De novo variants in the RNU4-2 snRNA cause a frequent neurodevelopmental syndrome.

Autor:	Chen Y; Big Data Institute, University of Oxford, Oxford, UK.; Centre for Human Genetics, University of Oxford, Oxford, UK., Dawes R; Big Data Institute, University of Oxford, Oxford, UK.; Centre for Human Genetics, University of Oxford, Oxford, UK., Kim HC; Big Data Institute, University of Oxford, Oxford, UK.; Centre for Human Genetics, University of Oxford, Oxford, UK., Ljungdahl A; Institute of Developmental and Regenerative Medicine, Department of Paediatrics, University of Oxford, Oxford, UK.; Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA., Stenton SL; Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA., Walker S; Genomics England, London, UK., Lord J; Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, UK., Lemire G; Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA., Martin-Geary AC; Big Data Institute, University of Oxford, Oxford, UK.; Centre for Human Genetics, University of Oxford, Oxford, UK., Ganesh VS; Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.; Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA., Ma J; Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA., Ellingford JM; Genomics England, London, UK.; Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, UK.; Division of Evolution, Infection and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicines and Health, University of Manchester, Manchester, UK., Delage E; Human Genetics, Wellcome Sanger Institute, Hinxton, UK., D'Souza EN; Big Data Institute, University of Oxford, Oxford, UK.; Centre for Human Genetics, University of Oxford, Oxford, UK., Dong S; Institute of Developmental and Regenerative Medicine, Department of Paediatrics, University of Oxford, Oxford, UK.; Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA., Adams DR; Undiagnosed Disesases Program, National Human Genome Research Institute, Bethesda, MD, USA., Allan K; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia., Bakshi M; Department of Clinical Genetics, Liverpool Hospital, Sydney, New South Wales, Australia., Baldwin EE; Division of Medical Genetics, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, UT, USA., Berger SI; Center for Genetic Medicine Research, Children's National Research Institute, Washington, DC, USA.; Division of Genetics and Metabolism, Children's National Hospital, Washington, DC, USA., Bernstein JA; Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA.; GREGoR Stanford Site, Stanford University School of Medicine, Stanford, CA, USA.; Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA, USA., Bhatnagar I; Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK., Blair E; Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK., Brown NJ; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.; Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia., Burrage LC; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA., Chapman K; Division of Genetics and Metabolism, Children's National Hospital, Washington, DC, USA., Coman DJ; Department of Metabolic Medicine, Queensland Children's Hospital, Brisbane, Queensland, Australia.; Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia.; School of Medicine, Griffith university, Gold Coast, Queensland, Australia., Compton AG; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.; Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia.; Murdoch Children's Research Institute, Melbourne, Victoria, Australia., Cunningham CA; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.; Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia., D'Souza P; Undiagnosed Disesases Program, National Human Genome Research Institute, Bethesda, MD, USA., Danecek P; Human Genetics, Wellcome Sanger Institute, Hinxton, UK., Délot EC; Center for Genetic Medicine Research, Children's National Research Institute, Washington, DC, USA., Dias KR; Neuroscience Research Australia, Sydney, New South Wales, Australia.; Prince of Wales Clinical School, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia., Elias ER; Department of Pediatrics, Children's Hospital Colorado, Aurora, CO, USA.; University of Colorado School of Medicine, University of Colorado, Aurora, CO, USA., Elmslie F; South West Thames Centre for Genomics, St George's University Hospitals NHS Foundation Trust, London, UK., Evans CA; Neuroscience Research Australia, Sydney, New South Wales, Australia.; New South Wales Health Pathology Randwick Genomics, Prince of Wales Hospital, Sydney, New South Wales, Australia., Ewans L; Discipline of Paediatrics and Child Health, Faculty of Medicine and Health, University of New South Wales, Sydney, New South Wales, Australia.; Centre for Clinical Genetics, Sydney Children's Hospitals Network, Randwick, New South Wales, Australia.; Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Darlinghurst, North South Wales, Australia., Ezell K; Division of Medical Genetics and Genomic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA., Fraser JL; Center for Genetic Medicine Research, Children's National Research Institute, Washington, DC, USA.; Division of Genetics and Metabolism, Children's National Hospital, Washington, DC, USA., Gallacher L; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.; Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia., Genetti CA; Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.; Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA., Goriely A; MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.; NIHR Biomedical Research Centre, Oxford, UK., Grant CL; Division of Genetics and Metabolism, Children's National Hospital, Washington, DC, USA., Haack T; Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany.; Center for Rare Diseases Tübingen, University of Tübingen, Tübingen, Germany., Higgs JE; Liverpool Centre for Genomic Medicine, Liverpool Women's Hospital, Liverpool, UK., Hinch AG; Centre for Human Genetics, University of Oxford, Oxford, UK., Hurles ME; Human Genetics, Wellcome Sanger