A method and server for predicting damaging missense mutations.
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Some of the more commonly used in-silico tools for missense variant interpretation in clinical laboratories include PolyPhen2, SIFT and MutationTaster.
“Some of the more commonly used in-silico tools for missense variant interpretation in clinical laboratories include PolyPhen2 19 , SIFT 20 and MutationTaster 21 .”
All TP53 mutations were either predicted to be deleterious or previously identified recurrent mutations.
“All were either predicted to be deleterious76,77 or previously identified recurrent mutations61”
From The origins and genetic interactions of KRAS mutations are allele- and tissue-specific (2021) · cites this paper as [77]
For probably damaging missense mutations (Mis3), risk is lower than for loss-of-function mutations, and allele frequency for ASD risk genes is lower than for non-ASD genes.
“Estimates reveal lower risk for these mutations, as expected, and lower for ASD risk genes compared with non-ASD genes (Table S1).”
From Integrated Model of De Novo and Inherited Genetic Variants Yields Greater Power to Identify Risk Genes (2013) · cites this paper as [9]
All variants tested were predicted as damaging by Polyphen2 DIV except Q1308R, which was identified only in controls and predicted as benign.
“All variants were predicted as damaging by Polyphen2 DIV except Q1308R identified only in controls and predicted as benign [41].”
From Genetic and Functional Analyses of SHANK2 Mutations Suggest a Multiple Hit Model of Autism Spectrum Disorders (2012) · cites this paper as [41]
In chromosome 4q25, index SNP rs4698775 is in strong linkage disequilibrium (r2=.88) with a potentially protein damaging variant in CCDC109B.
“In chromosome 4q25, index SNP rs4698775 is in strong linkage disequilibrium (r2=.88) with a potentially protein damaging variant in CCDC109B36, a coiled coil domain containing protein that may be involved in the regulation of gene expression.”
From Seven new loci associated with age-related macular degeneration (2013) · cites this paper as [36]
Non-synonymous archaic alleles are predicted to have less effect (as measured by deleteriousness scores) than non-synonymous non-archaic alleles (all P < 0.001).
“We found that non-synonymous archaic alleles are predicted to have less effect (as measured by the deleteriousness scores) than non-synonymous non-archaic alleles (all P < 0.001; Fig. 1; “Methods”).”
From Functional implications of Neandertal introgression in modern humans (2017) · cites this paper as [17]
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SIFT: predicting amino acid changes that affect protein function
Ng, P. C. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg509 · Cited by 6,601 · see citing works
Human non-synonymous SNPs: server and survey
Ramensky, V. E. (2002) · Nucleic Acids Research · doi:10.1093/nar/gkf493 · Cited by 2,267 · see citing works
Self-citationCapriotti, E., Calabrese, R., & Casadio, R. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl423 · Cited by 940 · see citing works
SNPs3D: Candidate gene and SNP selection for association studies
Yue, P., Melamud, E., & Moult, J. (2006) · BMC Bioinformatics · doi:10.1186/1471-2105-7-166 · Cited by 460 · see citing works
SNAP predicts effect of mutations on protein function
Bromberg, Y., Yachdav, G., & Rost, B. (2008) · Bioinformatics · doi:10.1093/bioinformatics/btn435 · Cited by 262 · see citing works
Hypermutable Non-Synonymous Sites Are under Stronger Negative Selection
Schmidt, S., Gerasimova, A. V., Kondrashov, F. A., Adzhubei, I. A., Kondrashov, A. S., & Sunyaev, S. R. (2008) · PLoS Genetics · doi:10.1371/journal.pgen.1000281 · Cited by 34 · see citing works
Self-citationCorrection: Hypermutable Non-Synonymous Sites Are under Stronger Negative Selection
