The CCR4-NOT complex, crucial in gene expression regulation, includes CNOT3, a subunit linked to neurodevelopmental disorders when mutated. This study investigates 51 patients from 42 families with heterozygous CNOT3 variants, aiming to expand the understanding of CNOT3-related neurodevelopmental disorders and explore genotype-phenotype correlations. Patients originated from various countries, reflecting the disorder's global significance. All patients exhibited developmental delays, particularly in the language area. Intellectual disability was found in 87% of patients and was typically mild to moderate. Behavioral issues, including autism spectrum disorders and attention deficits, were common, affecting over half of the patients. Dysmorphic features were highlighted and may help establishing the diagnosis. Epilepsy was uncommon (10%). Twenty-eight novel variants were identified, including missense, nonsense, frameshift, intronic variations and a deletion of 12 exons. Missense variants clustered at the N- and C-terminal regions of the protein, indicating critical functional roles. No clear genotype-phenotype correlation was observed, suggesting that all identified variants resulted in a loss-of-function effect. Finally, this work delineates the clinical and molecular spectrum of CNOT3-related disorders thanks to an in-depth characterization of a large cohort. Further research will be necessary to understand the functional consequences of the variants and enhance patient long-term outcomes.

Brotman Baty Institute for Precision Medicine Seattle WA USA

Center for Integrative Brain Research Seattle Children's Research Institute Seattle WA USA

Center for Medical Genetics Ghent University Hospital Ghent Belgium

Center for Medical Genetics Hôpital Erasme Hôpital Universitaire de Bruxelles Université Libre de Bruxelles Brussels Belgium

Center for Rare Diseases Pediatric and Adolescent Medicine Aarhus University Hospital Aarhus Denmark

Centre de référence « Surdités Génétiques » Service de Médecine génomique des Maladies rares Hôpital Necker Assistance Publique Hôpitaux de Paris Paris France

Centre for Rare Diseases Erlangen Erlangen Germany

Child Neuropsychiatry Unit IRCCS G Gaslini Institute Genoa Italy

CHU Lille Clinique de Génétique Lille France

Département de génétique médicale Hôpital Pitié Salpêtrière AP HP Sorbonne Université Paris France

Department of Biology and Medical Genetics Charles University 2nd Faculty of Medicine and University Hospital Motol Prague Czech Republic

Department of biomolecular medicine Ghent university Ghent Belgium

Department of Clinical Genetics Leiden University Medical Centre Leiden The Netherlands

Department of Genetics Hôpital Universitaire des Enfants Reine Fabiola Hôpital Universitaire de Bruxelles Université Libre de Bruxelles Brussels Belgium

Department of Human Genetics Radboud University Medical Center Nijmegen The Netherlands

Department of Medical Genetics and Metabolism Valley Children's Hospital Madera CA USA

Department of Medical Genetics Hospital de Santa Maria Centro Hospitalar Universitário Lisboa Norte Lisbon Portugal

Department of Medical Genetics Masaryk Hospital in Ústí nad Labem Regional Health Corporation Ústí nad Labem Czech Republic

Department of Medical Genetics University Hospital of Bordeaux and INSERM U1211 University of Bordeaux Bordeaux France

Department of Medicine and Surgery University of Milan Bicocca Monza Italy

Department of Neurobiology and Molecular Medicine IRCCS Fondazione Stella Maris Pisa Italy

Department of Neurology University of California San Francisco San Francisco CA USA

Department of Neurosciences Rehabilitation Ophthalmology Genetics Maternal and Child Health University of Genoa Genoa Italy

Department of Pediatrics Division of Clinical and Metabolic Genetics The Hospital for Sick Children Toronto ON Canada

Department of Pediatrics University of Washington Seattle WA USA

Division of Human Genetics Children's Hospital of Philadelphia Philadelphia PA USA

Epilepsy Center Kleinwachau Radeberg Germany

Fondazione Policlinico Universitario Agostino Gemelli IRCCS Roma Italy

Genetic Medicine University of California San Francisco Fresno Fresno CA USA

Genetica Medica Azienda Ospedaliera Universitaria Senese Siena Italy

Genetics and Metabolics Clinic McMaster Children's Hospital Hamilton ON Canada

Genetics Department AP HP Robert Debré University Hospital Paris France

Genomics and Clinical Genetics IRCCS Istituto Giannina Gaslini Genoa Italy

Institut de Génétique Médicale CHU Lille Avenue Oscar Lambret Lille France

Institut Imagine Paris France

Institute for Clinical Genetics University Hospital Carl Gustav Carus at TUD Dresden University of Technology Dresden Germany

Institute of Histology and Developmental Biology Faculty of Medicine University of Lisbon Lisbon Portugal

Institute of Human Genetics Universitätsklinikum Erlangen Friedrich Alexander Universität Erlangen Nürnberg 91054 Erlangen Germany

Institute of Human Genetics University Hospital Schleswig Holstein Kiel Germany

Institute of Human Genetics University Hospital Schleswig Holstein Lübeck Germany

Interuniversitary Institute of Bioinformatics in Brussels Université Libre de Bruxelles Brussels Belgium

Laboratoire Seqoia Paris France

Med Biotech Hub and Competence Center Department of Medical Biotechnologies University of Siena Siena Italy

Medical Genetics Unit IRCCS Istituto Giannina Gaslini Genoa Italy

Medical Genetics University of Siena Siena Italy

Necker Hospital APHP Reference Center for Intellectual Disability Genetics Department Institut Imagine University of Paris Paris France

NeuroDiderot UMR 1141 Inserm FHU I2 D2 Université de Paris Paris France

North East Thames Regional Genetic Service Great Ormond Street Hospital for Children NHS Foundation Trust London UK

Nottingham Clinical Genetics Service Nottingham University Hospitals NHS Trust City Hospital Campus Nottingham UK

Pediatric Neurology and Muscular Diseases Unit IRCCS Istituto Giannina Gaslini Genova Italy

Radboud University Medical Center Department of Neurology Nijmegen The Netherlands

Reference centre for Mendelian connective tissue disorders UZ Gent Ghent University Hospital UZ Gent Gent Belgium

Research Unit for Rare Diseases Department of Pediatrics and Inherited Metabolic Disorders 1st Faculty of Medicine Charles University Prague Prague Czech Republic

Service de Génétique Clinique et Oncogénétique CHU Amiens Picardie Amiens France

Service de Génétique Médicale Hôpital Purpan CHU de Toulouse Toulouse France

Service de génétique médicale Unité de génétique clinique CHU Hôtel Dieu 1 place Alexis Ricordeau Nantes France

Service of Medical Genetics Oncologic Institute of Southern Switzerland EOC Switzerland Switzerland

UF médecine génomique et génétique clinique Hôpital Jean Verdier Hôpitaux Universitaires de Paris Seine Saint Denis AP HP Bondy France

UFR de Santé Médecine et Biologie humaine Université Sorbonne Paris Nord Bobigny France

Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares FHU TRANSLAD CHU Dijon Bourgogne Dijon France

Université de Bourgogne INSERM UMR1231 GAD Génétique des Anomalies du Développement Dijon France

Université de Franche Comté Centre de Génétique Humaine CHU Besançon Besançon France

Université de Franche Comté CHU Besançon Oncobiologie Génétique Bioinformatique FHU TRANSLAD et Institut GIMI Besançon France

Université Montpellier Centre de référence anomalies du développement et syndromes malformatifs Génétique Clinique CHU Montpellier Montpellier France

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