ClinVar Miner

Variants in gene SCN2A

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Gene type:

If a variant has more than one submission, it may be counted in more than one significance column. If this is the case, the total number of variants will be less than the sum of the other cells.

pathogenic likely pathogenic uncertain significance likely benign benign not provided total
444 424 1405 861 197 89 3010

Condition and significance breakdown #

Total conditions: 82
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Condition pathogenic likely pathogenic uncertain significance likely benign benign not provided total
Seizures, benign familial infantile, 3; Developmental and epileptic encephalopathy, 11 211 98 771 704 53 2 1835
not provided 141 113 620 196 125 1 1138
Inborn genetic diseases 33 17 155 85 16 0 306
Developmental and epileptic encephalopathy, 11 75 93 90 5 6 0 256
not specified 0 0 56 99 71 0 209
Seizures, benign familial infantile, 3 29 28 67 21 55 0 195
Complex neurodevelopmental disorder 42 45 19 1 4 63 153
SCN2A-related disorder 12 24 28 28 4 6 101
Seizures, benign familial infantile, 3; Developmental and epileptic encephalopathy, 11; Episodic ataxia, type 9 7 6 22 7 0 0 41
Episodic ataxia, type 9 11 7 12 0 6 0 35
Developmental and epileptic encephalopathy 24 1 0 0 0 0 25
Intellectual disability 5 5 6 0 0 0 16
See cases 4 4 5 0 0 1 14
Seizure 5 8 1 1 0 0 14
West syndrome 12 0 0 0 0 0 12
West syndrome; Developmental and epileptic encephalopathy 11 0 0 0 0 0 11
Benign familial infantile epilepsy 9 0 0 0 0 0 9
Epileptic encephalopathy 2 6 0 0 0 0 8
Epilepsy of infancy with migrating focal seizures 2 3 0 0 0 0 5
Infantile spasms 1 4 0 0 0 0 5
Developmental disorder 1 1 1 1 0 0 4
Autism 1 2 0 0 0 0 3
Febrile seizure (within the age range of 3 months to 6 years) 1 0 2 0 0 0 3
Genetic developmental and epileptic encephalopathy 1 0 2 0 0 0 3
Lung cancer 0 0 0 0 0 3 3
unclassified developmental and epileptic encephalopathy 0 3 0 0 0 0 3
Autism spectrum disorder 2 0 0 0 0 0 2
Malignant migrating partial seizures of infancy 2 0 0 0 0 0 2
Neurodevelopmental delay 0 2 0 0 0 0 2
Neurodevelopmental disorder 0 1 1 0 0 0 2
SCN2A-related generalized epilepsy with febrile seizures plus 1 1 0 0 0 0 2
Seizures, benign familial infantile, 3; Developmental and epileptic encephalopathy, 1; Autism spectrum disorder; SCN2A-related generalized epilepsy with febrile seizures plus; West syndrome; Epilepsy with myoclonic atonic seizures; Non-syndromic intellectual disability; Lennox-Gastaut syndrome; Developmental and/or epileptic encephalopathy with spike-wave activation in sleep 0 0 0 0 0 2 2
Self-limited epilepsy with centrotemporal spikes 2 0 0 0 0 0 2
Squamous cell lung carcinoma 0 0 0 0 0 2 2
benign sporadic infantile epilepsy 0 2 0 0 0 0 2
