancer analysis of somatic allele frequency

2018
Sci Rep
PMCID: 5956099
PMID: 29769535
DOI: 10.1038/s41598-018-25462-0
call_split See protocol

[…] Functional annotations and conservation scores were extracted using the SeattleSeq annotation 147 (http://snp.gs.washington.edu/SeattleSeqAnnotation147/index.jsp). Pathogenicity was modeled using PolyPhen, CADD and FATHMM methods, and conservation was assessed based on GERP scores–. Transcription factor binding sites were analyzed using TRANSFAC 7.0. […]

library_books

Association of IL17RC and COL6A1 genetic polymorphisms with susceptibility to ossification of the thoracic posterior longitudinal ligament in Chinese patients

2018
PMCID: 5952594
PMID: 29764467
DOI: 10.1186/s13018-018-0817-y

[…] e assessed the causes of T-OPLL.In our previous whole-genome sequencing (WGS) study of 30 unrelated northern Chinese Han patients, four different algorithms [including SIFT(http://sift.jcvi.org/) [], PolyPhen-2 (http://genetics.bwh.harvard.edu/pph2/) [], MutationTaster (http://www.mutationtaster.org/) [], and GERP++ (http://mendel.stanford.edu/SidowLab/downloads/gerp/) []] were used to predict del […]

call_split

Case Report: Identification of an HNF1B p.Arg527Gln mutation in a Maltese patient with atypical early onset diabetes and diabetic nephropathy

2018
PMCID: 5952643
PMID: 29764441
DOI: 10.1186/s12902-018-0257-z
call_split See protocol

[…] ogenic. Non-exonic and synonymous variants were excluded from further analysis. Missense variants were evaluated for functional impact using a variety of in-silico prediction tools including SIFT [], Polyphen2 [], MelaLR [], MetaSVN [], fathmm-MKL [], DANN [], CADD [], MutationTaster [], Mutation Assesser [] and LRT []. […]

call_split

Molecular, Pathological, Radiological, and Immune Profiling of Non brainstem Pediatric High Grade Glioma from the HERBY Phase II Randomized Trial

2018
Cancer Cell
PMCID: 5956280
PMID: 29763623
DOI: 10.1016/j.ccell.2018.04.004
call_split See protocol

[…] ed exomes (n=3) were annotated by ExAc and ANNOVAR. Variants were annotated using the Ensembl Variant Effect Predictor v74 (ensembl.org/info/docs/variation/vep) incorporating SIFT (sift.jcvi.org) and PolyPhen (genetics.bwh.harvard.edu/pph2) predictions, COSMIC v64 (sanger.ac.uk/ genetics/CGP/cosmic/) and dbSNP build 137 (ncbi.nlm.nih.gov/sites/SNP) annotations. Copy number was obtained by calculat […]

library_books

A case of Raine syndrome presenting with facial dysmorphy and review of literature

2018
BMC Med Genet
PMCID: 5948820
PMID: 29751744
DOI: 10.1186/s12881-018-0593-x

[…] thy-1 (OMIM#251270). In silico analysis predicted the first variant (c.5327C > G/p.Ser1776Cys) to be disease-causing using the Mutation Taster, tolerated by SIFT (score 0.07) and probably damaging by PolyPhen (score 1.00). While second variant (c.3383G > A /p.Arg1128Lys) found to be a polymorphism by Mutation [email protected], tolerated by SIFT (score 0.65), and benign by PolyPhen (score 0.023). Second vari […]

Citations

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PolyPhen institution(s)
Division of Genetics, Brigham & Women’s Hospital, Harvard Medical School, Boston, MA, USA; Program in Biophysics, Harvard University, Cambridge, MA, USA

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