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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MutDB: update on development of tools for the biochemical analysis of genetic variation
Arti Singh,Adebayo Olowoyeye,Peter H. Baenziger,Jessica Dantzer,Maricel G. Kann,Predrag Radivojac,Randy Heiland,Sean D. Mooney +7 more
TL;DR: MutDB as discussed by the authors integrates annotated SNPs in dbSNP and amino acid substitutions in Swiss-Prot with protein structural information, links to scores that predict functional disruption and other useful annotations.
Journal ArticleDOI
ABCA4 Gene Screening by Next-Generation Sequencing in a British Cohort
Kaoru Fujinami,Jana Zernant,Ravinder K. Chana,Ravinder K. Chana,Genevieve A. Wright,Genevieve A. Wright,Kazushige Tsunoda,Yoko Ozawa,Kazuo Tsubota,Andrew R. Webster,Andrew R. Webster,Anthony T. Moore,Anthony T. Moore,Rando Allikmets,Michel Michaelides,Michel Michaelides +15 more
TL;DR: Application of the NGS platform for ABCA4 screening enabled detection of the second disease-associated allele in approximately half of the patients in a British cohort where one mutation had been detected with the arrayed primer extension (APEX) array.
Journal ArticleDOI
Characterization of the genetic profile of CYP2C19 in two South African populations
Britt I. Drögemöller,Galen E.B. Wright,Dana J.H. Niehaus,Liezl Koen,Stefanie Malan,Danielle M Da Silva,Renate Hillermann,Mauritz Venter,Louise Warnich +8 more
TL;DR: The data demonstrate that both the Xhosa and CMA populations exhibit unique genetic profiles that could influence the outcome of drug therapy in these populations.
Journal ArticleDOI
Prevalence of PALB2 mutations in Australasian multiple-case breast cancer families
Zhi Ling Teo,Daniel J. Park,Elena Provenzano,Catherine A Chatfield,Fabrice Odefrey,Tu Nguyen-Dumont,James G. Dowty,John L. Hopper,Ingrid Winship,Ingrid Winship,David E. Goldgar,Melissa C. Southey +11 more
TL;DR: About 1.5% (95% CI 0.6to 2.4) of Australasian multiple-case breast cancer families attending clinics are segregating protein-truncating mutations in PALB2, most being PALB 2 c.3113G>A, p.Trp1038*.
Journal ArticleDOI
Investigating the structural impacts of I64T and P311S mutations in APE1-DNA complex: a molecular dynamics approach.
TL;DR: Different parameters such as RMSD, RMSF, salt bridge, H-bonds and SASA applied in Molecular dynamic study reveals that predicted deleterious variants I64T and P311S alters the structure as well as affect the stability of APE1-DNA interacting functions.
References
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Journal ArticleDOI
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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.