Nat Protoc. 2009;4(7):1073-81. Epub 2009 Jun 25.

Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm.

Source

Department of Genomic Medicine, J. Craig Venter Institute, San Diego, California, USA.

Abstract

The effect of genetic mutation on phenotype is of significant interest in genetics. The type of genetic mutation that causes a single amino acid substitution (AAS) in a protein sequence is called a non-synonymous single nucleotide polymorphism (nsSNP). An nsSNP could potentially affect the function of the protein, subsequently altering the carrier's phenotype. This protocol describes the use of the 'Sorting Tolerant From Intolerant' (SIFT) algorithm in predicting whether an AAS affects protein function. To assess the effect of a substitution, SIFT assumes that important positions in a protein sequence have been conserved throughout evolution and therefore substitutions at these positions may affect protein function. Thus, by using sequence homology, SIFT predicts the effects of all possible substitutions at each position in the protein sequence. The protocol typically takes 5-20 min, depending on the input. SIFT is available as an online tool (http://sift.jcvi.org).

PMID:: 19561590; [PubMed - indexed for MEDLINE]

Publication Types, MeSH Terms, Substances, Grant Support

Publication Types

Research Support, N.I.H., Extramural

MeSH Terms

Substances

Proteins

Grant Support

R01 HG004701-01/HG/NHGRI NIH HHS/United States

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Related information

Related Citations
Calculated set of PubMed citations closely related to the selected article(s) retrieved using a word weight algorithm. Related articles are displayed in ranked order from most to least relevant, with the “linked from” citation displayed first.
SNP (Cited)
Nucleotide polymorphism records from dbSNP that have NCBI dbSNP identifiers reported in the PubMed abstract of the current articles.
Substance (MeSH Keyword)
PubChem chemical substance (submitted) records that are classified under the same Medical Subject Headings (MeSH) controlled vocabulary as the current articles.
Taxonomy via GenBank
Taxonomy records associated with the current articles through taxonomic information on related molecular database records (Nucleotide, Protein, Gene, SNP, Structure).
SNP
Nucleotide polymorphism records from dbSNP that have current articles as submitter-provided references.
Cited in PMC
Full-text articles in the PubMed Central Database that cite the current articles.

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