Up to 80% of rare disease patients remain undiagnosed after genomic sequencing1, with many probably involving pathogenic variants in yet to be discovered disease-gene associations. To search for such associations, we developed a rare variant gene burden analytical framework for Mendelian diseases, and applied it to protein-coding variants from whole-genome sequencing of 34,851 cases and their family members recruited to the 100,000 Genomes Project2. A total of 141 new associations were identified, including five for which independent disease-gene evidence was recently published. Following in silico triaging and clinical expert review, 69 associations were prioritized, of which 30 could be linked to existing experimental evidence. The five associations with strongest overall genetic and experimental evidence were monogenic diabetes with the known β cell regulator3,4 UNC13A, schizophrenia with GPR17, epilepsy with RBFOX3, Charcot-Marie-Tooth disease with ARPC3 and anterior segment ocular abnormalities with POMK. Further confirmation of these and other associations could lead to numerous diagnoses, highlighting the clinical impact of large-scale statistical approaches to rare disease-gene association discovery.

Aligning Science Across Parkinson's Collaborative Research Network Chevy Chase MD USA

Berlin Institute of Health Charité Universitätsmedizin Berlin Berlin Germany

Biosciences Institute Newcastle University Newcastle upon Tyne UK

Bristol Medical School University of Bristol Bristol UK

Cardiology Department St George's University Hospitals NHS Foundation Trust London UK

Cardiology Section Cardiovascular and Genomics Research Institute School of Health and Medical Sciences City St George's University of London London UK

Centre for Cell Biology and Cutaneous Research Blizard Institute QMUL London UK

Centre for Endocrinology William Harvey Research Institute Queen Mary University of London London UK

Centre for Human Genetics University of Oxford Oxford UK

Clinical Pharmacology and Precision Medicine William Harvey Research Institute Queen Mary University of London London UK

Department of Clinical and Biomedical Science University of Exeter Medical School Exeter UK

Department of Clinical Neurosciences School of Clinical Medicine University of Cambridge Cambridge UK

Department of Dermatology and NIHR Biomedical Research Centre Royal Victoria Infirmary Newcastle upon Tyne UK

Department of Genetics UMC Utrecht Utrecht Netherlands

Department of Medical Genetics NIHR Cambridge Biomedical Research Centre University of Cambridge Cambridge UK

Department of Medicine Royal College of Surgeons in Ireland and Department of Nephrology Beaumont Hospital Dublin Republic of Ireland

Department of Neurodegenerative Disease UCL Queen Square Institute of Neurology University College London London UK

Department of Neuromuscular Diseases UCL Institute of Neurology London UK

Department of Oncology University of Oxford Oxford UK

Department of Ophthalmology 1st Faculty of Medicine Charles University and General University Hospital Prague Prague Czech Republic

Department of Paediatrics and Inherited Metabolic Disorders 1st Faculty of Medicine Charles University and General University Hospital Prague Prague Czech Republic

Department of Renal Medicine University College London London UK

Division of Evolution Infection and Genomics University of Manchester Manchester UK

Division of Genetics and Epidemiology Institute of Cancer Research London UK

Division of Genetics and Epidemiology The Institute of Cancer Research London UK

Genetics and Genomic Medicine UCL Great Ormond Street Institute of Child Health University College London London UK

Great North Children's Hospital Newcastle upon Tyne UK

Institute of Cardiovascular Science University College London London UK

Institute of Translational and Clinical Research Newcastle University Newcastle upon Tyne UK

Kidney Genetics Group Division of Clinical Medicine School of Medicine and Population Health University of Sheffield Sheffield UK

Manchester Centre for Genomic Medicine Manchester University NHS Foundation Trust Manchester UK

Mc Gill University Montreal Quebec Canada

Medical Research Council Mitochondrial Biology Unit Cambridge Biomedical Campus University of Cambridge Cambridge UK

MRC Laboratory of Medical Sciences Imperial College London London UK

National Heart and Lung Institute Imperial College London London UK

National Hospital for Neurology and Neurosurgery London UK

National Institute of Health Research Biomedical Research Centre at Moorfields Eye Hospital London UK

Newcastle University Translational and Clinical Research Institute Newcastle upon Tyne UK

NIHR Biomedical Research Centre Newcastle University Newcastle upon Tyne UK

NIHR GOSH Biomedical Research Centre Great Ormond Street Institute of Child Health London UK

