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
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Comparison of mitochondrial mutation spectra in ageing human colonic epithelium and disease: absence of evidence for purifying selection in somatic mitochondrial DNA point mutations.
Laura C. Greaves,Joanna L. Elson,Marco Nooteboom,John P. Grady,Geoffrey A. Taylor,Robert W. Taylor,John C. Mathers,Thomas B. L. Kirkwood,Douglass M. Turnbull +8 more
TL;DR: It is shown that the mutations associated with ageing are randomly distributed throughout the genome, are more frequently non-synonymous or frameshift mutations than the general population, and are significantly more pathogenic than population variants.
Journal ArticleDOI
Relative contribution of simple mutations vs. copy number variations in five Parkinson disease genes in the Belgian population.
Karen Nuytemans,Bram Meeus,David Crosiers,Nathalie Brouwers,Dirk Goossens,Sebastiaan Engelborghs,Philippe Pals,Barbara A. Pickut,Marleen Van den Broeck,Ellen Corsmit,Patrick Cras,Peter Paul De Deyn,Jurgen Del-Favero,Christine Van Broeckhoven,Jessie Theuns +14 more
TL;DR: Though mutations is SNCA, PINK1, and PARK7 are rare, the identification of a SNCC duplication confirmed that screening of these genes remains meaningful, and the true pathogenic nature of some heterozygous mutations in recessive genes remains elusive.
Journal ArticleDOI
Predicting Functional Effects of Synonymous Variants: A Systematic Review and Perspectives
Zishuo Zeng,Yana Bromberg +1 more
TL;DR: While the methods differ in their ability to identify severe sSNV effects, no predictor appears capable of definitively recognizing subtle effects of such variants on a large scale.
Journal ArticleDOI
KD4v: comprehensible knowledge discovery system for missense variant
Tien-Dao Luu,Alin Rusu,Vincent Walter,Benjamin Linard,Laetitia Poidevin,Raymond Ripp,Luc Moulinier,Jean Muller,Wolfgang Raffelsberger,Nicolas Wicker,Odile Lecompte,Julie D. Thompson,Olivier Poch,Hoan Nguyen +13 more
TL;DR: The KD4v (Comprehensible Knowledge Discovery System for Missense Variant) server allows to characterize and predict the phenotypic effects (deleterious/neutral) of missense variants.
Journal ArticleDOI
SOX9 regulates ERBB signalling in pancreatic cancer development
Adrien Grimont,Andreia Av Pinho,Mark Cowley,Cécile Augereau,Amanda Mawson,Marc Giry-Laterriere,Geraldine Van den Steen,Nicola Waddell,Marina Pajic,Christine Sempoux,Jianmin Wu,Sean M. Grimmond,Andrew V. Biankin,Frédéric P. Lemaigre,Ilse Rooman,Patrick Jacquemin +15 more
TL;DR: By integrating data from patient samples and mouse models, this work found that SOX9 regulates the ERBB pathway throughout pancreatic tumourigenesis, which opens perspectives for therapy targeting tumoursigenic mechanisms.
References
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Journal ArticleDOI
Database resources of the National Center for Biotechnology Information
David L. Wheeler,Deanna M. Church,Ron Edgar,Scott Federhen,Wolfgang Helmberg,Thomas L. Madden,Joan Pontius,Gregory D. Schuler,Lynn M. Schriml,Edwin Sequeira,Tugba O. Suzek,Tatiana Tatusova,Lukas Wagner +12 more
TL;DR: In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides data analysis and retrieval resources for the data in GenBank and other biological data made available through NCBI’s website.
Journal ArticleDOI
dbSNP: the NCBI database of genetic variation
Stephen T. Sherry,Minghong Ward,Michael Kholodov,Jonathan Baker,Lon Phan,Elizabeth M. Smigielski,Karl Sirotkin +6 more
TL;DR: The dbSNP database is a general catalog of genome variation to address the large-scale sampling designs required by association studies, gene mapping and evolutionary biology, and is integrated with other sources of information at NCBI such as GenBank, PubMed, LocusLink and the Human Genome Project data.
Journal ArticleDOI
The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1999.
Amos Marc Bairoch,Rolf Apweiler +1 more
TL;DR: The Human Proteomics Initiative (HPI), a major project to annotate all known human sequences according to the quality standards of SWISS-PROT, is described.
Journal ArticleDOI
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
TL;DR: A World Wide Web server is presented to predict the effect of an nsSNP on protein structure and function and the dependence of selective pressure on the structural and functional properties of proteins is studied.