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Nucleic Acids Research, 2002, Vol. 30, No. 17 3894-3900
© 2002 Oxford University Press

Human non-synonymous SNPs: server and survey

Vasily Ramensky1,2,3, Peer Bork1,2 and Shamil Sunyaev*,1,3

1 European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany, 2 Max-Delbrueck Center for Molecular Medicine, Robert-Roessle-Strasse 10, 13122 Berlin, Germany and 3 Engelhardt Institute of Molecular Biology, Vavilova 32, 119991 Moscow, Russia

*To whom correspondence should be addressed at present address: Genetics Division, Department of Medicine, Brigham & Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA. Tel: +1 617 7325856; Fax: +1 617 7325123; Email: ssunyaev{at}rics.bwh.harvard.edu

Human single nucleotide polymorphisms (SNPs) represent the most frequent type of human population DNA variation. One of the main goals of SNP research is to understand the genetics of the human phenotype variation and especially the genetic basis of human complex diseases. Non-synonymous coding SNPs (nsSNPs) comprise a group of SNPs that, together with SNPs in regulatory regions, are believed to have the highest impact on phenotype. Here we present a World Wide Web server to predict the effect of an nsSNP on protein structure and function. The prediction method enabled analysis of the publicly available SNP database HGVbase, which gave rise to a dataset of nsSNPs with predicted functionality. The dataset was further used to compare the effect of various structural and functional characteristics of amino acid substitutions responsible for phenotypic display of nsSNPs. We also studied the dependence of selective pressure on the structural and functional properties of proteins. We found that in our dataset the selection pressure against deleterious SNPs depends on the molecular function of the protein, although it is insensitive to several other protein features considered. The strongest selective pressure was detected for proteins involved in transcription regulation.


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Association of the ARLTS1 Cys148Arg variant with sporadic and familial colorectal cancer
Carcinogenesis, August 1, 2007; 28(8): 1687 - 1691.
[Abstract] [Full Text] [PDF]

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 Nucleic Acids ResHome page
M. Brudno, A. Poliakov, S. Minovitsky, I. Ratnere, and I. Dubchak
Multiple whole genome alignments and novel biomedical applications at the VISTA portal
Nucleic Acids Res., July 13, 2007; 35(suppl_2): W669 - W674.
[Abstract] [Full Text] [PDF]

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 Nucleic Acids ResHome page
J. S. Kaminker, Y. Zhang, C. Watanabe, and Z. Zhang
CanPredict: a computational tool for predicting cancer-associated missense mutations
Nucleic Acids Res., July 13, 2007; 35(suppl_2): W595 - W598.
[Abstract] [Full Text] [PDF]

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 BioinformaticsHome page
F. Panitz, H. Stengaard, H. Hornshoj, J. Gorodkin, J. Hedegaard, S. Cirera, B. Thomsen, L. B. Madsen, A. Hoj, R. K. Vingborg, et al.
SNP mining porcine ESTs with MAVIANT, a novel tool for SNP evaluation and annotation
Bioinformatics, July 1, 2007; 23(13): i387 - i391.
[Abstract] [Full Text] [PDF]

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 Nucleic Acids ResHome page
Y. Bromberg and B. Rost
SNAP: predict effect of non-synonymous polymorphisms on function
Nucleic Acids Res., June 28, 2007; 35(11): 3823 - 3835.
[Abstract] [Full Text] [PDF]

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 BioinformaticsHome page
Z.-Q. Ye, S.-Q. Zhao, G. Gao, X.-Q. Liu, R. E. Langlois, H. Lu, and L. Wei
Finding new structural and sequence attributes to predict possible disease association of single amino acid polymorphism (SAP)
Bioinformatics, June 15, 2007; 23(12): 1444 - 1450.
[Abstract] [Full Text] [PDF]