Schmidt, S., Gerasimova, A. V., Kondrashov, F. A., Adzhubei, I. A., Kondrashov, A. S., & Sunyaev, S. R. (2008) · PLoS Genetics · doi:10.1371/annotation/a81b1fab-890c-447b-a308-5bc8ca3eb21d · Cited by 10 · see citing works
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Richards, S., Aziz, N., Bale, S., Bick, D., Das, S., Gastier-Foster, J., Grody, W. W., Hegde, M., Lyon, E., Spector, E., et al. (2015) · Genetics in Medicine · doi:10.1038/gim.2015.30 · Cited by 32,594 · see citing works
The Phyre2 web portal for protein modeling, prediction and analysis
Kelley, L. A., Mezulis, S., Yates, C. M., Wass, M. N., & Sternberg, M. J. E. (2015) · Nature Protocols · doi:10.1038/nprot.2015.053 · Cited by 9,652 · see citing works
The Ensembl Variant Effect Predictor
McLaren, W., Gil, L., Hunt, S. E., Riat, H. S., Ritchie, G. R. S., Thormann, A., Flicek, P., & Cunningham, F. (2016) · Genome Biology · doi:10.1186/s13059-016-0974-4 · Cited by 8,099 · see citing works
Mutational landscape determines sensitivity to PD-1 blockade in non–small cell lung cancer
Rizvi, N. A., Hellmann, M. D., Snyder, A., Kvistborg, P., Makarov, V., Havel, J. J., Lee, W., Yuan, J., Wong, P., Ho, T. S., et al. (2015) · Science · doi:10.1126/science.aaa1348 · Cited by 7,802 · see citing works
A general framework for estimating the relative pathogenicity of human genetic variants
Kircher, M., Witten, D. M., Jain, P., O'Roak, B. J., Cooper, G. M., & Shendure, J. (2014) · Nature Genetics · doi:10.1038/ng.2892 · Cited by 6,183 · see citing works
Genetic studies of body mass index yield new insights for obesity biology
Study, T. L. C., Locke, A. E., The ADIPOGen Consortium, The AGEN-BMI Working Group, The CARDIOGRAMplusC4D Consortium, The CKDGen Consortium, The, G. L. G. C., The, I. C. B. P., The MAGIC Investigators, The MuTHER Consortium, et al. (2015) · Nature · doi:10.1038/nature14177 · Cited by 4,534 · see citing works
Predicting Functional Effect of Human Missense Mutations Using PolyPhen‐2
Adzhubei, I., Jordan, D. M., & Sunyaev, S. R. (2013) · Current Protocols in Human Genetics · doi:10.1002/0471142905.hg0720s76 · Cited by 3,705 · see citing works
Self-citationCADD: predicting the deleteriousness of variants throughout the human genome
Rentzsch, P., Witten, D., Cooper, G. M., Shendure, J., & Kircher, M. (2019) · Nucleic Acids Research · doi:10.1093/nar/gky1016 · Cited by 3,534 · see citing works
<i>TREM2</i> Variants in Alzheimer's Disease
Guerreiro, R., Wojtas, A., Bras, J., Carrasquillo, M., Rogaeva, E., Majounie, E., Cruchaga, C., Sassi, C., Kauwe, J. S. K., Younkin, S., et al. (2013) · New England Journal of Medicine · doi:10.1056/nejmoa1211851 · Cited by 3,020 · see citing works
MutationTaster evaluates disease-causing potential of sequence alterations
Schwarz, J. M., Rödelsperger, C., Schuelke, M., & Seelow, D. (2010) · Nature Methods · doi:10.1038/nmeth0810-575 · Cited by 2,975 · see citing works
Alzheimer Disease Genetics Consortium (ADGC), Kunkle, B. W., The European Alzheimer’s Disease Initiative (EADI), Cohorts for Heart and Aging Research in Genomic Epidemiology Consortium (CHARGE), Genetic and Environmental Risk in AD/Defining Genetic, P. A. E. R. F. A. D. C. (., Grenier-Boley, B., Sims, R., Bis, J. C., Damotte, V., Naj, A. C., et al. (2019) · Nature Genetics · doi:10.1038/s41588-019-0358-2 · Cited by 2,946 · see citing works
REVEL: An Ensemble Method for Predicting the Pathogenicity of Rare Missense Variants
Ioannidis, N. M., Rothstein, J. H., Pejaver, V., Middha, S., McDonnell, S. K., Baheti, S., Musolf, A., Li, Q., Holzinger, E., Karyadi, D., et al. (2016) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2016.08.016 · Cited by 2,908 · see citing works
Predicting the Functional Effect of Amino Acid Substitutions and Indels
Choi, Y., Sims, G. E., Murphy, S., Miller, J. R., & Chan, A. P. (2012) · PLoS ONE · doi:10.1371/journal.pone.0046688 · Cited by 2,890 · see citing works
Synaptic, transcriptional and chromatin genes disrupted in autism
