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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Analysis of disease-linked rhodopsin mutations based on structure, function, and protein stability calculations.
Elizabeth Rakoczy,Christina Kiel,Richard McKeone,Francois Stricher,Luis Serrano,Luis Serrano +5 more
TL;DR: Detailed structural, functional, and energetic analysis provides a complete picture of the rhodopsin mutations and can guide mutation-specific therapies.
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Mammalian evolution and biomedicine: new views from phylogeny.
TL;DR: This work highlights the numerous applications to come from a well‐resolved phylogeny and genomic prospecting in multiple lineages of mammals, from identifying regulatory elements in mammalian genomes to assessing the functional consequences of mutations in human disease loci and those driving adaptive evolution.
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A Peroxisomal Disorder of Severe Intellectual Disability, Epilepsy, and Cataracts Due to Fatty Acyl-CoA Reductase 1 Deficiency
Rebecca Buchert,Hasan Tawamie,Christopher Smith,Steffen Uebe,A. Micheil Innes,A. Micheil Innes,Bassam Al Hallak,Arif B. Ekici,Heinrich Sticht,Bernd Schwarze,Ryan E. Lamont,Ryan E. Lamont,Jillian S. Parboosingh,Jillian S. Parboosingh,Francois P. Bernier,Francois P. Bernier,Rami Abou Jamra +16 more
TL;DR: The spectrum of clinical features associated with defects in plasmalogen biosynthesis is expanded to include FAR1 deficiency as a cause of syndromic severe intellectual disability with cataracts, epilepsy, and growth retardation but without rhizomelia.
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Clinical and Molecular Analysis of Stargardt Disease With Preserved Foveal Structure and Function
Kaoru Fujinami,Panagiotis I. Sergouniotis,Panagiotis I. Sergouniotis,Alice E. Davidson,Alice E. Davidson,Genevieve A. Wright,Genevieve A. Wright,Ravinder K. Chana,Ravinder K. Chana,Kazushige Tsunoda,Kazuo Tsubota,Catherine A Egan,Catherine A Egan,Anthony G. Robson,Anthony G. Robson,Anthony T. Moore,Anthony T. Moore,Graham E. Holder,Graham E. Holder,Michel Michaelides,Michel Michaelides,Andrew R. Webster,Andrew R. Webster +22 more
TL;DR: The presence of 2 distinct phenotypes of Stargardt disease (foveal sparing and foveal atrophy) suggests that there may be more than 1 disease mechanism in ABCA4 retinopathy.
Journal ArticleDOI
A combined functional annotation score for non-synonymous variants.
Margarida C. Lopes,Chris Joyce,Graham R. S. Ritchie,Sally John,Fiona Cunningham,Jennifer L. Asimit,Eleftheria Zeggini +6 more
TL;DR: Combined Annotation scoRing toOL (CAROL), which combines information from 2 bioinformatics tools: PolyPhen-2 and SIFT, in order to improve the prediction of the effect of non-synonymous coding variants, has higher predictive power and accuracy than each individual annotation tool.
References
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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
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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
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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.