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 Proc. Natl. Acad. Sci. USAHome page
G. Gasparre, A. M. Porcelli, E. Bonora, L. F. Pennisi, M. Toller, L. Iommarini, A. Ghelli, M. Moretti, C. M. Betts, G. N. Martinelli, et al.
Disruptive mitochondrial DNA mutations in complex I subunits are markers of oncocytic phenotype in thyroid tumors
PNAS, May 22, 2007; 104(21): 9001 - 9006.
[Abstract] [Full Text] [PDF]

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 Hum Mol GenetHome page
N. Johnson, O. Fletcher, C. Palles, M. Rudd, E. Webb, G. Sellick, I. dos Santos Silva, V. McCormack, L. Gibson, A. Fraser, et al.
Counting potentially functional variants in BRCA1, BRCA2 and ATM predicts breast cancer susceptibility
Hum. Mol. Genet., May 1, 2007; 16(9): 1051 - 1057.
[Abstract] [Full Text] [PDF]

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 J. Am. Soc. Nephrol.Home page
K. Tory, T. Lacoste, L. Burglen, V. Moriniere, N. Boddaert, M.-A. Macher, B. Llanas, H. Nivet, A. Bensman, P. Niaudet, et al.
High NPHP1 and NPHP6 Mutation Rate in Patients with Joubert Syndrome and Nephronophthisis: Potential Epistatic Effect of NPHP6 and AHI1 Mutations in Patients with NPHP1 Mutations
J. Am. Soc. Nephrol., May 1, 2007; 18(5): 1566 - 1575.
[Abstract] [Full Text] [PDF]

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 Physiol. GenomicsHome page
S. Savas, I. W. Taylor, J. L. Wrana, and H. Ozcelik
Functional nonsynonymous single nucleotide polymorphisms from the TGF-{beta} protein interaction network
Physiol Genomics, April 24, 2007; 29(2): 109 - 117.
[Abstract] [Full Text] [PDF]

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 BioinformaticsHome page
M. A. Care, C. J. Needham, A. J. Bulpitt, and D. R. Westhead
Deleterious SNP prediction: be mindful of your training data!
Bioinformatics, March 15, 2007; 23(6): 664 - 672.
[Abstract] [Full Text] [PDF]

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 Mol Biol EvolHome page
S. Seixas, G. Suriano, F. Carvalho, R. Seruca, J. Rocha, and A. Di Rienzo
Sequence Diversity at the Proximal 14q32.1 SERPIN Subcluster: Evidence for Natural Selection Favoring the Pseudogenization of SERPINA2
Mol. Biol. Evol., February 1, 2007; 24(2): 587 - 598.
[Abstract] [Full Text] [PDF]

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 Cancer Res.Home page
J. S. Kaminker, Y. Zhang, A. Waugh, P. M. Haverty, B. Peters, D. Sebisanovic, J. Stinson, W. F. Forrest, J. F. Bazan, S. Seshagiri, et al.
Distinguishing Cancer-Associated Missense Mutations from Common Polymorphisms
Cancer Res., January 15, 2007; 67(2): 465 - 473.
[Abstract] [Full Text] [PDF]

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 Nucleic Acids ResHome page
A. G. Jegga, S. Gowrisankar, J. Chen, and B. J. Aronow
PolyDoms: a whole genome database for the identification of non-synonymous coding SNPs with the potential to impact disease
Nucleic Acids Res., January 12, 2007; 35(suppl_1): D700 - D706.
[Abstract] [Full Text] [PDF]

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 BloodHome page
P. D. James, C. Notley, C. Hegadorn, J. Leggo, A. Tuttle, S. Tinlin, C. Brown, C. Andrews, A. Labelle, Y. Chirinian, et al.
The mutational spectrum of type 1 von Willebrand disease: results from a Canadian cohort study
Blood, January 1, 2007; 109(1): 145 - 154.
[Abstract] [Full Text] [PDF]