Study, T. D., De Rubeis, S., Autism, H. M. C. F., UK10K Consortium, The Autism Sequencing Consortium, He, X., Goldberg, A. P., Poultney, C. S., Samocha, K., Ercument Cicek, A., et al. (2014) · Nature · doi:10.1038/nature13772 · Cited by 2,746 · see citing works
Annotation of functional variation in personal genomes using RegulomeDB
Boyle, A. P., Hong, E. L., Hariharan, M., Cheng, Y., Schaub, M. A., Kasowski, M., Karczewski, K. J., Park, J., Hitz, B. C., Weng, S., et al. (2012) · Genome Research · doi:10.1101/gr.137323.112 · Cited by 2,722 · see citing works
A landscape of driver mutations in melanoma
Hodis, E., Watson, I. R., Kryukov, G. V., Arold, S. T., Imielinski, M., Theurillat, J.-P., Nickerson, E., Auclair, D., Li, L., Place, C., et al. (2012) · Cell · doi:10.1016/j.cell.2012.06.024 · Cited by 2,610 · see citing works
Zerbino, D. R., Achuthan, P., Akanni, W., Amode, M. R., Barrell, D., Bhai, J., Billis, K., Cummins, C., Gall, A., Girón, C. G., et al. (2018) · Nucleic Acids Research · doi:10.1093/nar/gkx1098 · Cited by 2,605 · see citing works
PROVEAN web server: a tool to predict the functional effect of amino acid substitutions and indels
Choi, Y., & Chan, A. P.-Y. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv195 · Cited by 2,560 · see citing works
The Mutational Landscape of Head and Neck Squamous Cell Carcinoma
Stransky, N., Egloff, A. M., Tward, A. D., Kostic, A. D., Cibulskis, K., Sivachenko, A., Kryukov, G. V., Lawrence, M. S., Sougnez, C. L., McKenna, A., et al. (2011) · Science · doi:10.1126/science.1208130 · Cited by 2,500 · see citing works
SIFT web server: predicting effects of amino acid substitutions on proteins
Sim, N.-L., Kumar, P. N., Hu, J., Henikoff, S., Schneider, G., & Ng, P. C. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks539 · Cited by 2,419 · see citing works
Satterstrom, F. K., Kosmicki, J. A., Wang, J., Breen, M. S., De Rubeis, S., An, J.-Y., Peng, M., Collins, R., Grove, J., Klei, L., et al. (2020) · Cell · doi:10.1016/j.cell.2019.12.036 · Cited by 2,321 · see citing works
Ward, L. D., & Kellis, M. (2012) · Nucleic Acids Research · doi:10.1093/nar/gkr917 · Cited by 2,229 · see citing works
De novo mutations revealed by whole-exome sequencing are strongly associated with autism
Sanders, S. J., Murtha, M. T., Gupta, A. R., Murdoch, J. D., Raubeson, M. J., Willsey, A. J., Ercan-Sencicek, A. G., DiLullo, N. M., Parikshak, N. N., Stein, J. L., et al. (2012) · Nature · doi:10.1038/nature10945 · Cited by 2,084 · see citing works
Initiative, T. A. D. N., Hollingworth, P., CHARGE consortium, EADI1 consortium, Harold, D., Sims, R., Gerrish, A., Lambert, J.-C., Carrasquillo, M. M., Abraham, R., et al. (2011) · Nature Genetics · doi:10.1038/ng.803 · Cited by 1,997 · see citing works
A high-coverage genome sequence from an archaic denisovan individual
Meyer, M., Kircher, M., Gansauge, M.-T., Li, H., Racimo, F., Mallick, S., Schraiber, J. G., Jay, F., Prüfer, K., de Filippo, C., et al. (2012) · Science · doi:10.1126/science.1224344 · Cited by 1,967 · see citing works
Schulze, K., Imbeaud, S., Letouzé, E., Alexandrov, L. B., Calderaro, J., Rebouissou, S., Couchy, G., Meiller, C., Shinde, J., Soysouvanh, F., et al. (2015) · Nature Genetics · doi:10.1038/ng.3252 · Cited by 1,803 · see citing works
Mapping the Hallmarks of Lung Adenocarcinoma with Massively Parallel Sequencing
Imielinski, M., Berger, A. H., Hammerman, P. S., Hernandez, B., Pugh, T. J., Hodis, E., Cho, J., Suh, J., Capelletti, M., Sivachenko, A., et al. (2012) · Cell · doi:10.1016/j.cell.2012.08.029 · Cited by 1,789 · see citing works
Patterns and rates of exonic de novo mutations in autism spectrum disorders
Neale, B. M., Kou, Y., Liu, L., Ma’ayan, A., Samocha, K. E., Sabo, A., Lin, C.-F., Stevens, C., Wang, L.-S., Makarov, V., et al. (2012) · Nature · doi:10.1038/nature11011 · Cited by 1,734 · see citing works
Self-citationExome sequencing as a tool for Mendelian disease gene discovery