Abnormal cerebral morphology 0 1 0 0 0 0 1
Adrenocortical carcinoma, hereditary 0 0 0 0 0 1 1
Autism Spectrum Disorder with Intellectual Disability 0 1 0 0 0 0 1
Autism spectrum disorder; unclassified developmental and epileptic encephalopathy 1 0 0 0 0 0 1
Autism; Seizures, benign familial infantile, 3; Episodic ataxia, type 9; Developmental and epileptic encephalopathy, 76 0 0 1 0 0 0 1
Benign Neonatal Epilepsy 1 0 0 0 0 0 1
Benign familial neonatal-infantile seizures 1; Developmental and epileptic encephalopathy, 11; Intellectual disability 0 0 0 0 0 1 1
Benign familial neonatal-infantile seizures 1; Seizures, benign familial infantile, 3; Developmental and epileptic encephalopathy, 11; SCN2A-related generalized epilepsy with febrile seizures plus 0 0 0 0 0 1 1
Cholangiocarcinoma 0 0 0 0 0 1 1
Clear cell carcinoma of kidney 0 0 0 0 0 1 1
Colon adenocarcinoma 0 0 0 0 0 1 1
Developmental and epileptic encephalopathy, 12 0 1 0 0 0 0 1
Developmental and epileptic encephalopathy, 30 1 0 0 0 0 0 1
Dystonia 12 0 1 0 0 0 0 1
Epilepsy 1 0 0 0 0 0 1
Epileptic encephalopathy, infantile or early childhood 1 0 0 0 0 0 1
Focal epilepsy 0 1 0 0 0 0 1
Gastric cancer 0 0 0 0 0 1 1
Generalized epilepsy with febrile seizures plus 1 0 0 0 0 0 1
Global developmental delay 0 0 1 0 0 0 1
Global developmental delay; Seizure; Movement disorder 0 1 0 0 0 0 1
Hemiplegia/hemiparesis 0 1 0 0 0 0 1
Hereditary episodic ataxia; Seizure; Vertigo 1 0 0 0 0 0 1
History of neurodevelopmental disorder 0 0 1 0 0 0 1
Intellectual disability, autosomal dominant 1 0 0 0 0 0 1
Lennox-Gastaut syndrome 0 0 1 0 0 0 1
Malignant tumor of urinary bladder 0 0 0 0 0 1 1
Marfanoid habitus and intellectual disability 0 1 0 0 0 0 1
Myoclonus 0 0 0 1 0 0 1
Non-syndromic intellectual disability 1 0 0 0 0 0 1
Nonpapillary renal cell carcinoma 0 0 0 0 0 1 1
Ovarian serous cystadenocarcinoma 0 0 0 0 0 1 1
Pulmonary fibrosis and/or bone marrow failure, Telomere-related, 3 0 0 1 0 0 0 1
Pyridoxine-dependent epilepsy 0 0 1 0 0 0 1
SCN2A-associated neurodevelopmental disorders 1 0 0 0 0 0 1
SCN2A-mediated disorder 0 1 0 0 0 0 1
SCN2A-related neurodevelopmental disorder 1 0 0 0 0 0 1
Seizures, benign familial infantile, 3; Developmental and epileptic encephalopathy, 11; Episodic ataxia, type 9; Complex neurodevelopmental disorder 0 0 0 0 0 1 1
Seizures, benign familial infantile, 3; Episodic ataxia, type 9 0 1 0 0 0 0 1
Seizures, benign familial infantile, 3; SCN2A-related generalized epilepsy with febrile seizures plus 0 0 0 0 0 1 1
Seizures, benign familial infantile, 5 1 0 0 0 0 0 1
Severe myoclonic epilepsy in infancy 0 1 0 0 0 0 1
Spastic ataxia 0 1 0 0 0 0 1
Uterine carcinosarcoma 0 0 0 0 0 1 1
Uterine corpus endometrial carcinoma 0 0 0 0 0 1 1
benign sporadic neonatal-infantile epilepsy 0 1 0 0 0 0 1
intellectual deficiency 0 1 0 0 0 0 1

