Genetic variants and phenotypic data curated for the CAGI6 intellectual disability panel challenge

Amberger JS, Bocchini CA, Scott AF, Hamosh A (2019) OMIM.org: Leveraging knowledge across phenotype–gene relationships. Nucleic Acids Res 47(D1):D1038–D1043. https://doi.org/10.1093/nar/gky1151

Article  CAS  PubMed  Google Scholar 

Aspromonte MC, Bellini M, Gasparini A, Carraro M, Bettella E, Polli R, Cesca F, Bigoni S, Boni S, Carlet O, Negrin S, Mammi I, Milani D, Peron A, Sartori S, Toldo I, Soli F, Turolla L, Stanzial F, Leonardi E (2019) Characterization of intellectual disability and autism comorbidity through gene panel sequencing. Hum Mutat 40(9):1346–1363. https://doi.org/10.1002/humu.23822

Article  CAS  PubMed  PubMed Central  Google Scholar 

Aspromonte MC, Del Conte A, Zhu S, Tan W, Shen Y, Zhang Y, Li Q, Wang MH, Babbi G, Bovo S, Martelli PL, Casadio R, Althagafi A, Toonsi S, Kulmanov M, Hoehndorf R, Katsonis P, Williams A, Lichtarge O, Leonardi E (2025) CAGI6 ID panel challenge: Assessment of phenotype and variant predictions in 415 children with neurodevelopmental disorders (NDDs). Human Genet. https://doi.org/10.1007/s00439-024-02722-w

Article  Google Scholar 

Aspromonte, M. C., Nugnes, M. V., Quaglia, F., Bouharoua, A., DisProt Consortium, Tosatto, S. C. E., & Piovesan, D (2023) DisProt in 2024: Improving function annotation of intrinsically disordered proteins. Nucleic Acids Res 52(1):D434–D441. https://doi.org/10.1093/nar/gkad928

Article  CAS  Google Scholar 

Barbosa S, Greville-Heygate S, Bonnet M, Godwin A, Fagotto-Kaufmann C, Kajava AV, Laouteouet D, Mawby R, Wai HA, Dingemans AJM, Hehir-Kwa J, Willems M, Capri Y, Mehta SG, Cox H, Goudie D, Vansenne F, Turnpenny P, Vincent M, Baralle D (2020) Opposite Modulation of RAC1 by Mutations in TRIO Is Associated with Distinct, Domain-Specific Neurodevelopmental Disorders. The Am J Human Genet 106(3):338–355. https://doi.org/10.1016/j.ajhg.2020.01.018

Article  CAS  Google Scholar 

Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (2000) The Protein Data Bank. Nucleic Acids Res 28(1):235–242. https://doi.org/10.1093/nar/28.1.235

Article  CAS  PubMed  PubMed Central  Google Scholar 

Burley SK, Bhikadiya C, Bi C, Bittrich S, Chao H, Chen L, Craig PA, Crichlow GV, Dalenberg K, Duarte JM, Dutta S, Fayazi M, Feng Z, Flatt JW, Ganesan S, Ghosh S, Goodsell DS, Green RK, Guranovic V, Zardecki C (2023) RCSB Protein Data Bank (RCSB.org): Delivery of experimentally-determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning. Nucleic Acids Res 51(D1):D488–D508

Article  CAS  PubMed  Google Scholar 

Carraro M, Monzon AM, Chiricosta L, Reggiani F, Aspromonte MC, Bellini M, Pagel K, Jiang Y, Radivojac P, Kundu K, Pal LR, Yin Y, Limongelli I, Andreoletti G, Moult J, Wilson SJ, Katsonis P, Lichtarge O, Chen J, Leonardi E (2019) Assessment of patient clinical descriptions and pathogenic variants from gene panel sequences in the CAGI-5 intellectual disability challenge. Hum Mutat 40(9):1330–1345. https://doi.org/10.1002/humu.23823