Bamshad, M. J., Ng, S. B. H., Bigham, A. W., Tabor, H. K., Emond, M. J., Nickerson, D. A., & Shendure, J. (2011) · Nature Reviews Genetics · doi:10.1038/nrg3031 · Cited by 1,659 · see citing works
Evolution and functional impact of rare coding variation from deep sequencing of human exomes
Tennessen, J. A., Bigham, A. W., O’Connor, T. D., Fu, W., Kenny, E. E., Gravel, S., McGee, S., Do, R., Liu, X., Jun, G., et al. (2012) · Science · doi:10.1126/science.1219240 · Cited by 1,613 · see citing works
Self-citationSIFT missense predictions for genomes
Vaser, R., Adusumalli, S., Leng, S. N., Sikic, M., & Ng, P. C. (2016) · Nature Protocols · doi:10.1038/nprot.2015.123 · Cited by 1,510 · see citing works
Guichard, C., Amaddeo, G., Imbeaud, S., Ladeiro, Y., Pelletier, L., Benmaad, I., Caldéraro, J., Bioulac‐Sage, P., Letexier, M., Degos, F., et al. (2012) · Nature Genetics · doi:10.1038/ng.2256 · Cited by 1,451 · see citing works
Association analysis identifies 65 new breast cancer risk loci
Michailidou, K., Lindström, S., Dennis, J., Beesley, J., Hui, S., Kar, S., Lemaçon, A., Soucy, P., Glubb, D. M., Rostamianfar, A., et al. (2017) · Nature · doi:10.1038/nature24284 · Cited by 1,380 · see citing works
Davoli, T., Uno, H., Wooten, E. C., & Elledge, S. J. (2017) · Science · doi:10.1126/science.aaf8399 · Cited by 1,325 · see citing works
Shihab, H. A., Gough, J., Cooper, D. N., Stenson, P. D., Barker, G., Edwards, K. J., Day, I. N. M., & Gaunt, T. R. (2012) · Human Mutation · doi:10.1002/humu.22225 · Cited by 1,319 · see citing works
Guidelines for investigating causality of sequence variants in human disease
MacArthur, D. G., Manolio, T. A., Dimmock, D. P., Rehm, H. L., Shendure, J., Abecasis, G. R., Adams, D. R., Altman, R. B., Antonarakis, S. E., Ashley, E. A., et al. (2014) · Nature · doi:10.1038/nature13127 · Cited by 1,224 · see citing works
Self-citationPersonal omics profiling reveals dynamic molecular and medical phenotypes
Chen, R., Mias, G. I., Li-Pook-Than, J., Jiang, L., Lam, H. Y. K., Chen, R., Miriami, E., Karczewski, K. J., Hariharan, M., Dewey, F. E., et al. (2012) · Cell · doi:10.1016/j.cell.2012.02.009 · Cited by 1,291 · see citing works
The human splicing code reveals new insights into the genetic determinants of disease
Xiong, H. Y., Alipanahi, B., Lee, L. J., Bretschneider, H., Merico, D., Yuen, R. K. C., Hua, Y., Gueroussov, S., Najafabadi, H. S., Hughes, T., et al. (2014) · Science · doi:10.1126/science.1254806 · Cited by 1,225 · see citing works
Exome sequencing in sporadic autism spectrum disorders identifies severe de novo mutations
O'Roak, B. J., Deriziotis, P., Lee, C., Vives, L., Schwartz, J. J., Girirajan, S., Karakoc, E., MacKenzie, A. P., Ng, S. B., Baker, C., et al. (2011) · Nature Genetics · doi:10.1038/ng.835 · Cited by 1,203 · see citing works
The genetic landscape of high-risk neuroblastoma
Pugh, T. J., Morozova, O., Attiyeh, E. F., Asgharzadeh, S., Wei, J. S., Auclair, D., Carter, S. L., Cibulskis, K., Hanna, M., Kieżun, A., et al. (2013) · Nature Genetics · doi:10.1038/ng.2529 · Cited by 1,170 · see citing works
Yates, A. D., Achuthan, P., Akanni, W. A., Allen, J., Allen, J., Álvarez-Jarreta, J., Amode, M. R., Armean, I. M., Azov, A. G., Bennett, R., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz966 · Cited by 1,162 · see citing works
Dong, C., Wei, P., Jian, X., Gibbs, R. A., Boerwinkle, E., Wang, K., & Liu, X. (2014) · Human Molecular Genetics · doi:10.1093/hmg/ddu733 · Cited by 1,106 · see citing works
Chemoresistance Evolution in Triple-Negative Breast Cancer Delineated by Single-Cell Sequencing
Kim, C. R., Gao, R., Sei, E., Brandt, R., Hartman, J., Hatschek, T., Crosetto, N., Foukakis, T., & Navin, N. E. (2018) · Cell · doi:10.1016/j.cell.2018.03.041 · Cited by 1,091 · see citing works
Advances in understanding cancer genomes through second-generation sequencing
Meyerson, M. M., Gabriel, S., & Getz, G. A. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2841 · Cited by 1,114 · see citing works