Submitter and significance breakdown #

Total submitters: 151
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Submitter pathogenic likely pathogenic uncertain significance likely benign benign not provided total
Labcorp Genetics (formerly Invitae), Labcorp 210 92 763 706 53 0 1824
GeneDx 122 80 469 159 158 0 988
Ambry Genetics 33 17 156 85 16 0 306
CeGaT Center for Human Genetics Tuebingen 13 19 88 96 7 0 223
Illumina Laboratory Services, Illumina 1 1 45 19 50 0 116
GenomeConnect - Simons Searchlight 39 33 12 0 0 0 84
PreventionGenetics, part of Exact Sciences 3 16 21 28 12 0 80
Genetic Services Laboratory, University of Chicago 5 4 28 21 14 0 72
Breakthrough Genomics, Breakthrough Genomics 2 0 4 13 45 0 64
Channelopathy-Associated Epilepsy Research Center 0 0 0 0 0 63 63
Neurology Department, Shenzhen Children's Hospital 58 1 0 0 0 0 59
Athena Diagnostics 4 3 13 7 19 0 46
Women's Health and Genetics/Laboratory Corporation of America, LabCorp 4 0 20 19 0 0 43
3billion 8 17 17 0 0 0 42
Institute of Human Genetics, University of Leipzig Medical Center 12 9 16 2 0 0 39
Revvity Omics, Revvity 5 3 31 0 0 0 39
Mayo Clinic Laboratories, Mayo Clinic 2 0 19 5 11 0 37
Eurofins Ntd Llc (ga) 1 3 25 1 6 0 36
Mendelics 14 12 5 1 3 0 35
Génétique des Maladies du Développement, Hospices Civils de Lyon 13 10 2 4 0 0 29
Neuberg Centre For Genomic Medicine, NCGM 2 4 23 0 0 0 29
Fulgent Genetics, Fulgent Genetics 3 0 15 5 0 0 23
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute 12 4 6 0 0 0 22
OMIM 20 0 0 0 0 0 20
ClinGen Epilepsy Sodium Channel Variant Curation Expert Panel, Clingen 2 8 4 1 4 0 19
Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego 7 7 4 0 0 0 18
Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan 1 2 1 0 14 0 18
Baylor Genetics 6 4 7 0 0 0 17
Department of Neurology, Children’s Hospital of Chongqing Medical University 3 11 2 0 0 0 16
Genomic Medicine Center of Excellence, King Faisal Specialist Hospital and Research Centre 2 4 9 0 0 0 15
Genome Diagnostics Laboratory, University Medical Center Utrecht 2 1 0 6 5 0 14
Diagnostic Laboratory, Strasbourg University Hospital 3 7 3 0 0 0 13
Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago 0 2 8 1 0 0 11
Dr. Peter K. Rogan Lab, Western University 0 0 0 0 0 11 11
MGZ Medical Genetics Center 1 2 8 0 0 0 11
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen 2 0 1 2 5 0 10
Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center 2 0 8 0 0 0 10
Equipe Genetique des Anomalies du Developpement, Université de Bourgogne 3 6 0 0 0 0 9
Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein 1 2 6 0 0 0 9
Laboratory of Inherited Metabolic Diseases, Research centre for medical genetics 2 3 4 0 0 0 9
Neurogenetics Laboratory - MEYER, AOU Meyer 3 6 0 0 0 0 9
Department of Genetics, Rouen University Hospital, Normandy Center for Genomic and Personalized Medicine 3 3 1 1 0 0 8
GenomeConnect, ClinGen 0 0 0 0 0 8 8
Institute of Human Genetics Munich, TUM University Hospital 6 2 0 0 0 0 8
Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen 4 4 0 0 0 0 8
Juno Genomics, Hangzhou Juno Genomics, Inc 3 2 3 0 0 0 8
MVZ Martinsried, Medicover Genetics 1 6 1 0 0 0 8
New York Genome Center 0 0 8 0 0 0 8
CENTOGENE GmbH and LLC - Guiding Precision Medicine 2 2 3 0 0 0 7
Cambridge Genomics Laboratory, East Genomic Laboratory Hub, NHS Genomic Medicine Service 2 0 5 0 0 0 7
Dasa 7 0 0 0 0 0 7
Diagnostic Genetics, Severance Hospital, Yonsei University College of Medicine 1 6 0 0 0 0 7
GenomeConnect - Brain Gene Registry 0 0 0 0 0 7 7
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories 0 1 2 1 2 0 6
Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard 3 3 0 0 0 0 6
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center 0 0 0 5 1 0 6
Genetics Laboratory, UDIAT-Centre Diagnòstic, Hospital Universitari Parc Tauli 4 2 0 0 0 0 6
Genome-Nilou Lab 0 0 0 0 6 0 6
Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden 1 3 2 0 0 0 6
Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics 1 0 3 1 0 0 5
Clinical Genetics Laboratory, University Hospital Schleswig-Holstein 2 0 3 0 0 0 5
Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics 3 1 1 0 0 0 5
HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology 2 2 1 0 0 0 5
Institute of Immunology and Genetics Kaiserslautern 4 1 0 0 0 0 5
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ 4 0 1 0 0 0 5
Laboratory of Genetics, Children's Clinical University Hospital Latvia 0 0 1 3 1 0 5
Laboratory of Molecular Genetics (Pr. Bezieau's lab), CHU de Nantes 1 1 3 0 0 0 5
MVZ Medizinische Genetik Mainz 0 4 1 0 0 0 5
NeuroMeGen, Hospital Clinico Santiago de Compostela 0 5 0 0 0 0 5
Centre de Biologie Pathologie Génétique, Centre Hospitalier Universitaire de Lille 2 1 1 0 0 0 4
Centre for Mendelian Genomics, University Medical Centre Ljubljana 0 1 3 0 0 0 4
Centre of Medical Genetics, University Hospital Muenster 1 2 1 0 0 0 4
Clinical Genomics Laboratory, Washington University in St. Louis 0 0 4 0 0 0 4
Institute of Human Genetics, University of Goettingen 0 1 3 0 0 0 4
Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India 2 1 1 0 0 0 4
Service de Génétique Moléculaire, Hôpital Robert Debré 1 3 0 0 0 0 4
Center for Molecular Medicine, Children’s Hospital of Fudan University 0 3 0 0 0 0 3
Center of Excellence for Medical Genomics, Chulalongkorn University 2 1 0 0 0 0 3
Diagnostics Services (NGS), CSIR - Centre For Cellular And Molecular Biology 1 1 1 0 0 0 3
Genomic Research Center, Shahid Beheshti University of Medical Sciences 0 0 1 2 0 0 3
Laboratoire de Génétique Moléculaire, CHU Bordeaux 3 0 0 0 0 0 3
Molecular Genetics Laboratory, Motol Hospital 3 0 0 0 0 0 3
Molecular Genetics, Royal Melbourne Hospital 0 1 2 0 0 0 3
Pittsburgh Clinical Genomics Laboratory, University of Pittsburgh Medical Center 2 0 1 0 0 0 3
UCLA Clinical Genomics Center, UCLA 0 3 0 0 0 0 3
AiLife Diagnostics, AiLife Diagnostics 1 1 0 0 0 0 2
Bioinformatics Core, Luxembourg Center for Systems Biomedicine 2 0 0 0 0 0 2
Blueprint Genetics 0 2 0 0 0 0 2
Center of Genomic medicine, Geneva, University Hospital of Geneva 1 1 0 0 0 0 2
Center of Human Genetics, Hôpital Erasme 0 2 0 0 0 0 2
Centre for Addiction & Mental Health, Centre for Addiction & Mental Health 0 2 0 0 0 0 2
Clinical Genetics Laboratory, Skane University Hospital Lund 1 1 0 0 0 0 2
Clinical Genomic Analysis (GENYSIS) Core, University of North Carolina at Chapel Hill 0 1 1 0 0 0 2
Consultorio y Laboratorio de Neurogenética, Hospital JM Ramos Mejia 0 2 0 0 0 0 2
Geisinger Autism and Developmental Medicine Institute, Geisinger Health System 0 1 1 0 0 0 2
Genetics and Genomic Medicine Centre, NeuroGen Healthcare, NeuroGen Healthcare 0 0 2 0 0 0 2
Groupe Hospitalier Pitie Salpetriere, Uf Genomique Du Developpement, Assistance Publique Hopitaux de Paris Sorbonne Université 1 1 0 0 0 0 2
Institute for Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin 1 0 1 0 0 0 2
Institute of Human Genetics, Cologne University 0 1 1 0 0 0 2
Johns Hopkins Genomics, Johns Hopkins University 0 0 2 0 0 0 2
Laboratory of Medical Genetics, National & Kapodistrian University of Athens 1 1 0 0 0 0 2
