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Human Molecular Genetics, 2001, Vol. 10, No. 6 591-597
© 2001 Oxford University Press

Prediction of deleterious human alleles

Shamil Sunyaev1,2,3, Vasily Ramensky3, Ina Koch3, Warren Lathe III1,2, Alexey S. Kondrashov4 and Peer Bork1,2,+

1European Molecular Biology Laboratory, Meyerhofstrasse 1, D-69117 Heidelberg, Germany, 2Max-Delbrueck Centre for Molecular Medicine, Robert-Roessle-Strasse 10, D-13122 Berlin, Germany, 3Engelhardt Institute of Molecular Biology, Vavilova 32, D-117984 Moscow, Russia and 4National Center for Biotechnology Information, National Institutes of Health, 45 Center Drive, MSC 6510, Bethesda, MD 20892-6510, USA

Single nucleotide polymorphisms (SNPs) constitute the bulk of human genetic variation, occurring with an average density of ~1/1000 nucleotides of a genotype. SNPs are either neutral allelic variants or are under selection of various strengths, and the impact of SNPs on fitness remains unknown. Identification of SNPs affecting human phenotype, especially leading to risks of complex disorders, is one of the key problems of medical genetics. SNPs in protein-coding regions that cause amino acid variants (non-synonymous cSNPs) are most likely to affect phenotypes. We have developed a straightforward and reliable method based on physical and comparative considerations that estimates the impact of an amino acid replacement on the three-dimensional structure and function of the protein. We estimate that ~20% of common human non-synonymous SNPs damage the protein. The average minor allele frequency of such SNPs in our data set was two times lower than that of benign non-synonymous SNPs. The average human genotype carries approximately 103 damaging non-synonymous SNPs that together cause a substantial reduction in fitness.

+ To whom correspondence should be addressed. Tel: +49 6221 387526; Fax: +49 6221 387517; Email: bork@embl-heidelberg.de


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 GeneticsHome page
A. L. Hughes, B. Packer, R. Welch, A. W. Bergen, S. J. Chanock, and M. Yeager
Effects of Natural Selection on Interpopulation Divergence at Polymorphic Sites in Human Protein-Coding Loci
Genetics, July 1, 2005; 170(3): 1181 - 1187.
[Abstract] [Full Text] [PDF]

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 BioinformaticsHome page
R. Karchin, M. Diekhans, L. Kelly, D. J. Thomas, U. Pieper, N. Eswar, D. Haussler, and A. Sali
LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sources
Bioinformatics, June 15, 2005; 21(12): 2814 - 2820.
[Abstract] [Full Text] [PDF]

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 BioinformaticsHome page
L. Bao and Y. Cui
Prediction of the phenotypic effects of non-synonymous single nucleotide polymorphisms using structural and evolutionary information
Bioinformatics, May 15, 2005; 21(10): 2185 - 2190.
[Abstract] [Full Text] [PDF]

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 BioinformaticsHome page
A. Cavallo and A. C. R. Martin
Mapping SNPs to protein sequence and structure data
Bioinformatics, April 15, 2005; 21(8): 1443 - 1450.
[Abstract] [Full Text] [PDF]

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 JNCI J Natl Cancer InstHome page
J. Sun, F. Wiklund, S. L. Zheng, B. Chang, K. Balter, L. Li, J.-E. Johansson, G. Li, H.-O. Adami, W. Liu, et al.
Sequence Variants in Toll-Like Receptor Gene Cluster (TLR6-TLR1-TLR10) and Prostate Cancer Risk
J Natl Cancer Inst, April 6, 2005; 97(7): 525 - 532.
[Abstract] [Full Text] [PDF]

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 Nucleic Acids ResHome page
S. Balasubramanian, Y. Xia, E. Freinkman, and M. Gerstein
Sequence variation in G-protein-coupled receptors: analysis of single nucleotide polymorphisms
Nucleic Acids Res., March 22, 2005; 33(5): 1710 - 1721.
[Abstract] [Full Text] [PDF]

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 Genome ResHome page
M. Blanchette, E. D. Green, W. Miller, and D. Haussler
Reconstructing large regions of an ancestral mammalian genome in silico
Genome Res., December 1, 2004; 14(12): 2412 - 2423.
[Abstract] [Full Text] [PDF]

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 Clin. Chem.Home page
D. Tchernitchko, M. Goossens, and H. Wajcman
In Silico Prediction of the Deleterious Effect of a Mutation: Proceed with Caution in Clinical Genetics
Clin. Chem., November 1, 2004; 50(11): 1974 - 1978.
[Abstract] [Full Text] [PDF]