Pleiotropy in complex traits: challenges and strategies
Solovieff, N., Cotsapas, C., Lee, P. H., Purcell, S. M., & Smoller, J. W. (2013) · Nature Reviews Genetics · doi:10.1038/nrg3461 · Cited by 1,085 · see citing works
Lee, S., Emond, M. J., Bamshad, M. J., Barnes, K. C., Rieder, M. J., Nickerson, D. A., Christiani, D. C., Wurfel, M. M., & Lin, X. (2012) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2012.06.007 · Cited by 1,040 · see citing works
mCSM: Predicting the effects of mutations in proteins using graph-based signatures
Pires, D. E. V., Ascher, D. B., & Blundell, T. L. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btt691 · Cited by 1,066 · see citing works
InterVar: Clinical Interpretation of Genetic Variants by the 2015 ACMG-AMP Guidelines
Li, Q., & Wang, K. (2017) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2017.01.004 · Cited by 1,035 · see citing works
Rare-Variant Association Analysis: Study Designs and Statistical Tests
Lee, S., Abecasis, G. R., Boehnke, M., & Lin, X. (2014) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2014.06.009 · Cited by 1,042 · see citing works
Clonal evolution in breast cancer revealed by single nucleus genome sequencing
Wang, Y., Waters, J., Leung, M. L., Unruh, A., Roh, W., Shi, X., Chen, K., Scheet, P., Vattathil, S., Liang, H., et al. (2014) · Nature · doi:10.1038/nature13600 · Cited by 1,029 · see citing works
Liu, X., Wu, C., Li, C., & Boerwinkle, E. (2015) · Human Mutation · doi:10.1002/humu.22932 · Cited by 957 · see citing works
Acquired Resistance and Clonal Evolution in Melanoma during BRAF Inhibitor Therapy
Shi, H., Hugo, W., Kong, X., Hong, A., Koya, R. C., Moriceau, G., Chodon, T., Guo, R., Johnson, D. B., Dahlman, K. B., et al. (2014) · Cancer Discovery · doi:10.1158/2159-8290.cd-13-0642 · Cited by 982 · see citing works
Exome sequencing in amyotrophic lateral sclerosis identifies risk genes and pathways
Cirulli, E. T., Lasseigne, B. N., Petrovski, S., Sapp, P. C., Dion, P. A., Leblond, C. S., Couthouis, J., Lu, Y.-F., Wang, Q., Krueger, B. J., et al. (2015) · Science · doi:10.1126/science.aaa3650 · Cited by 966 · see citing works
Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants
Fu, W., O’Connor, T. D., Jun, G., Kang, H. M., Abecasis, G. R., Leal, S. M., Gabriel, S., Rieder, M. J., Altshuler, D., Shendure, J., et al. (2012) · Nature · doi:10.1038/nature11690 · Cited by 951 · see citing works
Predicting Secretory Proteins with SignalP
Nielsen, H. (2017) · Methods in molecular biology · doi:10.1007/978-1-4939-7015-5_6 · Cited by 932 · see citing works
Identification of seven loci affecting mean telomere length and their association with disease
CARDIoGRAM consortium, Codd, V., Nelson, C. P., Albrecht, E., Mangino, M., Deelen, J., Buxton, J. L., Hottenga, J. J., Fischer, K., Esko, T., et al. (2013) · Nature Genetics · doi:10.1038/ng.2528 · Cited by 933 · see citing works
Inferring the molecular and phenotypic impact of amino acid variants with MutPred2
Pejaver, V., Urresti, J., Lugo-Martinez, J., Pagel, K. A., Lin, G. N., Nam, H.-J., Mort, M., Cooper, D. N., Sebat, J., Iakoucheva, L. M., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-19669-x · Cited by 923 · see citing works
Genic Intolerance to Functional Variation and the Interpretation of Personal Genomes
Petrovski, S., Wang, Q., Heinzen, E. L., Allen, A. S., & Goldstein, D. B. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003709 · Cited by 901 · see citing works
A Mutation in VPS35, Encoding a Subunit of the Retromer Complex, Causes Late-Onset Parkinson Disease
Zimprich, A. A., Benet‐Pagès, A., Struhal, W., Graf, E., Eck, S. H., Offman, M. N., Haubenberger, D., Spielberger, S., Schulte, E. C., Lichtner, P., et al. (2011) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2011.06.008 · Cited by 885 · see citing works
Sequencing of neuroblastoma identifies chromothripsis and defects in neuritogenesis genes
