ArticleAmerican journal of human genetics2021
SPEN haploinsufficiency causes a neurodevelopmental disorder overlapping proximal 1p36 deletion syndrome with an episignature of X chromosomes in females.
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Article in American journal of human genetics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 59 papers, 1 of them a synthesis that pooled it.
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59 citing papers in PubMed, 1 synthesis or guideline pooled it, 89 citations in OpenAlex.
- Matching heterogeneous cohorts by projected principal components reveals two novel Alzheimer's disease-associated genes in the Hispanic population.Alzheimer's & dementia : the journal of the Alzheimer's Association · 2026Pooled it
- SPEN Loss Drives Extrafollicular Diffuse Large B-cell Lymphoma with Female-Specific Lethality and Therapeutic Vulnerabilities.Cancer discovery · 2026Article
- A CLN8 biallelic missense variant causes epilepsy with severe treatment-resistant psychosis.Molecular genetics and genomics : MGG · 2026Article
- Two Cases of SPEN Haploinsufficiency Presenting with Dystonia: Expanding the Genotype and Phenotype.Movement disorders clinical practice · 2026Article
- A Novel HeterozygousInternational journal of molecular sciences · 2026Article
- A novel spliceosomopathy caused by de novo SF3B3 variants.Genome medicine · 2026Article
- Analysis Methods for Diagnosing Rare Neurodevelopmental Diseases with Episignatures: A Systematic Review of the Literature.Biomedicines · 2025Review
- Haploinsufficiency of brain-specific kinase BRSK1 causes epilepsy and neurodevelopmental disorders.Epilepsia · 2025Article
- Prenatally diagnosed chromosome 1p36 deletions: a retrospective case series, literature review, and genotype-phenotype correlations.BMC medical genomics · 2025Review
- Exome sequencing reveals broad genetic heterogeneity for neuromuscular disorders in consanguineous Pakistani Families.European journal of human genetics : EJHG · 2025Article
- Matching Heterogeneous Cohorts by Projected Principal Components Reveals Two Novel Alzheimer's Disease-Associated Genes in the Hispanic Population.medRxiv : the preprint server for health sciences · 2025Article
- DNA methylation dysregulation patterns in the 1p36 region instability.Journal of applied genetics · 2025Article
- BiallelicInternational journal of molecular sciences · 2025Article
- Syndromic congenital hypoacusis associated with premature birth and a variant of the SPEN gene: A case report and literature review.Experimental and therapeutic medicine · 2025Article
- Article
- The transcriptome of playfulness is sex biased in the juvenile rat medial amygdala: A role for inhibitory neurons.Cell reports · 2025Article
- Mutations in the small nuclear RNA gene RNU2-2 cause a severe neurodevelopmental disorder with prominent epilepsy.Nature genetics · 2025Article
- Article
- Deleterious coding variation associated with autism is consistent across populations, as exemplified by admixed Latin American populations.medRxiv : the preprint server for health sciences · 2025Article
- Dominantly acting variants in ATP6V1C1 and ATP6V1B2 cause a multisystem phenotypic spectrum by altering lysosomal and/or autophagosome function.HGG advances · 2024Article
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Authors and funding
114 authors at 20 institutions in 11 countries.
Francesca Clementina RadioGenetics and Rare Disease Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy.
Kaifang PangDivision of Neurology and Developmental Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA.
Andrea CiolfiGenetics and Rare Disease Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy.
Michael A LevyMolecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON N6A5W9, Canada.
Andrés Hernández-GarcíaDepartment of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
Lucia PedaceOncohaematology Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy.
Francesca PantaleoniGenetics and Rare Disease Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy.
Zhandong LiuDivision of Neurology and Developmental Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA.
Elke de BoerDepartment of Human Genetics, Radboudumc, 6525 GA Nijmegen, the Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboud University, 6525 GA Nijmegen, the Netherlands.
Adam JacksonDivision of Evolution & Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, M13 9 WL Manchester, UK; Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, M13 9WL Manchester, UK.
Alessandro BrusellesDepartment of Oncology and Molecular Medicine, Istituto Superiore di Sanità, 00161 Rome, Italy.
