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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Journal ArticleDOI
Paralog Studies Augment Gene Discovery: DDX and DHX Genes.
Ingrid S. Paine,Jennifer E. Posey,Christopher M. Grochowski,Shalini N. Jhangiani,Sarah Rosenheck,Robert Kleyner,Taylor Marmorale,Margaret Yoon,Kai Wang,Reid J. Robison,Gerarda Cappuccio,Michele Pinelli,Adriano Magli,Zeynep Coban Akdemir,Joannie Hui,Wai Lan Yeung,Bibiana K Y Wong,Lucia Ortega,Mir Reza Bekheirnia,Tatjana Bierhals,Maja Hempel,Jessika Johannsen,René Santer,Dilek Aktas,Mehmet Alikasifoglu,Sevcan Tug Bozdogan,Hatip Aydin,Ender Karaca,Yavuz Bayram,Hadas Ityel,Michael O. Dorschner,Janson White,Ekkehard Wilichowski,Saskia B. Wortmann,Erasmo Barbante Casella,Joao Paulo Kitajima,Fernando Kok,Fabíola Paoli Monteiro,Donna M. Muzny,Michael J. Bamshad,Richard A. Gibbs,V. Reid Sutton,Hilde Van Esch,Nicola Brunetti-Pierri,Friedhelm Hildebrandt,Ariel Brautbar,Ignatia B. Van den Veyver,Ian A. Glass,Davor Lessel,Gholson J. Lyon,James R. Lupski +50 more
TL;DR: 15 unrelated individuals who have DD and/or ID, central nervous system (CNS) dysfunction, vertebral anomalies, and dysmorphic features and were found to have probably damaging variants in DExD/H-box RNA helicase genes are described.
Proceedings Article
Adversarial Learning for Robust Deep Clustering
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Computational analysis of functional single nucleotide polymorphisms associated with the CYP11B2 gene.
TL;DR: This study investigated the pathogenic effect of 51 nsSNPs and 26 UTR SNPs in the CYP11B2 gene through computational platforms and cataloguing of deleterious SNPs is essential for narrowing down the number of CYP 11B2 mutations to be screened in genetic association studies.
Journal ArticleDOI
Monogenic diabetes syndromes: Locus-specific databases for Alström, Wolfram, and Thiamine-responsive megaloblastic anemia.
Dewi Astuti,Ataf Sabir,Piers Fulton,Malgorzata Zatyka,Denise Williams,Carol Hardy,Gabriella Milan,Francesca Favaretto,Patrick Yu-Wai-Man,Julia Rohayem,Miguel López de Heredia,Tamara Hershey,Lisbeth Tranebjærg,Jian-Hua Chen,Annabel Chaussenot,Virginia Nunes,Bess A. Marshall,Susan McAfferty,Vallo Tillmann,Pietro Maffei,Véronique Paquis-Flucklinger,Tarekign Geberhiwot,Wojciech Młynarski,Kay Parkinson,Virginie Picard,Gema Esteban Bueno,Renuka P Dias,Amy Arnold,Caitlin Richens,Richard B Paisey,Fumihiko Urano,Robert K. Semple,Richard O. Sinnott,Timothy Barrett,Timothy Barrett +34 more
TL;DR: A variant database for diabetes syndrome genes, using the Leiden Open Variation Database platform, containing observed phenotypes matched to the genetic variations, allowing prognostic predictions for other diabetes syndromes as next‐generation sequencing expands the repertoire of genotypes and phenotypes.
Journal ArticleDOI
Getting the Point—Mutations in Maize
Clifford F. Weil,Rita-Ann Monde +1 more
TL;DR: The Maize Targeting Induced Local Lesions IN Genomes (TILLING) Project has been established to provide reverse genetics resources that can screen ethyl methonyl sulfonate (EMS)-mutagenized populations of maize for individuals carrying point mutations in virtually any gene in the genome.
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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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