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 Genome ResHome page
R. J. Livingston, A. von Niederhausern, A. G. Jegga, D. C. Crawford, C. S. Carlson, M. J. Rieder, S. Gowrisankar, B. J. Aronow, R. B. Weiss, and D. A. Nickerson
Pattern of Sequence Variation Across 213 Environmental Response Genes
Genome Res., October 1, 2004; 14(10a): 1821 - 1831.
[Abstract] [Full Text] [PDF]

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 ScienceHome page
J. C. Cohen, R. S. Kiss, A. Pertsemlidis, Y. L. Marcel, R. McPherson, and H. H. Hobbs
Multiple Rare Alleles Contribute to Low Plasma Levels of HDL Cholesterol
Science, August 6, 2004; 305(5685): 869 - 872.
[Abstract] [Full Text] [PDF]

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 Cancer Epidemiol. Biomarkers Prev.Home page
S. Savas, D. Y. Kim, M. F. Ahmad, M. Shariff, and H. Ozcelik
Identifying Functional Genetic Variants in DNA Repair Pathway Using Protein Conservation Analysis
Cancer Epidemiol. Biomarkers Prev., May 1, 2004; 13(5): 801 - 807.
[Abstract] [Full Text] [PDF]

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 Proc. Natl. Acad. Sci. USAHome page
A. Y. Lau and D. I. Chasman
Functional classification of proteins and protein variants
PNAS, April 27, 2004; 101(17): 6576 - 6581.
[Abstract] [Full Text] [PDF]

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 Protein Eng Des SelHome page
B. Shen and M. Vihinen
Conservation and covariance in PH domain sequences: physicochemical profile and information theoretical analysis of XLA-causing mutations in the Btk PH domain
Protein Eng. Des. Sel., March 1, 2004; 17(3): 267 - 276.
[Abstract] [Full Text] [PDF]

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 Toxicol PatholHome page
H. W. Mohrenweiser
Genetic Variation and Exposure Related Risk Estimation: Will Toxicology Enter a New Era? DNA Repair and Cancer as a Paradigm
Toxicol Pathol, January 1, 2004; 32(1_suppl): 136 - 145.
[Abstract] [PDF]

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 Proc. Natl. Acad. Sci. USAHome page
A. L. Hughes, B. Packer, R. Welch, A. W. Bergen, S. J. Chanock, and M. Yeager
Widespread purifying selection at polymorphic sites in human protein-coding loci
PNAS, December 23, 2003; 100(26): 15754 - 15757.
[Abstract] [Full Text] [PDF]

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 Hum Mol GenetHome page
S. Sunyaev, F. A. Kondrashov, P. Bork, and V. Ramensky
Impact of selection, mutation rate and genetic drift on human genetic variation
Hum. Mol. Genet., December 15, 2003; 12(24): 3325 - 3330.
[Abstract] [Full Text] [PDF]

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 Nucleic Acids ResHome page
P. C. Ng and S. Henikoff
SIFT: predicting amino acid changes that affect protein function
Nucleic Acids Res., July 1, 2003; 31(13): 3812 - 3814.
[Abstract] [Full Text] [PDF]

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 Nucleic Acids ResHome page
S. D. Mooney, T. E. Klein, R. B. Altman, M. A. Trifiro, and B. Gottlieb
A functional analysis of disease-associated mutations in the androgen receptor gene
Nucleic Acids Res., April 15, 2003; 31(8): e42 - e42.
[Abstract] [Full Text] [PDF]

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 Nucleic Acids ResHome page
J. Zhang, W. L. Rowe, J. P. Struewing, and K. H. Buetow
HapScope: a software system for automated and visual analysis of functionally annotated haplotypes
Nucleic Acids Res., December 1, 2002; 30(23): 5213 - 5221.
[Abstract] [Full Text] [PDF]

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 Nucleic Acids ResHome page
V. Ramensky, P. Bork, and S. Sunyaev
Human non-synonymous SNPs: server and survey
Nucleic Acids Res., September 1, 2002; 30(17): 3894 - 3900.
[Abstract] [Full Text] [PDF]

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 Genome ResHome page
P. C. Ng and S. Henikoff
Accounting for Human Polymorphisms Predicted to Affect Protein Function
Genome Res., March 1, 2002; 12(3): 436 - 446.
[Abstract] [Full Text] [PDF]

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 Hum Mol GenetHome page
L. Goodstadt and C. P. Ponting
Sequence variation and disease in the wake of the draft human genome
Hum. Mol. Genet., October 1, 2001; 10(20): 2209 - 2214.
[Abstract] [Full Text] [PDF]

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 Hum Mol GenetHome page
M. P. Miller and S. Kumar
Understanding human disease mutations through the use of interspecific genetic variation
Hum. Mol. Genet., October 1, 2001; 10(21): 2319 - 2328.
[Abstract] [Full Text] [PDF]


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