title: Mutations in EBF3 Disturb Transcriptional Profiles and Cause Intellectual Disability, Ataxia, and Facial Dysmorphism.
abstract: From a GeneMatcher-enabled international collaboration, we identified ten individuals affected by intellectual disability, speech delay, ataxia, and facial dysmorphism and carrying a deleterious EBF3 variant detected by whole-exome sequencing. One 9-bp duplication and one splice-site, five missense, and two nonsense variants in EBF3 were found; the mutations occurred de novo in eight individuals, and the missense variant c.625C>T (p.Arg209Trp) was inherited by two affected siblings from their healthy mother, who is mosaic. EBF3 belongs to the early B cell factor family (also known as Olf, COE, or O/E) and is a transcription factor involved in neuronal differentiation and maturation. Structural assessment predicted that the five amino acid substitutions have damaging effects on DNA binding of EBF3. Transient expression of EBF3 mutant proteins in HEK293T cells revealed mislocalization of all but one mutant in the cytoplasm, as well as nuclear localization. By transactivation assays, all EBF3 mutants showed significantly reduced or no ability to activate transcription of the reporter gene CDKN1A, and in situ subcellular fractionation experiments demonstrated that EBF3 mutant proteins were less tightly associated with chromatin. Finally, in RNA-seq and ChIP-seq experiments, EBF3 acted as a transcriptional regulator, and mutant EBF3 had reduced genome-wide DNA binding and gene-regulatory activity. Our findings demonstrate that variants disrupting EBF3-mediated transcriptional regulation cause intellectual disability and developmental delay and are present in ∼0.1% of individuals with unexplained neurodevelopmental disorders.
authors.affiliation: Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany.
authors.forename: Frederike Leonie
authors.initials: FL
authors.lastname: Harms
authors.affiliation: Department of Medical Genetics, Kasturba Medical College, Manipal University, 576104 Manipal, India.
authors.forename: Katta M
authors.initials: KM
authors.lastname: Girisha
authors.affiliation: HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA; Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
authors.forename: Andrew A
authors.initials: AA
authors.lastname: Hardigan
authors.affiliation: Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany.
authors.forename: Fanny
authors.initials: F
authors.lastname: Kortüm
authors.affiliation: Department of Medical Genetics, Kasturba Medical College, Manipal University, 576104 Manipal, India.
authors.forename: Anju
authors.initials: A
authors.lastname: Shukla
authors.affiliation: Bioinformatics Service Facility, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; Center for Bioinformatics, University of Hamburg, 20246 Hamburg, Germany; Virus Genomics, Heinrich Pette Institute, Leibniz Institute for Experimental Virology, 20246 Hamburg, Germany.
authors.forename: Malik
authors.initials: M
authors.lastname: Alawi
authors.affiliation: Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, 500001 Hyderabad, Telangana, India.
authors.forename: Ashwin
authors.initials: A
authors.lastname: Dalal
authors.affiliation: Department of Pediatrics, McMaster University Medical Center, Hamilton, ON L8N 3Z5, Canada.
authors.forename: Lauren
authors.initials: L
authors.lastname: Brady
authors.affiliation: Department of Pediatrics, McMaster University Medical Center, Hamilton, ON L8N 3Z5, Canada.
authors.forename: Mark
authors.initials: M
authors.lastname: Tarnopolsky
authors.affiliation: Department of Pediatrics, University of California, San Diego, San Diego, CA 92123, USA; Division of Genetics/Dysmorphology, Rady Children's Hospital San Diego, San Diego, CA 92123, USA.
authors.forename: Lynne M
authors.initials: LM
authors.lastname: Bird
authors.affiliation: Division of Genetics/Dysmorphology, Rady Children's Hospital San Diego, San Diego, CA 92123, USA.
authors.forename: Sophia
authors.initials: S
authors.lastname: Ceulemans
authors.affiliation: Department of Neurology, University of Alabama at Birmingham, Birmingham, AL35294, USA.
authors.forename: Martina
authors.initials: M
authors.lastname: Bebin
authors.affiliation: HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA.
authors.forename: Kevin M
authors.initials: KM
authors.lastname: Bowling
authors.affiliation: HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA.
authors.forename: Susan M
authors.initials: SM
authors.lastname: Hiatt
authors.affiliation: Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
authors.forename: Edward J
authors.initials: EJ
authors.lastname: Lose
authors.affiliation: Department of Pediatrics and Medicine, Columbia University, New York, NY 10032, USA.
