A general framework for estimating the relative pathogenicity of human genetic variants

Kircher, Martin, Witten, Daniela M, Jain, Preti, O'Roak, Brian J, Cooper, Gregory M, Shendure, Jay·2014·Nature Genetics
DOI 10.1038/ng.2892

Cited by (152)

Items 101–152 of 152

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  2. Genetic Variants in SGLT1, Glucose Tolerance, and Cardiometabolic Risk
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  5. Network analysis reveals rare disease signatures across multiple levels of biological organization
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  6. GWAS4D: multidimensional analysis of context-specific regulatory variant for human complex diseases and traits
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  7. Desmoplakin variants are associated with idiopathic pulmonary fibrosis
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  8. De novo variants in SETD1B are associated with intellectual disability, epilepsy and autism
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  9. DeepPVP: phenotype-based prioritization of causative variants using deep learning
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  10. Predicting the pathogenicity of missense variants using features derived from AlphaFold2
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  11. De novo mutations from whole exome sequencing in neurodevelopmental and psychiatric disorders: From discovery to application
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  12. Whole-genome sequencing suggests a chemokine gene cluster that modifies age at onset in familial Alzheimer's disease
    Lalli, M A, Bettcher, B M, Arcila, M L, Garcia, G, Guzman, C, Madrigal, L, Ramirez, L, Acosta-Uribe, J, Baena, A, Wojta, K J et al. · 2015 · Molecular Psychiatry
  13. Deleterious ABCA7 mutations and transcript rescue mechanisms in early onset Alzheimer’s disease
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  14. Mutations in <i>HECW2</i> are associated with intellectual disability and epilepsy
    Halvardson, Jonatan, Zhao, Jin J, Zaghlool, Ammar, Wentzel, Christian, Georgii-Hemming, Patrik, Månsson, Else, Ederth Sävmarker, Helena, Brandberg, Göran, Soussi Zander, Cecilia, Thuresson, Ann-Charlotte et al. · 2016 · Journal of Medical Genetics
  15. TUBB1 mutations cause thyroid dysgenesis associated with abnormal platelet physiology
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  16. Individualized Iterative Phenotyping for Genome-wide Analysis of Loss-of-Function Mutations
    Johnston, Jennifer J., Lewis, Katie L., Ng, David, Singh, Larry N., Wynter, Jamila, Brewer, Carmen, Brooks, Brian P., Brownell, Isaac, Candotti, Fabio, Gonsalves, Steven G. et al. · 2015 · The American Journal of Human Genetics
  17. Genome-wide meta-analysis of macronutrient intake of 91,114 European ancestry participants from the cohorts for heart and aging research in genomic epidemiology consortium
    Merino, Jordi, Dashti, Hassan S., Li, Sherly X., Sarnowski, Chloé, Justice, Anne E., Graff, Misa, Papoutsakis, Constantina, Smith, Caren E., Dedoussis, George V., Lemaitre, Rozenn N. et al. · 2019 · Molecular Psychiatry
  18. Lysoplex: An efficient toolkit to detect DNA sequence variations in the autophagy-lysosomal pathway
    Di Fruscio, Giuseppina, Schulz, Angela, De Cegli, Rossella, Savarese, Marco, Mutarelli, Margherita, Parenti, Giancarlo, Banfi, Sandro, Braulke, Thomas, Nigro, Vincenzo, Ballabio, Andrea · 2015 · Autophagy
  19. Current perspectives in autism spectrum disorder: from genes to therapy
    Chahrour, Maria, O'Roak, Brian J., Santini, Emanuela, Samaco, Rodney C., Kleiman, Robin J., Manzini, M. Chiara · 2016 · The Journal of Neuroscience
  20. Phrank measures phenotype sets similarity to greatly improve Mendelian diagnostic disease prioritization
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  21. Genome-wide prediction of pathogenic gain- and loss-of-function variants from ensemble learning of a diverse feature set
    Stein, David, Kars, Meltem Ece, Wu, Yiming, Bayrak, Çiğdem Sevim, Stenson, Peter D., Cooper, David N., Schlessinger, Avner, Itan, Yuval · 2023 · Genome Medicine
  22. Adaptors for disorders of the brain? The cancer signaling proteins NEDD9, CASS4, and PTK2B in Alzheimer’s disease
    Beck, Tim N., Nicolas, Emmanuelle, Kopp, Meghan C., Golemis, Erica A. · 2014 · Oncoscience
  23. Neanderthal introgression reintroduced functional ancestral alleles lost in Eurasian populations