Article  CAS  PubMed  PubMed Central  Google Scholar 

Chen J (2019) A fully-automated event-based variant prioritizing solution to the CAGI5 intellectual disability gene panel challenge. Hum Mutat 40(9):1364–1372. https://doi.org/10.1002/humu.23781

Article  PubMed  PubMed Central  Google Scholar 

Chen S, Francioli LC, Goodrich JK, Collins RL, Kanai M, Wang Q, Alföldi J, Watts NA, Vittal C, Gauthier LD, Poterba T, Wilson MW, Tarasova Y, Phu W, Yohannes MT, Koenig Z, Farjoun Y, Banks E, Donnelly S, Karczewski KJ (2022) A genome-wide mutational constraint map quantified from variation in 76,156 human genomes. Biorxiv. https://doi.org/10.1101/2022.03.20.485034

Article  PubMed  PubMed Central  Google Scholar 

Coe BP, Stessman HAF, Sulovari A, Geisheker MR, Bakken TE, Lake AM, Dougherty JD, Lein ES, Hormozdiari F, Bernier RA, Eichler EE (2019) Neurodevelopmental disease genes implicated by de novo mutation and copy number variation morbidity. Nature Genet 51(1):106–116. https://doi.org/10.1038/s41588-018-0288-4

Article  CAS  PubMed  Google Scholar 

Cousin MA, Veale EL, Dsouza NR, Tripathi S, Holden RG, Arelin M, Beek G, Bekheirnia MR, Beygo J, Bhambhani V, Bialer M, Bigoni S, Boelman C, Carmichael J, Courtin T, Cogne B, Dabaj I, Doummar D, Fazilleau L, Klee EW (2022) Gain and loss of TASK3 channel function and its regulation by novel variation cause KCNK9 imprinting syndrome. Genome Med 14(1):62. https://doi.org/10.1186/s13073-022-01064-4

Article  CAS  PubMed  PubMed Central  Google Scholar 

Critical Assessment of Genome Interpretation Consortium (2024) CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods. Genome Biol 25:53. https://doi.org/10.1186/s13059-023-03113-6

Article  Google Scholar 

Davydov EV, Goode DL, Sirota M, Cooper GM, Sidow A, Batzoglou S (2010) Identifying a high fraction of the human genome to be under selective constraint using GERP++. PLoS Computat Biol 6(12):e1001025

Article  Google Scholar 

de Boer E, Ockeloen CW, Kampen RA, Hampstead JE, Dingemans AJM, Rots D, Lütje L, Ashraf T, Baker R, Barat-Houari M, Angle B, Chatron N, Denommé-Pichon A-S, Devinsky O, Dubourg C, Elmslie F, Elloumi HZ, Faivre L, Fitzgerald-Butt S, Kleefstra T (2022) Missense variants in ANKRD11 cause KBG syndrome by impairment of stability or transcriptional activity of the encoded protein. Genet Med 24(10):2051–2064

Article  PubMed  Google Scholar 

Desmet F-O, Hamroun D, Lalande M, Collod-Béroud G, Claustres M, Béroud C (2009) Human Splicing Finder: An online bioinformatics tool to predict splicing signals. Nucleic Acids Res 37(9):e67–e67. https://doi.org/10.1093/nar/gkp215

Article  CAS  PubMed  PubMed Central  Google Scholar 

Feliciano, P., Zhou, X., Astrovskaya, I., Turner, T. N., Wang, T., Brueggeman, L., Barnard, R., Hsieh, A., Snyder, L. G., Muzny, D. M., Sabo, A., SPARK Consortium, Gibbs, R. A., Eichler, E. E., O’Roak, B. J., Michaelson, J. J., Volfovsky, N., Shen, Y., & Chung, W. K (2019) Exome sequencing of 457 autism families recruited online provides evidence for autism risk genes. NPJ Genom Med 4:19. https://doi.org/10.1038/s41525-019-0093-8

