Predicting Functional Effect of Human Missense Mutations Using PolyPhen‐2
Open accessAbstract
PolyPhen‐2 (Polymorphism Phenotyping v2), available as software and via a Web server, predicts the possible impact of amino acid substitutions on the stability and function of human proteins using structural and comparative evolutionary considerations. It performs functional annotation of single‐nucleotide polymorphisms (SNPs), maps coding SNPs to gene transcripts, extracts protein sequence annotations and structural attributes, and builds conservation profiles. It then estimates the probability of the missense mutation being damaging based on a combination of all these properties. PolyPhen‐2 features include a high‐quality multiple protein sequence alignment pipeline and a prediction method employing machine‐learning classification. The software also integrates the UCSC Genome Browser's human genome annotations and MultiZ multiple alignments of vertebrate genomes with the human genome. PolyPhen‐2 is capable of analyzing large volumes of data produced by next‐generation sequencing projects, thanks to built‐in support for high‐performance computing environments like Grid Engine and Platform LSF. Curr. Protoc. Hum. Genet . 76:7.20.1‐7.20.41. © 2013 by John Wiley & Sons, Inc.
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This change is predicted as 'probably damaging' by PolyPhen.
“This change is predicted as ‘probably damaging’ by PolyPhen [51] (Table S3).”
From Neandertal introgression partitions the genetic landscape of neuropsychiatric disorders and associated behavioral phenotypes (2022) · cites this paper as [51]
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- Authors
- Adzhubei, I., Jordan, D. M., & Sunyaev, S. R.
- Affiliations
- Brigham and Women's Hospital (US)
- Venue
- Current Protocols in Human Genetics
- Publisher
- Wiley
- Published
- 2013-01
- Volume
- 76
- Issue
- 1
- Pages
- Unit7.20-Unit7.20
- ISSN
- 1934-8258 (ISSN-L)
- 1934-8266
- PMC
- PMC4480630
- OpenAlex
- W1563940013
- Cited by
- 3,705
- References
- 16
- Citations by year
- 2026: 178 · 2025: 330 · 2024: 408 · 2023: 326 · 2022: 349 · 2021: 421 · 2020: 329 · 2019: 362 · 2018: 317 · 2017: 240 · 2016: 183 · 2015: 148 · 2014: 83 · 2013: 27 · 2012: 2
- FWCI
- 97.54
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Current Protocols in Human Genetics (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Institute of Mental Health (R01MH101244)
- National Institute of General Medical Sciences (R01GM078598)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Keywords
- PolyPhen-2, missense mutations, amino acid substitutions, protein stability, protein function prediction, single nucleotide polymorphisms, conservation profiles, multiple sequence alignment, machine learning classification, human genome annotation, next-generation sequencing data analysis
- MeSH terms
- Humans, Protein Conformation, Proteins, Software, Computational Biology, Mutation, Missense, Internet, Polymorphism, Single Nucleotide, Databases, Genetic, Search Engine
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