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PMID: 11875032 Published · ppublish English Comparative Study Journal Article Research Support, U.S. Gov't, P.H.S.

Accounting for human polymorphisms predicted to affect protein function.

Genome research ·Vol. 12 ·No. 3 ·2002-03-00 ·Pages 436-46

Ng PC, Henikoff S

Abstract

A major interest in human genetics is to determine whether a nonsynonymous single-base nucleotide polymorphism (nsSNP) in a gene affects its protein product and, consequently, impacts the carrier's health. We used the SIFT (Sorting Intolerant From Tolerant) program to predict that 25% of 3084 nsSNPs from dbSNP, a public SNP database, would affect protein function. Some of the nsSNPs predicted to affect function were variants known to be associated with disease. Others were artifacts of SNP discovery. Two reports have indicated that there are thousands of damaging nsSNPs in an individual's human genome; we find the number is likely to be much lower.

MeSH Terms
Amino Acid Motifs/genetics,physiology Amino Acid Sequence Amino Acid Substitution/genetics Chromosome Mapping/methods,standards,statistics & numerical data Databases, Protein/statistics & numerical data False Positive Reactions Genes Humans Molecular Sequence Data Mutation/genetics,physiology Polymorphism, Genetic Polymorphism, Single Nucleotide Proteins/genetics,physiology Pseudogenes/genetics Sequence Analysis, DNA/methods,standards,statistics & numerical data Software
Chemicals
Proteins
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Ng Pauline C
Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
Henikoff Steven
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37 references, click to expand
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Article Info
Journal
Genome research
Abbr.
Genome Res
ISSN
1088-9051
DOI
10.1101/gr.212802
Published
2002-03-00
Pages
436-46
Language
English
Region
United States
NLM ID
9518021
PMCID
PMC155281
Subset
IM
Grants
NIGMS NIH HHS · GM 20009 · United States
External Links
PubMed source DOI: 10.1101/gr.212802 PMC Full Text View journal details
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