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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Comprehensive annotation of BRCA1 and BRCA2 missense variants by functionally validated sequence-based computational prediction models
Steven N. Hart,Tanya L. Hoskin,Hermela Shimelis,Raymond Moore,Bing Jian Feng,Abigail Thomas,Noralane M. Lindor,Eric C. Polley,David E. Goldgar,Edwin S. Iversen,Alvaro N.A. Monteiro,Vera J. Suman,Fergus J. Couch +12 more
TL;DR: The recalibrated algorithms and new metapredictors significantly improved upon current models for predicting the impact of variants in cancer risk–associated domains of B RCA1 and BRCA2.
Journal ArticleDOI
A bioinformatics approach for the phenotype prediction of nonsynonymous single nucleotide polymorphisms in human cytochromes P450.
TL;DR: This prediction analysis of nsSNPs in human CYP genes would be useful for further genotype-phenotype studies on individual differences in drug clearance and clinical response and a significant concordance between the predicted results using the SIFT and PolyPhen algorithms.
Journal Article
Mitochondrial DNA analysis in primary congenital glaucoma.
TL;DR: A total of 44 novel mtDNA variations were identified and may adversely affect respiratory chain, impair OXPHOS pathway result in low ATP production, high ROS production and impair growth, development and differentiation of TM lead to trabecular-dysgenesis and consequently RGC’s death.
Journal ArticleDOI
Further delineation of an entity caused by CREBBP and EP300 mutations but not resembling Rubinstein-Taybi syndrome
Leonie A. Menke,Thatjana Gardeitchik,Peter Hammond,Ketil Heimdal,Gunnar Houge,Sophia B. Hufnagel,Jianling Ji,Stefan Johansson,Sarina G. Kant,Esther Kinning,Eyby Leon,Ruth Newbury-Ecob,Stefano Paolacci,Rolph Pfundt,Nicola K. Ragge,Tuula Rinne,Claudia A. L. Ruivenkamp,Sulagna C. Saitta,Yu Sun,Marco Tartaglia,Paulien A. Terhal,Anthony J. van Essen,Magnus Dehli Vigeland,Bing Xiao,Raoul C.M. Hennekam +24 more
TL;DR: In this paper, missense variants in parts of exons 30 and 31 of CREBBP can cause a phenotype that differs from Rubinstein-Taybi syndrome (RSTS).
Journal ArticleDOI
Contemporary genetic testing in inherited cardiac disease: tools, ethical issues, and clinical applications.
Francesca Girolami,Giulia Frisso,Matteo Benelli,Lia Crotti,Maria Iascone,Ruggiero Mango,Cristina Mazzaccara,Kalliope Pilichou,Eloisa Arbustini,Benedetta Tomberli,Giuseppe Limongelli,Cristina Basso,Iacopo Olivotto +12 more
TL;DR: This document reflects the multidisciplinary, ‘real-world’ experience required when implementing genetic testing in cardiomyopathies and arrhythmic syndromes, along the recommendations of various guidelines.
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
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.