Haley McConkeyMolecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON N6A5W9, Canada.
Emilia StellacciDepartment of Oncology and Molecular Medicine, Istituto Superiore di Sanità, 00161 Rome, Italy.
Stefania Lo CiceroDepartment of Oncology and Molecular Medicine, Istituto Superiore di Sanità, 00161 Rome, Italy.
Marialetizia MottaGenetics and Rare Disease Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy.
Rosalba CarrozzoGenetics and Rare Disease Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy.
Maria Lisa DenticiGenetics and Rare Disease Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy.
Kirsty McWalterGeneDx, Gaithersburg, MD 20877, USA.
Megha DesaiGeneDx, Gaithersburg, MD 20877, USA.
Kristin G MonaghanGeneDx, Gaithersburg, MD 20877, USA.
Aida TelegrafiGeneDx, Gaithersburg, MD 20877, USA.
Christophe PhilippeInserm UMR 1231 GAD (Génétique des Anomalies du Développement), Université de Bourgogne, 21070 Dijon, France; UF Innovation en Diagnostic Génomique des Maladies Rares, CHU, Dijon Bourgogne, 21079 Dijon, France.
Antonio VitobelloInserm UMR 1231 GAD (Génétique des Anomalies du Développement), Université de Bourgogne, 21070 Dijon, France; UF Innovation en Diagnostic Génomique des Maladies Rares, CHU, Dijon Bourgogne, 21079 Dijon, France.
Margaret AuDivision of Medical Genetics, Department of Pediatrics, Cedars Sinai Medical Center, David Geffen School of Medicine at UCLA, Los Angeles, CA 90048, USA.
Katheryn GrandDivision of Medical Genetics, Department of Pediatrics, Cedars Sinai Medical Center, David Geffen School of Medicine at UCLA, Los Angeles, CA 90048, USA.
Pedro A Sanchez-LaraDivision of Medical Genetics, Department of Pediatrics, Cedars Sinai Medical Center, David Geffen School of Medicine at UCLA, Los Angeles, CA 90048, USA.
Joanne BaezDivision of Medical Genetics, Department of Pediatrics, Cedars Sinai Medical Center, David Geffen School of Medicine at UCLA, Los Angeles, CA 90048, USA.
Kristin LindstromPhoenix Children's Hospital, Phoenix, AZ 85016, USA.
Peggy KulchPhoenix Children's Hospital, Phoenix, AZ 85016, USA.
Jessica SebastianDivision of Medical Genetics, Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA.
Suneeta Madan-KhetarpalDivision of Medical Genetics, Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA.
Chelsea RoadhouseMcMaster Children's Hospital, Hamilton, ON L8N 3Z5, Canada.
Jennifer J MacKenzieMcMaster Children's Hospital, Hamilton, ON L8N 3Z5, Canada.
Berrin MonteleoneClinical genetics, NYU Langone Long Island School of Medicine, Mineola, NY 11501, USA.
Carol J SaundersCenter for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, MO 64108, USA.
July K Jean CuevasCenter for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, MO 64108, USA.
Laura CrossCenter for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, MO 64108, USA.
Dihong ZhouCenter for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, MO 64108, USA.
Taila HartleyChildren's Hospital of Eastern Ontario, Ottawa, ON K1H 8L1, Canada.
Sarah L SawyerChildren's Hospital of Eastern Ontario, Ottawa, ON K1H 8L1, Canada.
Fabíola Paoli MonteiroMendelics Genomic Analysis, Campo Belo - São Paulo 04013-000, Brazil.
Tania Vertemati SecchesMendelics Genomic Analysis, Campo Belo - São Paulo 04013-000, Brazil.
Fernando KokMendelics Genomic Analysis, Campo Belo - São Paulo 04013-000, Brazil.
Laura E Schultz-RogersCenter for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA.
Erica L MackeCenter for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA.
Eva MoravaCenter for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA; Department of Clinical Genomics, Mayo Clinic, Rochester, MN 55905, USA.
Eric W KleeCenter for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA.