    Rinker, David C., Simonti, Corinne N., McArthur, Evonne, Shaw, Douglas, Hodges, Emily, Capra, John A. · 2020 · Nature Ecology &amp; Evolution
  24. Shared genetic architecture between irritable bowel syndrome and psychiatric disorders reveals molecular pathways of the gut-brain axis
    Tesfaye, Markos, Jaholkowski, Piotr, Hindley, Guy F. L., Shadrin, Alexey A., Rahman, Zillur, Bahrami, Shahram, Lin, Aihua, Holen, Børge, Parker, Nadine, Cheng, Weiqiu et al. · 2023 · Genome Medicine
  25. Integrating healthcare and research genetic data empowers the discovery of 28 novel developmental disorders
    Kaplanis, Joanna, Samocha, Kaitlin E., Wiel, Laurens, Zhang, Zhancheng, Arvai, Kevin J., Eberhardt, Ruth Y., Gallone, Giuseppe, Lelieveld, Stefan H., Martin, Hilary C., McRae, Jeremy F. et al. · 2019
  26. Single suture craniosynostosis: Identification of rare variants in genes associated with syndromic forms
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  27. IW-Scoring: an Integrative Weighted Scoring framework for annotating and prioritizing genetic variations in the noncoding genome
    Wang, Jun, Dayem Ullah, Abu Z, Chelala, Claude · 2018 · Nucleic Acids Research
  28. VIPdb, a genetic variant impact predictor database
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  29. Genome-wide Analysis of Insomnia (N=1,331,010) Identifies Novel Loci and Functional Pathways
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  31. Sequencing Analysis at 8p23 Identifies Multiple Rare Variants in DLC1 Associated with Sleep-Related Oxyhemoglobin Saturation Level
    Liang, Jingjing, Cade, Brian E., He, Karen Y., Wang, Heming, Lee, Jiwon, Sofer, Tamar, Williams, Stephanie, Li, Ruitong, Chen, Han, Gottlieb, Daniel J. et al. · 2019 · The American Journal of Human Genetics
  32. A test for ancient selective sweeps and an application to candidate sites in modern humans
    Racimo, Fernando, Kuhlwilm, Martin, Slatkin, Montgomery · 2014 · Molecular Biology and Evolution
  33. Deleterious Variation in BRSK2 Associates with a Neurodevelopmental Disorder
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  34. Defects in fatty acid amide hydrolase 2 in a male with neurologic and psychiatric symptoms
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  35. The evolutionary history of human spindle genes includes back-and-forth gene flow with Neandertals
    Peyrégne, Stéphane, Kelso, Janet, Peter, Benjamin M, Pääbo, Svante · 2022 · eLife
  36. A selection pressure landscape for 870 human polygenic traits
    Song, Weichen, Shi, Yueqi, Wang, Weidi, Pan, Weihao, Qian, Wei, Yu, Shunying, Zhao, Min, Lin, Guan Ning · 2021 · Nature Human Behaviour
  37. Personalised analytics for rare disease diagnostics
    Anderson, Denise, Baynam, Gareth, Blackwell, Jenefer M., Lassmann, Timo · 2019 · Nature Communications
  38. Contribution of rare whole-genome sequencing variants to plasma protein levels and the missing heritability
    Kierczak, Marcin, Rafati, Nima, Höglund, Julia, Gourlé, Hadrien, Lo Faro, Valeria, Schmitz, Daniel, Ek, Weronica E., Gyllensten, Ulf, Enroth, Stefan, Ekman, Diana et al. · 2022 · Nature Communications
  39. Genetic associations with age at dementia onset in the <i>PSEN1 E280A</i> Colombian kindred
    Cochran, Jesse Nicholas, Acosta‐Uribe, Juliana, Esposito, Bianca T., Madrigal, Lucia, Aguillón, David, Giraldo, Margarita M., Taylor, Jared W., Bradley, Joseph, Fulton‐Howard, Brian, Andrews, Shea J. et al. · 2023 · Alzheimer's &amp; Dementia
  40. A microglia clonal inflammatory disorder in Alzheimer’s disease
    Vicario, Rocio, Fragkogianni, Stamatina, Weber, Leslie, Lazarov, Tomi, Hu, Yang, Hayashi, Samantha Y, Craddock, Barbara, Socci, Nicholas D, Alberdi, Araitz, Baako, Ann et al. · 2025 · eLife
  41. A biallelic truncating <i>AEBP1</i> variant causes connective tissue disorder in two siblings
    Hebebrand, Moritz, Vasileiou, Georgia, Krumbiegel, Mandy, Kraus, Cornelia, Uebe, Steffen, Ekici, Arif B., Thiel, Christian T., Reis, André, Popp, Bernt · 2019 · American Journal of Medical Genetics Part A
  42. Resequencing and association analysis of coding regions at twenty candidate genes suggest a role for rare risk variation at AKAP9 and protective variation at NRXN1 in schizophrenia susceptibility
    Suárez-Rama, José Javier, Arrojo, Manuel, Sobrino, Beatriz, Amigo, Jorge, Brenlla, Julio, Agra, Santiago, Paz, Eduardo, Brión, María, Carracedo, Ángel, Páramo, Mario et al. · 2015 · Journal of Psychiatric Research