Institute, Hinxton, UK., Kuechler A; Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Essen, Germany., Lachlan KL; Wessex Clinical Genetics Service, University Hospital Southampton NHS Trust, Southampton, UK.; Department of Human Genetics and Genomic Medicine, Southampton University, Southampton, UK., Lalani SR; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA., Lecoquierre F; University of Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, Rouen, France., Leitão E; Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Essen, Germany., Fevre AL; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia., Leventer RJ; Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia.; Murdoch Children's Research Institute, Melbourne, Victoria, Australia.; Royal Children's Hospital, Melbourne, Victoria, Australia., Liebelt JE; Paediatric and Reproductive Genetics Unit, South Australian Clinical Genetics Service, Women's and Children's Hospital, North Adelaide, South Australia, Australia.; Repromed, Dulwich, South Australia, Australia., Lindsay S; Human Genetics, Wellcome Sanger Institute, Hinxton, UK., Lockhart PJ; Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia.; Bruce Lefroy Centre, Murdoch Children's Research Institute, Melbourne, Victoria, Australia., Ma AS; Department of Clinical Genetics, Sydney Children's Hospitals Network Westmead, Sydney, New South Wales, Australia.; Specialty of Genomic Medicine, University of Sydney, Sydney, New South Wales, Australia., Macnamara EF; Undiagnosed Disesases Program, National Human Genome Research Institute, Bethesda, MD, USA., Mansour S; South West Thames Centre for Genomics, St George's University Hospitals NHS Foundation Trust, London, UK., Maurer TM; GREGoR Stanford Site, Stanford University School of Medicine, Stanford, CA, USA.; Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA, USA.; Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA., Mendez HR; GREGoR Stanford Site, Stanford University School of Medicine, Stanford, CA, USA.; Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA, USA.; Department of Medicine - Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA., Metcalfe K; Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK., Montgomery SB; GREGoR Stanford Site, Stanford University School of Medicine, Stanford, CA, USA.; Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA, USA.; Department of Pathology, Department of Genetics, Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA., Moosajee M; UCL Institute of Ophthalmology, London, UK.; The Francis Crick Institute, London, UK.; Moorfields Eye Hospital NHS Foundation Trust, London, UK., Nassogne MC; Service de Neurologie Pédiatrique, Cliniques Universitaires Saint-Luc, UCLouvain, Brussels, Belgium.; Institut des Maladies Rares, Cliniques Universitaires Saint-Luc, UCLouvain, Brussels, Belgium., Neumann S; Division of Medical Genetics and Genomic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA., O'Donoghue M; Nottingham University Hospitals NHS Trust, Nottingham, UK., O'Leary M; Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA., Palmer EE; Discipline of Paediatrics and Child Health, Faculty of Medicine and Health, University of New South Wales, Sydney, New South Wales, Australia.; Centre for Clinical Genetics, Sydney Children's Hospitals Network, Randwick, New South Wales, Australia., Pattani N; South West Thames Centre for Genomics, St George's University Hospitals NHS Foundation Trust, London, UK., Phillips J; Division of Medical Genetics and Genomic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA., Pitsava G; Institute for Clinical and Translational Research, University of California Irvine, Irvine, CA, USA., Pysar R; Discipline of Paediatrics and Child Health, Faculty of Medicine and Health, University of New South Wales, Sydney, New South Wales, Australia.; Centre for Clinical Genetics, Sydney Children's Hospitals Network, Randwick, New South Wales, Australia.; Department of Clinical Genetics, The Children's Hospital at Westmead, Westmead, New South Wales, Australia., Rehm HL; Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA., Reuter CM; GREGoR Stanford Site, Stanford University School of Medicine, Stanford, CA, USA.; Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA, USA.; Department of Medicine - Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA., Revencu N; Center for Human Genetics, Cliniques Universitaires Saint-Luc, Université Catholique de Louvain, Brussels, Belgium., Riess A; Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany., Rius R; Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia.; Centre for Population Genomics, Garvan Institute of Medical Research and UNSW Sydney, Sydney, New South Wales, Australia.; Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, Victoria, Australia., Rodan L; Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA., Roscioli T; Neuroscience Research Australia, Sydney, New South Wales, Australia.; Prince of Wales Clinical School, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia.; New South Wales Health Pathology Randwick Genomics, Prince of Wales Hospital, Sydney, New South Wales, Australia., Rosenfeld JA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA., Sachdev R; Discipline of Paediatrics and Child Health, Faculty of Medicine and Health, University of New South Wales, Sydney, New South Wales, Australia.; Centre for Clinical Genetics, Sydney Children's Hospitals Network, Randwick, New South Wales, Australia., Shaw-Smith CJ; Department of Clinical Genetics, Peninsula Regional Clinical Genetics Service, Royal Devon University Hospital, Exeter, UK., Simons C; Centre for Population Genomics, Garvan Institute of Medical Research and UNSW Sydney, Sydney, New South Wales, Australia.; Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, Victoria, Australia., Sisodiya SM; Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology, London, UK.; UK and Chalfont Centre for Epilepsy, Chalfont St Peter, UK., Snell P; Bruce Lefroy Centre, Murdoch