Article  CAS  PubMed  Google Scholar 

Fu JM, Satterstrom FK, Peng M, Brand H, Collins RL, Dong S, Wamsley B, Klei L, Wang L, Hao SP, Stevens CR, Cusick C, Babadi M, Banks E, Collins B, Dodge S, Gabriel SB, Gauthier L, Lee SK, Talkowski ME (2022) Rare coding variation provides insight into the genetic architecture and phenotypic context of autism. Nature Genet 54(9):1320–1331. https://doi.org/10.1038/s41588-022-01104-0

Article  CAS  PubMed  Google Scholar 

Gehin C, Lone MA, Lee W, Capolupo L, Ho S, Adeyemi AM, Gerkes EH, Stegmann APA, López-Martín E, Bermejo-Sánchez E, Martínez-Delgado B, Zweier C, Kraus C, Popp B, Strehlow V, Gräfe D, Knerr I, Jones ER, Zamuner S, Gennarino VA (2023) CERT1 mutations perturb human development by disrupting sphingolipid homeostasis. The J Clin Investigation. https://doi.org/10.1172/JCI165019

Article  Google Scholar 

Grove J, Ripke S, Als TD, Mattheisen M, Walters RK, Won H, Pallesen J, Agerbo E, Andreassen OA, Anney R, Awashti S, Belliveau R, Bettella F, Buxbaum JD, Bybjerg-Grauholm J, Bækvad-Hansen M, Cerrato F, Chambert K, Christensen JH, Børglum AD (2019) Identification of common genetic risk variants for autism spectrum disorder. Nature Genet 51(3):431–444. https://doi.org/10.1038/s41588-019-034

Article  CAS  PubMed  Google Scholar 

Huggenvik JI, Michelson RJ, Collard MW, Ziemba AJ, Gurley P, Mowen KA (1998) Characterization of a Nuclear Deformed Epidermal Autoregulatory Factor-1 (DEAF-1)-Related (NUDR) Transcriptional Regulator Protein. Mol Endocrinol 12(10):1619–1639. https://doi.org/10.1210/mend.12.10.0181

Article  CAS  PubMed  Google Scholar 

Iossifov I, O’Roak BJ, Sanders SJ, Ronemus M, Krumm N, Levy D, Stessman HA, Witherspoon KT, Vives L, Patterson KE, Smith JD, Paeper B, Nickerson DA, Dea J, Dong S, Gonzalez LE, Mandell JD, Mane SM, Murtha MT, Wigler M (2014) The contribution of de novo coding mutations to autism spectrum disorder. Nature 515(7526):216–221. https://doi.org/10.1038/nature13908

Article  CAS  PubMed  PubMed Central  Google Scholar 

Jensen M, Girirajan S (2017) Mapping a shared genetic basis for neurodevelopmental disorders. Genome Med 9(1):109. https://doi.org/10.1186/s13073-017-0503-4

Article  PubMed  PubMed Central  Google Scholar 

Jumper J, Evans R, Pritzel A, Green T, Figurnov M, Ronneberger O, Tunyasuvunakool K, Bates R, Žídek A, Potapenko A, Bridgland A, Meyer C, Kohl SAA, Ballard AJ, Cowie A, Romera-Paredes B, Nikolov S, Jain R, Adler J, Hassabis D (2021) Highly accurate protein structure prediction with AlphaFold. Nature 596(7873):583–589. https://doi.org/10.1038/s41586-021-03819-2

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kaplanis J, Samocha KE, Wiel L, Zhang Z, Arvai KJ, Eberhardt RY, Gallone G, Lelieveld SH, Martin HC, McRae JF, Short PJ, Torene RI, de Boer E, Danecek P, Gardner EJ, Huang N, Lord J, Martincorena I, Pfundt R, Retterer K (2020) Evidence for 28 genetic disorders discovered by combining healthcare and research data. Nature 586(7831):757–762. https://doi.org/10.1038/s41586-020-2832-5

Article  CAS  PubMed  PubMed Central  Google Scholar 

Karczewski KJ, Francioli LC, Tiao G, Cummings BB, Alföldi J, Wang Q, Collins RL, Laricchia KM, Ganna A, Birnbaum DP, Gauthier LD, Brand H, Solomonson

Comments (0)

No login
gif