Jennifer KemppainenCenter for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA.
Maria IasconeOspedale Papa Giovanni XXIII, 24127 Bergamo, Italy.
Angelo SelicorniAzienda Socio Sanitaria Territoriale Lariana, 22100 Como, Italy.
Romano TenconiDipartimento di Pediatria, Università di Padova, 35137 Padua, Italy.
David J AmorVictorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia; Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Melbourne, VIC 3052, Australia.
Lynn PaisMedical and Populations Genetics Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Lyndon GallacherVictorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia; Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Melbourne, VIC 3052, Australia.
Peter D TurnpennyRoyal Devon & Exeter NHS Foundation Trust, Exeter EX2 5DW, UK.
Karen StalsRoyal Devon & Exeter NHS Foundation Trust, Exeter EX2 5DW, UK.
Sian EllardRoyal Devon & Exeter NHS Foundation Trust, Exeter EX2 5DW, UK.
Sara CabetDepartment of Genetics, Hospices Civils de Lyon, Groupement Hospitalier Est, Claude Bernard Lyon 1 University, 69002 Lyon, France.
Gaetan LescaDepartment of Genetics, Hospices Civils de Lyon, Groupement Hospitalier Est, Claude Bernard Lyon 1 University, 69002 Lyon, France.
Joset PascalInstitute of Medical Genetics, University of Zurich, 8952 Schlieren, Zurich, Switzerland.
Katharina SteindlInstitute of Medical Genetics, University of Zurich, 8952 Schlieren, Zurich, Switzerland.
Sarit RavidPediatric Neurology Unit, Ruth Children's Hospital, Rambam Health Care Campus, Haifa 3109601, Israel.
Karin WeissGenetics Institute, Rambam Health Care Campus, Rappaport Faculty of Medicine, Israel Institute of Technology, Haifa 3109601, Israel.
Alison M R CastleDepartment of Genetics, CHEO, University of Ottawa, Ottawa, ON K1N 6N5, Canada.
Melissa T CarterDepartment of Genetics, CHEO, University of Ottawa, Ottawa, ON K1N 6N5, Canada.
Louisa KalsnerConnecticut Children's Medical Center, University of Connecticut School of Medicine, Farmington, CT 06032, USA.
Bert B A de VriesDepartment of Human Genetics, Radboudumc, 6525 GA Nijmegen, the Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboud University, 6525 GA Nijmegen, the Netherlands.
Bregje W van BonDepartment of Human Genetics, Radboudumc, 6525 GA Nijmegen, the Netherlands.
Marijke R WeversDepartment of Human Genetics, Radboudumc, 6525 GA Nijmegen, the Netherlands.
Rolph PfundtDepartment of Human Genetics, Radboudumc, 6525 GA Nijmegen, the Netherlands.
Alexander P A StegmannDepartment of Human Genetics, Radboudumc, 6525 GA Nijmegen, the Netherlands; Department of Clinical Genetics, Maastricht University Medical Center+, 6229 HX Maastricht, the Netherlands.
Bronwyn KerrManchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, M13 9WL Manchester, UK.
Helen M KingstonManchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, M13 9WL Manchester, UK.
Kate E ChandlerManchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, M13 9WL Manchester, UK.
Willow SheehanDepartment of Medical Genetics, Shodair Children's Hospital, Helena, MT 59601, USA.
Abdallah F EliasDepartment of Medical Genetics, Shodair Children's Hospital, Helena, MT 59601, USA.
Deepali N ShindeAmbry Genetics, Aliso Viejo, CA 92656, USA.
Meghan C TowneAmbry Genetics, Aliso Viejo, CA 92656, USA.
Nathaniel H RobinDepartment of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
Dana GoodloeDepartment of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
Adeline VanderverDivision of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
Omar SherbiniDepartment of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
Krista BluskeIllumina Clinical Services Laboratory, San Diego, CA 92122, USA.
R Tanner HagelstromIllumina Clinical Services Laboratory, San Diego, CA 92122, USA.
Caterina ZanusInstitute for Maternal and Child Health, IRCCS "Burlo Garofolo," 34137 Trieste, Italy.