Children's Research Institute, Melbourne, Victoria, Australia., St Clair L; Department of Clinical Genetics, Sydney Children's Hospitals Network Westmead, Sydney, New South Wales, Australia., Stark Z; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.; Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia., Stewart HS; Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK., Tan TY; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.; Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia., Tan NB; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia., Temple SEL; Department of Clinical Genetics, Liverpool Hospital, Sydney, New South Wales, Australia.; School of Women's and Children's Health, University of New South Wales, Sydney, New South Wales, Australia., Thorburn DR; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.; Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia.; Murdoch Children's Research Institute, Melbourne, Victoria, Australia., Tifft CJ; Undiagnosed Disesases Program, National Human Genome Research Institute, Bethesda, MD, USA., Uebergang E; Murdoch Children's Research Institute, Melbourne, Victoria, Australia., VanNoy GE; Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA., Vasudevan P; Medical Genetics, University of Leicester, Leicester Royal Infirmary, Leicester, UK., Vilain E; Institute for Clinical and Translational Science, University of California Irvine, Irvine, CA, USA., Viskochil DH; Division of Medical Genetics, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, UT, USA., Wedd L; Centre for Population Genomics, Garvan Institute of Medical Research and UNSW Sydney, Sydney, New South Wales, Australia.; Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, Victoria, Australia., Wheeler MT; GREGoR Stanford Site, Stanford University School of Medicine, Stanford, CA, USA.; Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA, USA.; Department of Medicine - Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA., White SM; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.; Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia., Wojcik M; Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.; Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.; Division of Newborn Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA., Wolfe LA; Undiagnosed Disesases Program, National Human Genome Research Institute, Bethesda, MD, USA., Wolfenson Z; Undiagnosed Disesases Program, National Human Genome Research Institute, Bethesda, MD, USA., Wright CF; Department of Clinical and Biomedical Sciences, University of Exeter, Exeter, UK., Xiao C; Department of Neurology, University of California Irvine, Irvine, CA, USA., Zocche D; North West Thames Regional Genetics Service, Northwick Park and St Mark's Hospitals, London, UK., Rubenstein JL; Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA., Markenscoff-Papadimitriou E; Department of Psychiatry, Langley Porter Psychiatric Institute, UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA., Fica SM; Department of Biochemistry, University of Oxford, Oxford, UK., Baralle D; School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK.; National Institute for Health Research (NIHR) Southampton Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton, UK., Depienne C; Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Essen, Germany., MacArthur DG; Centre for Population Genomics, Garvan Institute of Medical Research and UNSW Sydney, Sydney, New South Wales, Australia.; Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, Victoria, Australia., Howson JMM; Human Genetics Centre of Excellence, Novo Nordisk Research Centre, Oxford, UK., Sanders SJ; Institute of Developmental and Regenerative Medicine, Department of Paediatrics, University of Oxford, Oxford, UK.; Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA., O'Donnell-Luria A; Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.; Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA., Whiffin N; Big Data Institute, University of Oxford, Oxford, UK. nwhiffin@well.ox.ac.uk.; Centre for Human Genetics, University of Oxford, Oxford, UK. nwhiffin@well.ox.ac.uk.; Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA. nwhiffin@well.ox.ac.uk.
Jazyk:	angličtina
Zdroj:	Nature [Nature] 2024 Aug; Vol. 632 (8026), pp. 832-840. Date of Electronic Publication: 2024 Jul 11.
DOI:	10.1038/s41586-024-07773-7
Abstrakt:	Around 60% of individuals with neurodevelopmental disorders (NDD) remain undiagnosed after comprehensive genetic testing, primarily of protein-coding genes 1 . Large genome-sequenced cohorts are improving our ability to discover new diagnoses in the non-coding genome. Here we identify the non-coding RNA RNU4-2 as a syndromic NDD gene. RNU4-2 encodes the U4 small nuclear RNA (snRNA), which is a critical component of the U4/U6.U5 tri-snRNP complex of the major spliceosome 2 . We identify an 18 base pair region of RNU4-2 mapping to two structural elements in the U4/U6 snRNA duplex (the T-loop and stem III) that is severely depleted of variation in the general population, but in which we identify heterozygous variants in 115 individuals with NDD. Most individuals (77.4%) have the same highly recurrent single base insertion (n.64_65insT). In 54 individuals in whom it could be determined, the de novo variants were all on the maternal allele. We demonstrate that RNU4-2 is highly expressed in the developing human brain, in contrast to RNU4-1 and other U4 homologues. Using RNA sequencing, we show how 5' splice-site use is systematically disrupted in individuals with RNU4-2 variants, consistent with the known role of this region during spliceosome activation. Finally, we estimate that variants in this 18 base pair region explain 0.4% of individuals with NDD. This work underscores the importance of non-coding genes in rare disorders and will provide a diagnosis to thousands of individuals with NDD worldwide. (© 2024. The Author(s).)
Databáze:	MEDLINE
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