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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De novo Mutations From Whole Exome Sequencing in Neurodevelopmental and Psychiatric Disorders: From Discovery to Application.
TL;DR: This review will assist researchers and clinicians in the interpretation of variants obtained from WES studies, and highlights the need to develop consensus analytical protocols and validated lists of genes appropriate for clinical laboratory analysis, in order to reach the growing demands.
Journal ArticleDOI
Novel PRRT2 mutations in paroxysmal dyskinesia patients with variant inheritance and phenotypes.
Xiao Rong Liu,M. Wu,Na He,H. Meng,L. Wen,J.-L. Wang,M.-P. Zhang,W.-B. Li,X. Mao,J.-M. Qin,Bing-Mei Li,Bin Tang,Y.-H. Deng,Yi-Wu Shi,Tao Su,Yong-Hong Yi,Beisha Tang,Wei-Ping Liao +17 more
TL;DR: It is confirmed that PRRT2 mutations are the most common cause of familial PDs, displaying both dominant and recessive inheritance.
Journal ArticleDOI
Evidence for Diversifying Selection in a Set of Mycobacterium tuberculosis Genes in Response to Antibiotic- and Nonantibiotic-Related Pressure
Nuno S. Osório,Fernando Rodrigues,Sebastien Gagneux,Sebastien Gagneux,Jorge Pedrosa,Marta Pinto-Carbó,António G. Castro,Douglas B. Young,Douglas B. Young,Iñaki Comas,Margarida Saraiva +10 more
TL;DR: Diversifying selection is identified in specific codons of the genes Rv0176 and Rv1872c coding for MCE1-associated transmembrane protein and a putative l-lactate dehydrogenase, illustrating that diversifying selection in MTBC is happening as a consequence of both antibiotic treatment and other evolutionary pressures.
Journal ArticleDOI
Peripheral motor neuropathy is associated with defective kinase regulation of the KCC3 cotransporter
Kristopher T. Kahle,Bianca Flores,Diana Bharucha-Goebel,Jinwei Zhang,Sandra Donkervoort,Madhuri Hegde,Gulnaz Hussain,Daniel Duran,Bo Liang,Dandan Sun,Carsten G. Bönnemann,Eric Delpire +11 more
TL;DR: The results suggest that the function of the peripheral nervous system depends on finely tuned, kinase-regulated KCC3 activity and implicate abnormal cell volume homeostasis as a previously unreported mechanism of axonal degeneration.
Journal ArticleDOI
New mutations in the Wilson disease gene, ATP7B: implications for molecular testing.
TL;DR: Mutation analysis was carried out on 300 WND patients of various origins, and new mutations not previously reported were identified, and all but one missense variant have strong evidence for classification as disease-causing mutations.
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.