Molenaar, J. J., Köster, J., Zwijnenburg, D. A., Sluis, P. V., Valentijn, L. J., van der Ploeg, I., Hamdi, M., van Nes, J., Westerman, B. A., van Arkel, J., et al. (2012) · Nature · doi:10.1038/nature10910 · Cited by 869 · see citing works
Flicek, P., Ahmed, I., Amode, M. R., Barrell, D. G., Beal, K. M., Brent, S., Carvalho‐Silva, D., Clapham, P., Coates, G. M. P., Fairley, S., et al. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1236 · Cited by 869 · see citing works
Rausch, T., Jones, D. T. W., Zapatka, M., Stütz, A. M., Zichner, T., Weischenfeldt, J., Jäger, N., Remke, M., Shih, D., Northcott, P. A., et al. (2012) · Cell · doi:10.1016/j.cell.2011.12.013 · Cited by 865 · see citing works
Genomic variant annotation and prioritization with ANNOVAR and wANNOVAR
Yang, H., & Wang, K. (2015) · Nature Protocols · doi:10.1038/nprot.2015.105 · Cited by 845 · see citing works
Cortés, A., Hadler, J. S., Robinson, P. C., Leo, P., Cremin, K., Pryce, K., Harris, J., Bradbury, L. A., Kenna, T., Yang, J., et al. (2013) · Nature Genetics · doi:10.1038/ng.2667 · Cited by 855 · see citing works
PredictSNP: Robust and Accurate Consensus Classifier for Prediction of Disease-Related Mutations
Bendl, J. M., Štourač, J., Šalanda, O., Pavelka, A., Wieben, E. D., Zendulka, J., Brezovský, J., & Damborský, J. (2014) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003440 · Cited by 850 · see citing works
Jagadeesh, K. A., Wenger, A. M., Berger, M. J., Guturu, H., Stenson, P. D., Cooper, D. N., Bernstein, J. A., & Bejerano, G. (2016) · Nature Genetics · doi:10.1038/ng.3703 · Cited by 831 · see citing works
Whole genome sequencing resource identifies 18 new candidate genes for autism spectrum disorder
C Yuen, R. K., Merico, D., Bookman, M., L Howe, J., Thiruvahindrapuram, B., Patel, R. V., Whitney, J., Deflaux, N., Bingham, J., Wang, Z., et al. (2017) · Nature Neuroscience · doi:10.1038/nn.4524 · Cited by 844 · see citing works
Whole-genome sequencing of 234 bulls facilitates mapping of monogenic and complex traits in cattle
Daetwyler, H. D., Capitan, A., Pausch, H., Stothard, P., van Binsbergen, R., Brøndum, R. F., Liao, X., Djari, A., Rodriguez, S. C., Grohs, C., et al. (2014) · Nature Genetics · doi:10.1038/ng.3034 · Cited by 838 · see citing works
Pathogenic Germline Variants in 10,389 Adult Cancers
Huang, K., Mashl, R. J., Wu, Y., Ritter, D., Wang, J., Oh, C., Paczkowska, M., Reynolds, S. M., Wyczalkowski, M. A., Oak, N., et al. (2018) · Cell · doi:10.1016/j.cell.2018.03.039 · Cited by 838 · see citing works
dbNSFP: A lightweight database of human nonsynonymous SNPs and their functional predictions
Liu, X., Jian, X., & Boerwinkle, E. (2011) · Human Mutation · doi:10.1002/humu.21517 · Cited by 816 · see citing works
Flicek, P., Amode, M. R., Barrell, D. G., Beal, K. M., Brent, S., Carvalho‐Silva, D., Clapham, P., Coates, G. M. P., Fairley, S., Fitzgerald, S. F., et al. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr991 · Cited by 818 · see citing works
Davoli, T., Xu, A. W., Mengwasser, K. E., Sack, L. M., Yoon, J. C., Park, P. J., & Elledge, S. J. (2013) · Cell · doi:10.1016/j.cell.2013.10.011 · Cited by 815 · see citing works
Yan, X., Xu, J., Gu, Z., Pan, C., Lü, G., Shen, Y., Shi, J., Zhu, Y., Tang, L., Zhang, X., et al. (2011) · Nature Genetics · doi:10.1038/ng.788 · Cited by 806 · see citing works
Exploiting the Mutanome for Tumor Vaccination
Castle, J. C., Kreiter, S., Diekmann, J., Löwer, M., van de Roemer, N., de Graaf, J., Selmi, A., Diken, M., Boegel, S., Paret, C., et al. (2012) · Cancer Research · doi:10.1158/0008-5472.can-11-3722 · Cited by 802 · see citing works
Stenson, P. D., Mort, M. E., Ball, E. V., Chapman, M., Evans, K., Azevedo, L., Hayden, M., Heywood, S., Millar, D. S., Phillips, A. D., et al. (2020) · Human Genetics · doi:10.1007/s00439-020-02199-3 · Cited by 793 · see citing works