  43. Meta-analysis of ACE inhibitor-induced angioedema identifies novel risk locus.
    Mathey, Carina M., Maj, Carlo, Eriksson, Niclas, Krebs, Kristi, Westmeier, Julia, David, Friederike S., Koromina, Maria, Scheer, Annika B., Szabo, Nora, Wedi, Bettina et al. · 2024 · Journal of Allergy and Clinical Immunology
  44. PreMode predicts mode-of-action of missense variants by deep graph representation learning of protein sequence and structural context
    Zhong, Guojie, Zhao, Yige, Zhuang, Demi, Chung, Wendy K., Shen, Yufeng · 2025 · Nature Communications
  45. Using the Neandertal genome to study the evolution of small insertions and deletions in modern humans
    Chintalapati, Manjusha, Dannemann, Michael, Prüfer, Kay · 2017 · BMC Evolutionary Biology
  46. TM2D genes regulate Notch signaling and neuronal function in Drosophila
    Salazar, Jose L., Yang, Sheng-An, Lin, Yong Qi, Li-Kroeger, David, Marcogliese, Paul C., Deal, Samantha L., Neely, G. Gregory, Yamamoto, Shinya · 2021 · PLOS Genetics
  47. Genome-wide association study meta-analysis of the Alcohol Use Disorder Identification Test (AUDIT) in two population-based cohorts (N=141,932)
    Sanchez-Roige, Sandra, Palmer, Abraham A., Fontanillas, Pierre, Elson, Sarah L., The 23andMe Research Team, Substance Use Disorder Working Group of the Psychiatric Genomics Consortium, Adams, Mark J., Howard, David M., Edenberg, Howard J., Davies, Gail et al. · 2018
  48. Calibrating variant-scoring methods for clinical decision making
    Benevenuta, Silvia, Capriotti, Emidio, Fariselli, Piero · 2021 · Bioinformatics
  49. Evaluating pathogenicity of variants of unknown significance in APP, PSEN1, and PSEN2
    Marsh, Jacob A., Huang, Guangming, Bowling, Kevin, Renton, Alan E., Ziegemeier, Ellen, Ball, Torri, Pottier, Cyril, Cruchaga, Carlos, Day, Gregory S., Bateman, Randall J. et al. · 2025 · Neurotherapeutics
  50. Human genetic adaptation related to cellular zinc homeostasis
    Roca-Umbert, Ana, Garcia-Calleja, Jorge, Vogel-González, Marina, Fierro-Villegas, Alejandro, Ill-Raga, Gerard, Herrera-Fernández, Víctor, Bosnjak, Anja, Muntané, Gerard, Gutiérrez, Esteban, Campelo, Felix et al. · 2023 · PLoS Genetics
  51. Regional Adipose Distribution Reveals Differential Genetic Risk Patterns for Cardiometabolic Diseases
    Wu, Qian, Yang, Fan, An, Qi, Liu, Ying, Tian, Hexian, Du, Yamin, Cai, Wenjie, Lei, Minghuan, Xu, Jinglei, Deng, Linlin et al. · 2026 · Journal of the American Heart Association
  52. Whole‐Genome Sequencing and Single‐Cell Transcriptomics Identify Human Leukocyte Antigen Loci and a <i>COG5</i> Variant in Aortic Dissection
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