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 Cancer Epidemiol. Biomarkers Prev.Home page
A. Koushik, P. Kraft, C. S. Fuchs, S. E. Hankinson, W. C. Willett, E. L. Giovannucci, and D. J. Hunter
Nonsynonymous Polymorphisms in Genes in the One-Carbon Metabolism Pathway and Associations with Colorectal Cancer
Cancer Epidemiol. Biomarkers Prev., December 1, 2006; 15(12): 2408 - 2417.
[Abstract] [Full Text] [PDF]

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 BioinformaticsHome page
E. Capriotti, R. Calabrese, and R. Casadio
Predicting the insurgence of human genetic diseases associated to single point protein mutations with support vector machines and evolutionary information
Bioinformatics, November 15, 2006; 22(22): 2729 - 2734.
[Abstract] [Full Text] [PDF]

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 Hum Mol GenetHome page
E. L. Webb, M. F. Rudd, G. S. Sellick, R. El Galta, L. Bethke, W. Wood, O. Fletcher, S. Penegar, L. Withey, M. Qureshi, et al.
Search for low penetrance alleles for colorectal cancer through a scan of 1467 non-synonymous SNPs in 2575 cases and 2707 controls with validation by kin-cohort analysis of 14 704 first-degree relatives
Hum. Mol. Genet., November 1, 2006; 15(21): 3263 - 3271.
[Abstract] [Full Text] [PDF]

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 Am J EpidemiolHome page
P. Bhatti, D. M. Church, J. L. Rutter, J. P. Struewing, and A. J. Sigurdson
Candidate Single Nucleotide Polymorphism Selection using Publicly Available Tools: A Guide for Epidemiologists
Am. J. Epidemiol., October 15, 2006; 164(8): 794 - 804.
[Abstract] [Full Text] [PDF]

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 DiabetesHome page
S. Onengut-Gumuscu, J. H. Buckner, and P. Concannon
A Haplotype-Based Analysis of the PTPN22 Locus in Type 1 Diabetes.
Diabetes, October 1, 2006; 55(10): 2883 - 2889.
[Abstract] [Full Text] [PDF]

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 J ANIM SCIHome page
A. Tomas, J. Casellas, O. Ramirez, G. Munoz, J. L. Noguera, and A. Sanchez
High amino acid variation in the intracellular domain of the pig prolactin receptor (PRLR) and its relation to ovulation rate and piglet survival traits
J Anim Sci, August 1, 2006; 84(8): 1991 - 1998.
[Abstract] [Full Text] [PDF]

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 BloodHome page
M. F. Rudd, G. S. Sellick, E. L. Webb, D. Catovsky, and R. S. Houlston
Variants in the ATM-BRCA2-CHEK2 axis predispose to chronic lymphocytic leukemia
Blood, July 15, 2006; 108(2): 638 - 644.
[Abstract] [Full Text] [PDF]

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 IOVSHome page
L. S. Sullivan, S. J. Bowne, D. G. Birch, D. Hughbanks-Wheaton, J. R. Heckenlively, R. A. Lewis, C. A. Garcia, R. S. Ruiz, S. H. Blanton, H. Northrup, et al.
Prevalence of disease-causing mutations in families with autosomal dominant retinitis pigmentosa: a screen of known genes in 200 families.
Invest. Ophthalmol. Vis. Sci., July 1, 2006; 47(7): 3052 - 3064.
[Abstract] [Full Text] [PDF]

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 Nucleic Acids ResHome page
H.-Y. Yuan, J.-J. Chiou, W.-H. Tseng, C.-H. Liu, C.-K. Liu, Y.-J. Lin, H.-H. Wang, A. Yao, Y.-T. Chen, and C.-N. Hsu
FASTSNP: an always up-to-date and extendable service for SNP function analysis and prioritization.
Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W635 - W641.
[Abstract] [Full Text] [PDF]

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 Nucleic Acids ResHome page
A. Han, H. J. Kang, Y. Cho, S. Lee, Y. J. Kim, and S. Gong
SNP@Domain: a web resource of single nucleotide polymorphisms (SNPs) within protein domain structures and sequences.
Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W642 - W644.
[Abstract] [Full Text] [PDF]


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