Northern Genetics Centre The Newcastle upon Tyne NHS Foundation Trust Newcastle upon Tyne UK

Nuffield Department of Surgical Sciences University of Oxford Oxford UK

Oxford Centre for Genomic Medicine Oxford University Foundation Trust Oxford UK

Oxford NIHR Biomedical Research Centre Oxford UK

Paediatric Nephrology University Hospital and Catholic University Leuven Leuven Belgium

Pediatric Cardiology CHU Sainte Justine University of Montreal Montreal Quebec Canada

Renal Services The Newcastle upon Tyne NHS Foundation Trust Hospitals Newcastle upon Tyne UK

School of Cellular and Molecular Medicine University of Bristol Bristol UK

School of Pharmacy and Biomolecular Sciences Royal College of Surgeons in Ireland Dublin Republic of Ireland

Sheffield Kidney Institute Sheffield Teaching Hospitals NHS Foundation Trust Sheffield UK

The Jackson Laboratory for Genomic Medicine Farmington CT USA

UCL Ear Institute University College London London UK

UCL Genetics Institute University College London London UK

UCL Institute of Neurology London UK

UCL Institute of Ophthalmology University College London London UK

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medRxiv. 2023 Dec 21:2023.12.20.23300294. doi: 10.1101/2023.12.20.23300294. PubMed

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100,000 Genomes Project Pilot Investigators et al. 100,000 Genomes pilot on rare-disease diagnosis in health care—preliminary report. N. Engl. J. Med. 385, 1868–1880 (2021). DOI

Turnbull, C. et al. The 100 000 Genomes Project: bringing whole genome sequencing to the NHS. BMJ 361, k1687 (2018). PubMed DOI

Cataldo, L. R. et al. MAFA and MAFB regulate exocytosis-related genes in human β-cells. Acta Physiol. 234, e13761 (2022). DOI

Kang, L. et al. Munc13-1 is required for the sustained release of insulin from pancreatic beta cells. Cell Metab. 3, 463–468 (2006). PubMed DOI

Nguengang Wakap, S. et al. Estimating cumulative point prevalence of rare diseases: analysis of the Orphanet database. Eur. J. Hum. Genet. 28, 165–173 (2020). PubMed DOI

Amberger, J. S., Bocchini, C. A., Scott, A. F. & Hamosh, A. Omim.org: leveraging knowledge across phenotype-gene relationships. Nucleic Acids Res. 47, D1038–D1043 (2019). PubMed DOI

Xiao, S. et al. Functional filter for whole-genome sequencing data identifies HHT and stress-associated non-coding SMAD4 polyadenylation site variants >5 kb from coding DNA. Am. J. Hum. Genet. 110, 1903–1918 (2023). PubMed DOI PMC

Splinter, K. et al. Effect of genetic diagnosis on patients with previously undiagnosed disease. N. Engl. J. Med. 379, 2131–2139 (2018). PubMed DOI PMC

Baxter, S. M. et al. Centers for Mendelian Genomics: a decade of facilitating gene discovery. Genet. Med. 24, 784–797 (2022). PubMed DOI PMC

Wright, C. F. et al. Genetic diagnosis of developmental disorders in the DDD study: a scalable analysis of genome-wide research data. Lancet 385, 1305–1314 (2015). PubMed DOI PMC

Bone, W. P. et al. Computational evaluation of exome sequence data using human and model organism phenotypes improves diagnostic efficiency. Genet. Med. 18, 608–617 (2016). PubMed DOI

Farazi Fard, M. A. et al. Truncating mutations in UBAP1 cause hereditary spastic paraplegia. Am. J. Hum. Genet. 104, 767–773 (2019). PubMed DOI PMC

Wallmeier, J. et al. De novo mutations in FOXJ1 result in a motile ciliopathy with hydrocephalus and randomization of left/right body asymmetry. Am. J. Hum. Genet. 105, 1030–1039 (2019). PubMed DOI PMC

Cortese, A. et al. Biallelic mutations in SORD cause a common and potentially treatable hereditary neuropathy with implications for diabetes. Nat. Genet. 52, 473–481 (2020). PubMed DOI PMC

Havrilla, J. M., Pedersen, B. S., Layer, R. M. & Quinlan, A. R. A map of constrained coding regions in the human genome. Nat. Genet. 51, 88–95 (2019). PubMed DOI