Flavio FaletraInstitute for Maternal and Child Health, IRCCS "Burlo Garofolo," 34137 Trieste, Italy.
Luciana MusanteInstitute for Maternal and Child Health, IRCCS "Burlo Garofolo," 34137 Trieste, Italy.
Evangeline C Kurtz-NelsonDepartment of Psychiatry & Behavioral Sciences, University of Washington, Seattle, WA 98195, USA.
Rachel K EarlDepartment of Psychiatry & Behavioral Sciences, University of Washington, Seattle, WA 98195, USA.
Britt-Marie AnderlidDepartment of Molecular Medicine and Surgery, Karolinska Institutet and Department of Clinical Genetics, Karolinska University Hospital, 17176 Stockholm, Sweden.
Gilles MorinCA de Génétique Clinique & Oncogénétique, CHU Amiens-Picardie, 80054 Amiens, France.
Marjon van SlegtenhorstDepartment of Clinical Genetics, Erasmus MC University Medical Center, 3015 GD Rotterdam, the Netherlands.
Karin E M DiderichDepartment of Clinical Genetics, Erasmus MC University Medical Center, 3015 GD Rotterdam, the Netherlands.
Alice S BrooksDepartment of Clinical Genetics, Erasmus MC University Medical Center, 3015 GD Rotterdam, the Netherlands.
Joost GribnauDepartment of Developmental Biology, Oncode Institute, Erasmus MC, University Medical Center, 3015 GD Rotterdam, the Netherlands.
Ruben G BoersDepartment of Developmental Biology, Oncode Institute, Erasmus MC, University Medical Center, 3015 GD Rotterdam, the Netherlands.
Teresa Robert FinestraDepartment of Developmental Biology, Oncode Institute, Erasmus MC, University Medical Center, 3015 GD Rotterdam, the Netherlands.
Lauren B CarterDepartment of Pediatrics, Division of Medical Genetics, Levine Children's Hospital Atrium Health, Charlotte, NC 28203, USA.
Anita RauchInstitute of Medical Genetics, University of Zurich, 8952 Schlieren, Zurich, Switzerland.
Paolo GaspariniInstitute for Maternal and Child Health, IRCCS "Burlo Garofolo," 34137 Trieste, Italy; Department of Medicine, Surgery & Health Science, University of Trieste, 34143 Trieste, Italy.
Kym M BoycottChildren's Hospital of Eastern Ontario, Ottawa, ON K1H 8L1, Canada.
Tahsin Stefan BarakatDepartment of Clinical Genetics, Erasmus MC University Medical Center, 3015 GD Rotterdam, the Netherlands.
John M GrahamDivision of Medical Genetics, Department of Pediatrics, Cedars Sinai Medical Center, David Geffen School of Medicine at UCLA, Los Angeles, CA 90048, USA.
Laurence FaivreCentre de Référence Maladies Rares « Anomalies du Développement et Syndromes Malformatifs », Centre de Génétique, FHU-TRANSLAD et Institut GIMI, 77908 Dijon, France; UMR 1231 GAD, Inserm - Université Bourgogne-Franche Comté, 77908 Dijon, France.
Siddharth BankaDivision of Evolution & Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, M13 9 WL Manchester, UK; Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, M13 9WL Manchester, UK.
Tianyun WangDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA.
Evan E EichlerDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.
Manuela PrioloUOSD Genetica Medica del Grande Ospedale Metropolitano "Bianchi Melacrino Morelli" di Reggio Calabria, 89124 Reggio Calabria, Italy.
Bruno DallapiccolaGenetics and Rare Disease Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy.
Lisenka E L M VissersDepartment of Human Genetics, Radboudumc, 6525 GA Nijmegen, the Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboud University, 6525 GA Nijmegen, the Netherlands.
Bekim SadikovicMolecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON N6A5W9, Canada.
Daryl A ScottDepartment of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA.
Jimmy Lloyd HolderDivision of Neurology and Developmental Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA.
Marco TartagliaGenetics and Rare Disease Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy. Electronic address: marco.tartaglia@opbg.net.
