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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High-Resolution Mapping of Complex Traits with a Four-Parent Advanced Intercross Yeast Population
Francisco A. Cubillos,Francisco A. Cubillos,Leopold Parts,Leopold Parts,Francisco Salinas,Anders Bergström,Eugenio Scovacricchi,Amin Zia,Christopher J. R. Illingworth,Ville Mustonen,Sebastian Ibstedt,Jonas Warringer,Edward J. Louis,Edward J. Louis,Richard Durbin,Gianni Liti +15 more
TL;DR: The most parsimonious model for the majority of loci mapped using either approach was the effect of an allele private to one founder, which could validate examples of pleiotropic effects and complex allelic series at a locus.
Journal ArticleDOI
Evidence that the recessive bymovirus resistance locus rym4 in barley corresponds to the eukaryotic translation initiation factor 4E gene
Konstantin Kanyuka,Arnis Druka,David G. Caldwell,A. Tymon,Nicola McCallum,Robbie Waugh,Michael J. Adams +6 more
TL;DR: Evidence that the barley rym4 gene locus, controlling immunity to viruses in the genus Bymovirus, corresponds to eIF4E is provided, providing evidence that monocotyledonous and dicotylingonous plants have evolved a similar strategy to combat VPg-encoding virus in the family Potyviridae.
Journal ArticleDOI
Protein interactions in human genetic diseases
TL;DR: A novel method that combines protein structure information with protein interaction data to identify residues that form part of an interaction interface and can retrieve interaction hotspots with an accuracy of 60% is presented.
Journal ArticleDOI
Mutations in SLC20A2 are a major cause of familial idiopathic basal ganglia calcification.
Sandy Chan Hsu,Renee L. Sears,R. R. Lemos,Beatriz Quintáns,Alden Y. Huang,Elizabeth Spiteri,Elizabeth Spiteri,Lisette Nevarez,Catherine Mamah,Catherine Mamah,Mayana Zatz,Kerrie D. Pierce,Janice M. Fullerton,Janice M. Fullerton,John C. Adair,Jon E. Berner,Matthew Bower,Henry Brodaty,Olga Carmona,Valerija Dobricic,Brent L. Fogel,Daniel García-Estevez,Jill Goldman,John L. Goudreau,Suellen Hopfer,Suellen Hopfer,Milena Jankovic,Serge Jaumà,Joanna C. Jen,Suppachok Kirdlarp,Joerg Klepper,Vladimir S. Kostic,Anthony E. Lang,Agnès Linglart,Melissa K. Maisenbacher,Bala V. Manyam,Pietro Mazzoni,Z. Miedzybrodzka,Witoon Mitarnun,Philip B. Mitchell,Jennifer Mueller,Ivana Novakovic,Martin Paucar,Henry L. Paulson,Sheila A Simpson,Per Svenningsson,Paul J. Tuite,Jerrold L. Vitek,Suppachok Wetchaphanphesat,Charles A. Williams,Michele Yang,Michele Yang,Peter R. Schofield,Peter R. Schofield,João Ricardo Mendes de Oliveira,María Jesús Sobrido,Daniel H. Geschwind,Giovanni Coppola +57 more
TL;DR: It is demonstrated that mutations in SLC20A2 are a major cause of familial IBGC, and non-perfect segregation patterns of predicted deleterious variants highlight the challenges of phenotypic assessment in this condition with highly variable clinical presentation.
Journal ArticleDOI
Mutations in IFT172 cause isolated retinal degeneration and Bardet-Biedl syndrome.
Kinga M. Bujakowska,Qi Zhang,Anna M. Siemiatkowska,Qin Liu,Emily Place,Marni J. Falk,Mark Consugar,Marie-Elise Lancelot,Aline Antonio,Christine Lonjou,Wassila Carpentier,Saddek Mohand-Said,Anneke I. den Hollander,Frans P.M. Cremers,Bart P. Leroy,Xiaowu Gai,José-Alain Sahel,L. Ingeborgh van den Born,Rob W.J. Collin,Christina Zeitz,Isabelle Audo,Eric A. Pierce +21 more
TL;DR: The findings expand the spectrum of disease associated with mutations in IFT172 and suggest that mutations in genes originally reported to be associated with syndromic ciliopathies should also be considered in subjects with non-syndromic retinal dystrophy.
References
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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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