Laboratory of Medical Genetics, University of Torino 0 2 0 0 0 0 2
Pediatric Department, Xiangya Hospital, Central South University 0 2 0 0 0 0 2
Pediatrics, MediClubGeorgia 1 1 0 0 0 0 2
Service de Génétique Médicale, Centre Hospitalier Universitaire de Nice-Université Côte d'Azur 0 2 0 0 0 0 2
Yale Center for Mendelian Genomics, Yale University 0 2 0 0 0 0 2
ARUP Laboratories, Cytogenetics and Genomic Microarray, ARUP Laboratories 0 0 1 0 0 0 1
Beijing Key Laboratry for Genetics of Birth Defects, Beijing Children's Hospital 0 1 0 0 0 0 1
Biochemical Molecular Genetic Laboratory, King Abdulaziz Medical City 0 1 0 0 0 0 1
Breda Genetics srl, Breda Genetics srl 0 0 1 0 0 0 1
Bruce Lefroy Centre, Murdoch Childrens Research Institute 1 0 0 0 0 0 1
CGC Genetics, Unilabs 0 1 0 0 0 0 1
Center of Medical Genomics-TUH, Thammasat University 1 0 0 0 0 0 1
Centre for Medical Genetics, Mumbai 0 0 0 1 0 0 1
Clinical Genomics Laboratory, Stanford Medicine 1 0 0 0 0 0 1
Clinical Molecular Genetics Laboratory, Johns Hopkins All Children's Hospital 0 0 1 0 0 0 1
Cytogenetics and Genomics Lab, Cyprus Institute Of Neurology and Genetics 1 0 0 0 0 0 1
DECIPHER, Wellcome Sanger Institute 0 0 0 0 0 1 1
Daryl Scott Lab, Baylor College of Medicine 0 0 1 0 0 0 1
Department of Human Genetics, Hannover Medical School 0 1 0 0 0 0 1
Department of Molecular Genetics, Istishari Arab Hospital 0 1 0 0 0 0 1
Department of Pathology and Laboratory Medicine, Sinai Health System 0 0 1 0 0 0 1
Genetics and Molecular Pathology, SA Pathology 1 0 0 0 0 0 1
Genetics and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University 0 1 0 0 0 0 1
Genomic Medicine Lab, University of California San Francisco 1 0 0 0 0 0 1
Genomics England Pilot Project, Genomics England 0 1 0 0 0 0 1
ISCA site 1 0 1 0 0 0 0 1
Institute of Human Genetics, Clinical Exome/Genome Diagnostics Group, University Hospital Bonn 1 0 0 0 0 0 1
Institute of Human Genetics, University Hospital of Duesseldorf 0 1 0 0 0 0 1
Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital 0 1 0 0 0 0 1
Kariminejad - Najmabadi Pathology & Genetics Center 0 1 0 0 0 0 1
Laboratoire Génétique Moléculaire, CHRU TOURS 0 0 1 0 0 0 1
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine 0 0 1 0 0 0 1
Laboratory of Molecular Genetics, CHU Rennes 0 1 0 0 0 0 1
Laboratory of genome editing, Research Centre for Medical Genetics 0 1 0 0 0 0 1
Lifecell International Pvt. Ltd 0 1 0 0 0 0 1
Medical Genetics Center, Maternal and Child Health Hospital of Hubei Province 1 0 0 0 0 0 1
Medical Molecular Genetics Department, Human Genetics and Genome Research Division, National Research Centre 0 1 0 0 0 0 1
Molecular Genetics Lab, CHRU Brest 0 1 0 0 0 0 1
Molecular Genetics Laboratory, BC Children's and BC Women's Hospitals 0 1 0 0 0 0 1
Molecular Medicine for Neurodegenerative and Neuromuscular Diseases Unit, IRCCS Fondazione Stella Maris 0 1 0 0 0 0 1
NIHR Bioresource Rare Diseases, University of Cambridge 0 1 0 0 0 0 1
Pediatric Genetics Clinic, Sheba Medical Center 1 0 0 0 0 0 1
Provincial Medical Genetics Program of British Columbia, University of British Columbia 0 1 0 0 0 0 1
Research Centre for Medical Genetics, Research Centre for Medical Genetics 0 1 0 0 0 0 1
Servicio de Genética Del Instituto Nacional de Salud Del Niño, Ministerio de Salud 0 0 1 0 0 0 1
Solve-RD Consortium 0 1 0 0 0 0 1
Suma Genomics 0 0 0 1 0 0 1
Sydney Genome Diagnostics, Children's Hospital Westmead 1 0 0 0 0 0 1
Undiagnosed Diseases Network, NIH 1 0 0 0 0 0 1
Zotz-Klimas Genetics Lab, MVZ Zotz Klimas 0 0 1 0 0 0 1

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