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

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-dna.org).

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Figure 1: 'Sorting Tolerant From Intolerant' (SIFT) algorithm flowchart for scoring individual amino acid substitutions (AASs).
Figure 2
Figure 3: Input screen for the 'Sorting Tolerant From Intolerant' (SIFT) batch tool that takes as an input a list of protein identifiers with corresponding amino acid substitutions (AASs).
Figure 4: Input screen for a single protein that takes as an input the protein sequence along with corresponding amino acid substitutions (AASs).
Figure 5
Figure 6: Results summary screen for a single protein.
Figure 7: Output prediction for all substitutions for a single protein.
Figure 8: Output scaled probability matrix for a single protein.
Figure 9

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Acknowledgements

Development of the SIFT server at the J. Craig Venter Institute was funded by the National Human Genome Research Institute (R01 HG004701-01).

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Correspondence to Pauline C Ng.

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Kumar, P., Henikoff, S. & Ng, P. Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat Protoc 4, 1073–1081 (2009). https://doi.org/10.1038/nprot.2009.86

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