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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Reduced secreted clusterin as a mechanism for Alzheimer-associated CLU mutations
Karolien Bettens,Steven Vermeulen,Caroline Van Cauwenberghe,Bavo Heeman,Bob Asselbergh,Caroline Robberecht,Sebastiaan Engelborghs,Mathieu Vandenbulcke,Rik Vandenberghe,Peter Paul De Deyn,Peter Paul De Deyn,Marc Cruts,Christine Van Broeckhoven,Kristel Sleegers +13 more
TL;DR: Functional analyses suggest reduced secretion of the CLU protein as the mode of action for three patient-specific CLU mutations, possibly interfering with heterodimerization of the α- and β-chain of CLU.
Journal ArticleDOI
A case of autism spectrum disorder arising from a de novo missense mutation in POGZ.
Ryoko Fukai,Yoko Hiraki,Hiroko Yofune,Yoshinori Tsurusaki,Mitsuko Nakashima,Hirotomo Saitsu,Fumiaki Tanaka,Noriko Miyake,Naomichi Matsumoto +8 more
TL;DR: A novel mutation is reported in the pogo transposable element-derived protein with zinc finger domain gene (POGZ) identified by trio-based whole exome sequencing, the first de novo missense mutation in the centromere protein B-like DNA-binding domain in ASD.
Journal ArticleDOI
GEMME: A Simple and Fast Global Epistatic Model Predicting Mutational Effects
TL;DR: GEMME is an original and fast method that predicts mutational outcomes by explicitly modeling the evolutionary history of natural sequences by accounting for all positions in a sequence when estimating the effect of a given mutation.
Journal ArticleDOI
A missense mutation in TUBD1 is associated with high juvenile mortality in Braunvieh and Fleckvieh cattle.
Hermann Schwarzenbacher,Johann Burgstaller,F Seefried,Christine Wurmser,Monika Hilbe,Simone Jung,Christian Fuerst,Nora Dinhopl,Herbert Weissenböck,Birgit Fuerst-Waltl,Marlies Dolezal,Reinhard Winkler,Oskar Grueter,Ulrich Bleul,Thomas Wittek,Ruedi Fries,Hubert Pausch +16 more
TL;DR: Clinical and pathological findings revealed that homozygous calves suffered from chronic airway disease possibly resulting from defective cilia in the respiratory tract, demonstrating for the first time that deleterious alleles may segregate across closed cattle breeds without recent admixture.
Journal ArticleDOI
Functional analysis of BMP4 mutations identified in pediatric CAKUT patients.
Mansoureh Tabatabaeifar,Karl-Peter Schlingmann,Mieczysław Litwin,Sevinç Emre,Aysin Bakkaloglu,Otto Mehls,Corinne Antignac,Franz Schaefer,Stefanie Weber,Stefanie Weber +9 more
TL;DR: Functional data is presented demonstrating a lower level of messenger RNA (mRNA) abundance in BMP4 mutants that indicates a possible negative feedback of the mutants on their own mRNA expression and/or stability, and the formation of alternative protein complexes induced by the S91C-BMP4 mutation are described.
References
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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.