Martin, A. R. et al. PanelApp crowdsources expert knowledge to establish consensus diagnostic gene panels. Nat. Genet. 51, 1560–1565 (2019). PubMed DOI

Guillen Sacoto, M. J. et al. De novo variants in the ATPase module of MORC2 cause a neurodevelopmental disorder with growth retardation and variable craniofacial dysmorphism. Am. J. Hum. Genet. 107, 352–363 (2020). PubMed DOI PMC

Tolchin, D. et al. De novo SOX6 variants cause a neurodevelopmental syndrome associated with ADHD, craniosynostosis, and osteochondromas. Am. J. Hum. Genet. 106, 830–845 (2020). PubMed DOI PMC

Marom, R. et al. COPB2 loss of function causes a coatopathy with osteoporosis and developmental delay. Am. J. Hum. Genet. 108, 1710–1724 (2021). PubMed DOI PMC

Senum, S. R. et al. Monoallelic IFT140 pathogenic variants are an important cause of the autosomal dominant polycystic kidney-spectrum phenotype. Am. J. Hum. Genet. 109, 136–156 (2022). PubMed DOI

Jackson, A. et al. Biallelic TUFT1 variants cause woolly hair, superficial skin fragility and desmosomal defects. Br. J. Dermatol. 188, 75–83 (2023). PubMed DOI

Karczewski, K. J. et al. The mutational constraint spectrum quantified from variation in 141,456 humans. Nature 581, 434–443 (2020). PubMed DOI PMC

Singer-Berk, M. et al. Advanced variant classification framework reduces the false positive rate of predicted loss-of-function variants in population sequencing data. Am. J. Hum. Genet. 110, 1496–1508 (2023). PubMed DOI PMC

Szklarczyk, D. et al. The STRING database in 2023: protein-protein association networks and functional enrichment analyses for any sequenced genome of interest. Nucleic Acids Res. 51, D638–D646 (2023). PubMed DOI

Rehm, H. L. et al. ClinGen—the clinical genome resource. N. Engl. J. Med. 372, 2235–2242 (2015). PubMed DOI PMC

Kwan, E. P. et al. Munc13-1 deficiency reduces insulin secretion and causes abnormal glucose tolerance. Diabetes 55, 1421–1429 (2006). PubMed DOI

Wang, H.-Y. et al. RBFOX3/NeuN is required for hippocampal circuit balance and function. Sci. Rep. 5, 17383 (2015). PubMed DOI PMC

Lal, D. et al. RBFOX1 and RBFOX3 mutations in rolandic epilepsy. PLoS ONE 8, e73323 (2013). PubMed DOI PMC

Huang, D.-F. et al. Neuronal splicing regulator RBFOX3 mediates seizures via regulating Vamp1 expression preferentially in NPY-expressing GABAergic neurons. Proc. Natl Acad. Sci. USA 119, e2203632119 (2022). PubMed DOI PMC

Muñoz-Lasso, D. C., Romá-Mateo, C., Pallardó, F. V. & Gonzalez-Cabo, P. Much more than a scaffold: cytoskeletal proteins in neurological disorders. Cells 9, 358 (2020). PubMed DOI PMC

Lippi, G. et al. Targeting of the Arpc3 actin nucleation factor by miR-29a/b regulates dendritic spine morphology. J. Cell Biol. 194, 889–904 (2011). PubMed DOI PMC

Zuchero, J. B. et al. CNS myelin wrapping is driven by actin disassembly. Dev. Cell 34, 152–167 (2015). PubMed DOI PMC

Reis, L. M. et al. Comprehensive phenotypic and functional analysis of dominant and recessive FOXE3 alleles in ocular developmental disorders. Hum. Mol. Genet. 30, 1591–1606 (2021). PubMed DOI PMC

Chen, Y. et al. Identification of novel molecular markers through transcriptomic analysis in human fetal and adult corneal endothelial cells. Hum. Mol. Genet. 22, 1271–1279 (2013). PubMed DOI

Bath, C. et al. Transcriptional dissection of human limbal niche compartments by massive parallel sequencing. PLoS ONE 8, e64244 (2013). PubMed DOI PMC

Di Costanzo, S. et al. POMK mutations disrupt muscle development leading to a spectrum of neuromuscular presentations. Hum. Mol. Genet. 23, 5781–5792 (2014). PubMed DOI PMC