authors.forename: Michelle
authors.initials: M
authors.lastname: Primiano
authors.affiliation: Department of Pediatrics and Medicine, Columbia University, New York, NY 10032, USA.
authors.forename: Wendy K
authors.initials: WK
authors.lastname: Chung
authors.affiliation: GeneDx, Gaithersburg, MD 20877, USA.
authors.forename: Jane
authors.initials: J
authors.lastname: Juusola
authors.affiliation: Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
authors.forename: Zeynep C
authors.initials: ZC
authors.lastname: Akdemir
authors.affiliation: Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA.
authors.forename: Matthew
authors.initials: M
authors.lastname: Bainbridge
authors.affiliation: Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
authors.forename: Wu-Lin
authors.initials: WL
authors.lastname: Charng
authors.affiliation: Cook Children's Genetic Clinic, Fort Worth, TX 76102, USA.
authors.forename: Margaret
authors.initials: M
authors.lastname: Drummond-Borg
authors.affiliation: Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
authors.forename: Mohammad K
authors.initials: MK
authors.lastname: Eldomery
authors.affiliation: Division of Clinical Genetics and Metabolic Disorders, Department of Pediatrics, Tawam Hospital, 15258 Al-Ain, United Arab Emirates.
authors.forename: Ayman W
authors.initials: AW
authors.lastname: El-Hattab
authors.affiliation: Section of Medical Genetics, Children's Hospital, King Fahad Medical City, 11564 Riyadh, Saudi Arabia.
authors.forename: Mohammed A M
authors.initials: MAM
authors.lastname: Saleh
authors.affiliation: Service de Génétique Médicale, Centre Hospitalier Universitaire Nantes, 44093 Nantes Cedex 1, France.
authors.forename: Stéphane
authors.initials: S
authors.lastname: Bézieau
authors.affiliation: Service de Génétique Médicale, Centre Hospitalier Universitaire Nantes, 44093 Nantes Cedex 1, France.
authors.forename: Benjamin
authors.initials: B
authors.lastname: Cogné
authors.affiliation: Service de Génétique Médicale, Centre Hospitalier Universitaire Nantes, 44093 Nantes Cedex 1, France; INSERM UMR-S 957, 44035 Nantes, France.
authors.forename: Bertrand
authors.initials: B
authors.lastname: Isidor
authors.affiliation: Service de Génétique Médicale, Centre Hospitalier Universitaire Nantes, 44093 Nantes Cedex 1, France.
authors.forename: Sébastien
authors.initials: S
authors.lastname: Küry
authors.affiliation: Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
authors.forename: James R
authors.initials: JR
authors.lastname: Lupski
authors.affiliation: HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA.
authors.forename: Richard M
authors.initials: RM
authors.lastname: Myers
authors.affiliation: HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA. Electronic address: gcooper@hudsonalpha.org.
authors.forename: Gregory M
authors.initials: GM
authors.lastname: Cooper
authors.affiliation: Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany. Electronic address: kkutsche@uke.de.
authors.forename: Kerstin
authors.initials: K
authors.lastname: Kutsche
mesh_terms: D000293:Adolescent; D000328:Adult; D019943:Amino Acid Substitution; D001259:Ataxia / Q000235:genetics*; D002648:Child; D002675:Child, Preschool; D002843:Chromatin / Q000235:genetics / Q000378:metabolism; D050759:Cyclin-Dependent Kinase Inhibitor p21 / Q000235:genetics; D002658:Developmental Disabilities / Q000235:genetics; D059472:Exome / Q000235:genetics; D005145:Face / Q000002:abnormalities*; D005260:Female; D005786:Gene Expression Regulation / Q000235:genetics; D017930:Genes, Reporter; D057809:HEK293 Cells; D006801:Humans; D008607:Intellectual Disability / Q000235:genetics*; D007805:Language Development Disorders / Q000235:genetics*; D008297:Male; D008958:Models, Molecular; D009030:Mosaicism; D009154:Mutation; D065886:Neurodevelopmental Disorders / Q000235:genetics*; D021381:Protein Transport / Q000235:genetics; D013577:Syndrome; D014157:Transcription Factors / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D014158:Transcription, Genetic / Q000235:genetics*
chemical_list: C493956:CDKN1A protein, human; D002843:Chromatin; D050759:Cyclin-Dependent Kinase Inhibitor p21; C000605678:EBF3 protein, human; D014157:Transcription Factors
keywords: EBF3; de novo mutation; developmental delay; gene regulation; intellectual disability; transcription factor