Liu, L., Okada, S., Kong, X., Kreins, A. Y., Cypowyj, S., Abhyankar, A., Toubiana, J., Itan, Y., Audry, M., Nitschké, P., et al. (2011) · The Journal of Experimental Medicine · doi:10.1084/jem.20110958 · Cited by 799 · see citing works
Disease variant prediction with deep generative models of evolutionary data
Frazer, J., Notin, P., Dias, M., Gomez, A., Min, J. K., Brock, K., Gal, Y., & Marks, D. S. (2021) · Nature · doi:10.1038/s41586-021-04043-8 · Cited by 791 · see citing works
Seven new loci associated with age-related macular degeneration
The AMD Gene Consortium (2013) · Nature Genetics · doi:10.1038/ng.2578 · Cited by 788 · see citing works
The ExAC browser: displaying reference data information from over 60 000 exomes
Karczewski, K. J., Weisburd, B., Thomas, B., Solomonson, M., Ruderfer, D. M., Kavanagh, D., Hamamsy, T., Lek, M., Samocha, K. E., Cummings, B. B., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw971 · Cited by 767 · see citing works
Mutation effects predicted from sequence co-variation
Hopf, T. A., Ingraham, J. B., Poelwijk, F. J., Schärfe, C. P. I., Springer, M., Sander, C., & Marks, D. S. (2017) · Nature Biotechnology · doi:10.1038/nbt.3769 · Cited by 775 · see citing works
Multi-ethnic genome-wide association study for atrial fibrillation
Roselli, C., Chaffin, M. D., Weng, L.-C. C., Aeschbacher, S., Ahlberg, G., Albert, C. M., Almgren, P., Alonso, Á., Anderson, C. D., Aragam, K. G., et al. (2018) · Nature Genetics · doi:10.1038/s41588-018-0133-9 · Cited by 754 · see citing works
González-Pérez, A., & López-Bigas, N. (2011) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2011.03.004 · Cited by 765 · see citing works
The BioMart community portal: an innovative alternative to large, centralized data repositories
Smedley, D., Haider, S., Durinck, S., Pandini, L., Provero, P., Allen, J., Arnaiz, O., Awedh, M. H., Baldock, R., Barbiera, G., et al. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv350 · Cited by 755 · see citing works
Pooled Association Tests for Rare Variants in Exon-Resequencing Studies
Price, A. L., Kryukov, G. V., de Bakker, P. I. W., Purcell, S. M., Staples, J., Wei, L.-J., & Sunyaev, S. R. (2010) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2010.04.005 · Cited by 755 · see citing works
Self-citationThe International IBD Genetics Consortium (IIBDGC), Ellinghaus, D., International Genetics of Ankylosing Spondylitis Consortium (IGAS), International PSC Study Group (IPSCSG), Genetic Analysis of Psoriasis Consortium (GAPC), Psoriasis Association Genetics Extension (PAGE), Jostins, L., Spain, S. L., Cortes, A., Bethune, J., et al. (2016) · Nature Genetics · doi:10.1038/ng.3528 · Cited by 751 · see citing works
Wright, C., Fitzgerald, T. W., Jones, W., Clayton, S., McRae, J., van Kogelenberg, M., King, D. A., Ambridge, K., Barrett, D. M., Bayzetinova, T., et al. (2015) · The Lancet · doi:10.1016/s0140-6736(14)61705-0 · Cited by 1,794 · see citing works
Dulak, A. M., Stojanov, P., Peng, S., Lawrence, M. S., Fox, C., Stewart, C., Bandla, S., Imamura, Y., Schumacher, S. E., Shefler, E., et al. (2013) · Nature Genetics · doi:10.1038/ng.2591 · Cited by 736 · see citing works
Bouaoun, L., Sonkin, D., Ardin, M., Hollstein, M., Byrnes, G., Zavadil, J., & Olivier, M. (2016) · Human Mutation · doi:10.1002/humu.23035 · Cited by 730 · see citing works
Linking disease associations with regulatory information in the human genomePreprint
Schaub, M. A., Boyle, A. P., Kundaje, A. B., Batzoglou, S., & Snyder, M. P. (2012) · Genome Research · doi:10.1101/gr.136127.111 · Cited by 715 · see citing works
Validating therapeutic targets through human genetics
Plenge, R. M., Scolnick, E. M., & Altshuler, D. (2013) · Nature Reviews Drug Discovery · doi:10.1038/nrd4051 · Cited by 712 · see citing works
GATA2 deficiency: a protean disorder of hematopoiesis, lymphatics, and immunity
Spinner, M. A., Sanchez, L. A., Hsu, A. P., Shaw, P. A., Zerbe, C. S., Calvo, K. R., Arthur, D. C., Gu, W., Gould, C. M., Brewer, C. C., et al. (2013) · Blood · doi:10.1182/blood-2013-07-515528 · Cited by 712 · see citing works