Lu, C. et al. G-protein-coupled receptor Gpr17 regulates oligodendrocyte differentiation in response to lysolecithin-induced demyelination. Sci. Rep. 8, 4502 (2018). PubMed DOI PMC

Bean, L. J. H. et al. Diagnostic gene sequencing panels: from design to report-a technical standard of the American College of Medical Genetics and Genomics (ACMG). Genet. Med. 22, 453–461 (2020). PubMed DOI

DiStefano, M. T. et al. The Gene Curation Coalition: a global effort to harmonize gene-disease evidence resources. Genet. Med. 24, 1732–1742 (2022). PubMed DOI PMC

Nicolae, D. L. Association tests for rare variants. Annu. Rev. Genomics Hum. Genet. 17, 117–130 (2016). PubMed DOI

Mbatchou, J. et al. Computationally efficient whole-genome regression for quantitative and binary traits. Nat. Genet. 53, 1097–1103 (2021). PubMed DOI

Jiang, L. et al. A resource-efficient tool for mixed model association analysis of large-scale data. Nat. Genet. 51, 1749–1755 (2019). PubMed DOI

Loh, P.-R., Kichaev, G., Gazal, S., Schoech, A. P. & Price, A. L. Mixed-model association for biobank-scale datasets. Nat. Genet. 50, 906–908 (2018). PubMed DOI PMC

Zhou, W. et al. Efficiently controlling for case-control imbalance and sample relatedness in large-scale genetic association studies. Nat. Genet. 50, 1335–1341 (2018). PubMed DOI PMC

Kuonen, D. Miscellanea. Saddlepoint approximations for distributions of quadratic forms in normal variables. Biometrika 86, 929–935 (1999). DOI

Firth, D. Bias reduction of maximum likelihood estimates. Biometrika 80, 27 (1993). DOI

Greene, D., NIHR BioResource, Richardson, S. & Turro, E. A fast association test for identifying pathogenic variants involved in rare diseases. Am. J. Hum. Genet. 101, 104–114 (2017). PubMed DOI PMC

Greene, D. et al. Genetic association analysis of 77,539 genomes reveals rare disease etiologies. Nat. Med. 29, 679–688 (2023). PubMed DOI PMC

Köhler, S. et al. The Human Phenotype Ontology in 2021. Nucleic Acids Res. 49, D1207–D1217 (2021). PubMed DOI

Rimmer, A. et al. Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications. Nat. Genet. 46, 912–918 (2014). PubMed DOI PMC

Morgenthaler, S. & Thilly, W. G. A strategy to discover genes that carry multi-allelic or mono-allelic risk for common diseases: a cohort allelic sums test (CAST). Mutat. Res. 615, 28–56 (2007). PubMed DOI

Benjamini, Y. & Hochberg, Y. On the adaptive control of the false discovery rate in multiple testing with independent statistics. J. Educ. Behav. Stat. 25, 60 (2000). DOI

Uhlén, M. et al. Proteomics. Tissue-based map of the human proteome. Science 347, 1260419 (2015). PubMed DOI

Zhang, W., Wang, C. & Zhang, X. Mutplot: an easy-to-use online tool for plotting complex mutation data with flexibility. PLoS ONE 14, e0215838 (2019). PubMed DOI PMC

Smedley, D. et al. PhenoDigm: analyzing curated annotations to associate animal models with human diseases. Database 2013, bat025 (2013). PubMed DOI PMC

García-Ruiz, S. et al. CoExp: a web tool for the exploitation of co-expression networks. Front. Genet. 12, 630187 (2021). PubMed DOI PMC

Li, D. et al. Endogenous plasma resuspension of peripheral blood mononuclear cells prevents preparative-associated stress that modifies polyA-enriched RNA responses to subsequent acute stressors. Cell Stress 11, 112–124 (2024).

Elhassan, E. A. E. et al. The utility of a genetic kidney disease clinic employing a broad range of genomic testing platforms: experience of the Irish Kidney Gene Project. J. Nephrol. 35, 1655–1665 (2022). PubMed DOI PMC

Cipriani, V., Vestito, L. & Smedley, D. whri-phenogenomics/geneBurdenRD: zenodo-v3 (zenodo-v3. Zenodo https://doi.org/10.5281/zenodo.14500039 (2024).