SIFT: predicting amino acid changes that affect protein function
Pauline C. Ng,Steven Henikoff +1 more
TLDR
SIFT is a program that predicts whether an amino acid substitution affects protein function so that users can prioritize substitutions for further study and can distinguish between functionally neutral and deleterious amino acid changes in mutagenesis studies and on human polymorphisms.Abstract:
Single nucleotide polymorphism (SNP) studies and random mutagenesis projects identify amino acid substitutions in protein-coding regions. Each substitution has the potential to affect protein function. SIFT (Sorting Intolerant From Tolerant) is a program that predicts whether an amino acid substitution affects protein function so that users can prioritize substitutions for further study. We have shown that SIFT can distinguish between functionally neutral and deleterious amino acid changes in mutagenesis studies and on human polymorphisms. SIFT is available at http://blocks.fhcrc.org/sift/SIFT.html.read more
Citations
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Computational approaches to identify functional genetic variants in cancer genomes.
Abel Gonzalez-Perez,Ville Mustonen,Boris Reva,Graham R. S. Ritchie,Pau Creixell,Rachel Karchin,Miguel Vazquez,J. Lynn Fink,Karin S. Kassahn,John V. Pearson,Gary D. Bader,Paul C. Boutros,Lakshmi Muthuswamy,B. F. Francis Ouellette,Jüri Reimand,Rune Linding,Tatsuhiro Shibata,Alfonso Valencia,Adam Butler,Serge Dronov,Paul Flicek,Nick B. Shannon,Hannah Carter,Li Ding,Chris Sander,Josh M. Stuart,Lincoln Stein,Nuria Lopez-Bigas +27 more
TL;DR: The result of discussions within the ICGC on how to address the challenge of identifying mutations that contribute to oncogenesis, tumor maintenance or response to therapy is presented, and computational techniques to annotate somatic variants and predict their impact on cancer phenotype are recommended.
Journal ArticleDOI
PHYTOCHROME C plays a major role in the acceleration of wheat flowering under long-day photoperiod
Andrew Chen,Chin-Shang Li,Wei Hu,Mei Yee Lau,Huiqiong Lin,Nathan C. Rockwell,Shelley S. Martin,Judith A. Jernstedt,J. Clark Lagarias,Jorge Dubcovsky +9 more
TL;DR: These results implicate light-dependent, PHYC-mediated activation of PPD1 expression in the acceleration of wheat flowering under inductive long days, and highlight important differences in the photoperiod pathways of the temperate grasses with those of well-studied model plant species.
Journal ArticleDOI
PMut: a web-based tool for the annotation of pathological variants on proteins, 2017 update
Víctor López-Ferrando,Andrea Gazzo,Xavier de la Cruz,Modesto Orozco,Josep Lluís Gelpí,Josep Lluís Gelpí +5 more
TL;DR: The PMut internal engine has been renewed, and converted into a fully featured standalone training and prediction engine that not only powers PMut web portal, but that can generate custom predictors with alternative training sets or validation schemas.
Journal ArticleDOI
The Spectrum of Mutations in Progranulin: A Collaborative Study Screening 545 Cases of Neurodegeneration
Chang En Yu,Thomas D. Bird,Lynn M. Bekris,Thomas J. Montine,James B. Leverenz,Ellen J. Steinbart,Nichole M. Galloway,Howard Feldman,Randall L. Woltjer,Carol A. Miller,Carol A. Miller,Elisabeth M. Wood,Murray Grossman,Leo McCluskey,Christopher M. Clark,Manuela Neumann,Adrian Danek,Douglas Galasko,Steven E. Arnold,Alice Chen-Plotkin,Anna Karydas,Bruce L. Miller,John Q. Trojanowski,Virginia M.-Y. Lee,Gerard D. Schellenberg,Vivianna M. Van Deerlin +25 more
TL;DR: To delineate the range of clinical presentations associated with GRN mutations and to define pathogenic candidacy of rare GRN variants, a large study of patients with frontotemporal dementia and non-FTD cases identified 58 genetic variants that included 26 previously unknown changes.
Journal ArticleDOI
Missense mutations in TCF8 cause late-onset Fuchs corneal dystrophy and interact with FCD4 on chromosome 9p.
S. Amer Riazuddin,Norann A. Zaghloul,Amr Al-Saif,Lisa Davey,Bill H. Diplas,Danielle N. Meadows,Allen O. Eghrari,Mollie A. Minear,Yi-Ju Li,Gordon K. Klintworth,Natalie A. Afshari,Simon G. Gregory,John D. Gottsch,Nicholas Katsanis,Nicholas Katsanis +14 more
TL;DR: The data suggest that PPCD and FCD are allelic variants of the same disease continuum and that genetic interaction between genes that cause corneal dystrophies can modulate the expressivity of the phenotype.
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Predicting Deleterious Amino Acid Substitutions
Pauline C. Ng,Steven Henikoff +1 more
TL;DR: A tool that uses sequence homology to predict whether a substitution affects protein function is constructed, which may be used to identify plausible disease candidates among the SNPs that cause missense substitutions.
Journal ArticleDOI
Human non‐synonymous SNPs: server and survey
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