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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Polymorphisms in the Trace Amine Receptor 4 (TRAR4) Gene on Chromosome 6q23.2 Are Associated with Susceptibility to Schizophrenia
Jubao Duan,Maria Martinez,Alan R. Sanders,C Hou,Naruya Saitou,Takashi Kitano,Bryan J. Mowry,Bryan J. Mowry,Raymond R. Crowe,Jeremy M. Silverman,Douglas F. Levinson,Pablo V. Gejman +11 more
TL;DR: Genotyped 192 European-ancestry and African American pedigrees with schizophrenia from samples that previously showed linkage evidence to 6q13-q26, focusing on the MOXD1-STX7-TRARs gene cluster at 6q23.2, and revealed strong preliminary evidence that TRAR4 is a candidate gene for schizophrenia.
Journal ArticleDOI
Mutation analysis of the paraplegin gene (SPG7) in patients with hereditary spastic paraplegia.
N. Elleuch,C. Depienne,Ali Benomar,A. M. Ouvrard Hernandez,Xavier Ferrer,B. Fontaine,D. Grid,Chantal M. E. Tallaksen,R. Zemmouri,Giovanni Stevanin,Alexandra Durr,Alexis Brice +11 more
TL;DR: Cerebellar signs or cerebellar atrophy on brain imaging were the most frequent additional features in patients with SPG7 HSP, complicating routine diagnosis.
Journal ArticleDOI
The Wilms tumor gene, Wt1, is critical for mouse spermatogenesis via regulation of sertoli cell polarity and is associated with non-obstructive azoospermia in humans.
Xiao Na Wang,Ze Song Li,Ze Song Li,Yu Ren,Tao Jiang,Ya Qing Wang,Min Chen,Jun Zhang,Jian Xiu Hao,Yanbo Wang,Ri Na Sha,Yi Huang,Yi Huang,Xiao Liu,Jing Chu Hu,Guang Qing Sun,Hong Gang Li,Cheng Liang Xiong,Jun Xie,Zhi Mao Jiang,Zhi Ming Cai,Zhi Ming Cai,Jun Wang,Jian Wang,Vicki Huff,Yaoting Gui,Fei Gao +26 more
TL;DR: It is suggested that Wt1 is important in spermatogenesis by regulating the polarity of SCs via Wnt signaling pathway and that WT1 mutation is one of the genetic causes of NOA in humans.
Journal ArticleDOI
Mutations in PVRL4, Encoding Cell Adhesion Molecule Nectin-4, Cause Ectodermal Dysplasia-Syndactyly Syndrome
Francesco Brancati,Francesco Brancati,Paola Fortugno,Irene Bottillo,Marc Lopez,Emmanuelle Josselin,Omar Boudghene-Stambouli,Emanuele Agolini,Laura Bernardini,Emanuele Bellacchio,Miriam Iannicelli,Alfredo De Rossi,Amina Dib-Lachachi,Liborio Stuppia,Giandomenico Palka,Stefan Mundlos,Sigmar Stricker,Uwe Kornak,Giovanna Zambruno,Bruno Dallapiccola +19 more
TL;DR: Together with cleft lip and/or palate ectodermal dysplasia (CLPED1, or Zlotogora-Ogur syndrome) due to an impaired function of nECTin-1, EDSS is the second known "nectinopathy" caused by mutations in a nectin adhesion molecule.
Journal ArticleDOI
The Limits of Natural Selection in a Nonequilibrium World.
TL;DR: It is argued that substantial care is needed to appropriately test whether species and populations show meaningful differences in selection efficacy, and a move toward model-based inferences that explicitly incorporate nonequilibrium dynamics provides a promising approach to more accurately contrast selection efficacy across populations.
References
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Stephen T. Sherry,Minghong Ward,Michael Kholodov,Jonathan Baker,Lon Phan,Elizabeth M. Smigielski,Karl Sirotkin +6 more
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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.