Bambino Gesù Children's Hospital · ITBaylor College of Medicine · USCedars-Sinai Medical Center · USErasmus MC · NLRadboud University Nijmegen · NLChildren's Mercy Hospital · USIRCCS Materno Infantile Burlo Garofolo · ITMayo Clinic · USChildren's Hospital of Eastern Ontario · CAIstituti di Ricovero e Cura a Carattere Scientifico · ITIstituto Superiore di Sanità · ITLondon Health Sciences Centre · CARoyal Devon & Exeter NHS Foundation Trust · GBUniversity of Alabama at Birmingham · USUniversity of Washington · USUniversity of Zurich · CHAmbry Genetics (United States) · USChildren's Hospital of Pittsburgh · USGenomic (Brazil) · BRIllumina (United States) · US
Funding
Joint Center for Mendelian GenomicsUM1HG008900 · NHGRI · BROAD INSTITUTE, INC. · PI O'DONNELL-LURIA, ANNE, REHM, HEIDI L · 2016 to 2020
$16.5MSporadic Mutations and Autism Spectrum DisordersR01MH101221 · NIMH · UNIVERSITY OF WASHINGTON · PI EICHLER, EVAN · 2013 to 2025
$9.2MA powerful web-based discovery platform for rare disease geneticsR01HG009141 · NHGRI · BROAD INSTITUTE, INC. · PI QUINLAN, AARON R, REHM, HEIDI L · 2017 to 2020
$2.9MMechanisms of Abnormal Diaphragm and Cardiac DevelopmentR01HD098458 · NICHD · BAYLOR COLLEGE OF MEDICINE · PI Daryl Armstrong Scott · 2020 to 2026
$2.8MNHGRI NIH HHS R01 HG009141NHGRI NIH HHS UM1 HG008900NICHD NIH HHS R01 HD098458NIMH NIH HHS R01 MH101221Wellcome Trust
Abstract
Deletion 1p36 (del1p36) syndrome is the most common human disorder resulting from a terminal autosomal deletion. This condition is molecularly and clinically heterogeneous. Deletions involving two non-overlapping regions, known as the distal (telomeric) and proximal (centromeric) critical regions, are sufficient to cause the majority of the recurrent clinical features, although with different facial features and dysmorphisms. SPEN encodes a transcriptional repressor commonly deleted in proximal del1p36 syndrome and is located centromeric to the proximal 1p36 critical region. Here, we used clinical data from 34 individuals with truncating variants in SPEN to define a neurodevelopmental disorder presenting with features that overlap considerably with those of proximal del1p36 syndrome. The clinical profile of this disease includes developmental delay/intellectual disability, autism spectrum disorder, anxiety, aggressive behavior, attention deficit disorder, hypotonia, brain and spine anomalies, congenital heart defects, high/narrow palate, facial dysmorphisms, and obesity/increased BMI, especially in females. SPEN also emerges as a relevant gene for del1p36 syndrome by co-expression analyses. Finally, we show that haploinsufficiency of SPEN is associated with a distinctive DNA methylation episignature of the X chromosome in affected females, providing further evidence of a specific contribution of the protein to the epigenetic control of this chromosome, and a paradigm of an X chromosome-specific episignature that classifies syndromic traits. We conclude that SPEN is required for multiple developmental processes and SPEN haploinsufficiency is a major contributor to a disorder associated with deletions centromeric to the previously established 1p36 critical regions.
Indexed as
AdolescentAutism Spectrum DisorderChildChild, PreschoolChromosome DeletionChromosome DisordersChromosomes, Human, Pair 1Chromosomes, Human, XDNA-Binding ProteinsDNA MethylationEpigenesis, GeneticFemaleHaploinsufficiencyHumansIntellectual DisabilityNeurodevelopmental DisordersDNA-Binding ProteinsRNA-Binding ProteinsSPEN protein, human1p36distal 1p36 deletion syndromeDNA methylome analysisepisignaturegenotype-phenotype correlationsneurodevelopmental disorderobesityproximal 1p36 deletion syndromeSPENX chromosome
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