Rodrigues, C. H. M., Pires, D. E. V., & Ascher, D. B. (2020) · Protein Science · doi:10.1002/pro.3942 · Cited by 687 · see citing works
MuSiC: Identifying mutational significance in cancer genomesPreprint
Dees, N. D., Zhang, Q., Kandoth, C., Wendl, M. C., Schierding, W. S., Koboldt, D. C., Mooney, T. B., Callaway, M. B., Dooling, D. J., Mardis, E. R., et al. (2012) · Genome Research · doi:10.1101/gr.134635.111 · Cited by 669 · see citing works
Liu, X., Li, C., Mou, C., Dong, Y., & Tu, Y.-C. (2020) · Genome Medicine · doi:10.1186/s13073-020-00803-9 · Cited by 652 · see citing works
Sex-dependent dominance at a single locus maintains variation in age at maturity in salmon
Barson, N. J., Aykanat, T., Hindar, K., Baranski, M., Bolstad, G. H., Fiske, P., Jacq, C., Jensen, A. J., Johnston, S. E., Karlsson, S., et al. (2015) · Nature · doi:10.1038/nature16062 · Cited by 627 · see citing works
Strong signatures of selection in the domestic pig genome
Rubin, C.-J., Megens, H.-J., Barrio, A. M., Maqbool, K., Sayyab, S., Schwochow, D., Wang, C., Carlborg, Ö., Jern, P., Jørgensen, C. B., et al. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1217149109 · Cited by 652 · see citing works
Shi, H., Moriceau, G., Kong, X., Lee, M., Lee, H., Koya, R. C., Ng, C., Chodon, T., Scolyer, R. A., Dahlman, K. B., et al. (2012) · Nature Communications · doi:10.1038/ncomms1727 · Cited by 637 · see citing works
Searching for missing heritability: Designing rare variant association studies
Zuk, O., Schaffner, S. F., Samocha, K., Do, R., Hechter, E., Kathiresan, S., Daly, M. J., Neale, B. M., Sunyaev, S. R., & Lander, E. S. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1322563111 · Cited by 635 · see citing works
Self-citationLanguage models enable zero-shot prediction of the effects of mutations on protein function
Meier, J., Rao, R., Verkuil, R., Liu, J., Sercu, T., & Rives, A. (2021) · doi:10.1101/2021.07.09.450648 · Cited by 635 · see citing works
Hsu, A. P., Sampaio, E. P., Khan, J. I., Calvo, K. R., Lemieux, J. E., Patel, S. Y., Frucht, D. M., Vinh, D. C., Auth, R., Freeman, A. F., et al. (2011) · Blood · doi:10.1182/blood-2011-05-356352 · Cited by 635 · see citing works
- Authors
- Adzhubei, I. A., Schmidt, S., Peshkin, L., Ramensky, V. E., Gerasimova, A., Bork, P., Kondrashov, A. S., & Sunyaev, S. R.
- Affiliations
- Brigham and Women's Hospital (US)
- Max Planck Institute for Developmental Biology (DE)
- Harvard University (US)
- Engelhardt Institute of Molecular Biology (RU)
- University of Michigan (US)
- Corresponding author
- Sunyaev, Shamil R
- ORCID
- Venue
- Nature Methods
- Published
- 2010-04
- Volume
- 7
- Issue
- 4
- Pages
- 248-249
- ISSN
- 1548-7091 (ISSN-L)
- 1548-7105
- PMC
- PMC2855889
- OpenAlex
- W2059145105
- Cited by
- 13,194
- References
- 7
- Citations by year
- 2026: 407 · 2025: 634 · 2024: 749 · 2023: 748 · 2022: 884 · 2021: 1046 · 2020: 978 · 2019: 1041 · 2018: 959 · 2017: 979 · 2016: 1030 · 2015: 1037 · 2014: 979 · 2013: 832 · 2012: 565
- FWCI
- 307.36
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Methods (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Institute of Mental Health (R01MH084676)
- National Institute of General Medical Sciences (R01GM078598)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer Genomics and Diagnostics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Keywords
- mutation prediction, protein structure, protein stability, protein-ligand binding, protein-protein interaction, protein solubility, protein localization, protein phosphorylation, ubiquitination, protein degradation, protein dimerization, protein aggregation, protein conformational change
- MeSH terms
- Data Interpretation, Statistical, Humans, Models, Genetic, Software, Genetic Variation, Mutation, Missense
About these checks
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