ClinVar Miner

Variants studied for autosomal recessive non-syndromic intellectual disability

Included ClinVar conditions (71):
Minimum submission review status: Collection method:
Minimum conflict level:
Gene type:
ClinVar version:

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
408 300 1187 779 222 24 2756

Gene and significance breakdown #

Total genes and gene combinations: 92
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Gene or gene combination pathogenic likely pathogenic uncertain significance likely benign benign not provided total
VRK1 64 38 148 258 14 1 494
MAN1B1 26 12 175 171 42 0 387
PGAP1 23 12 111 117 27 1 284
EXOSC3 31 23 66 116 10 2 224
PRSS12 1 2 92 11 10 2 115
TRAPPC9 24 13 63 4 11 2 114
NSUN2 9 14 56 8 18 1 103
TUSC3 8 5 26 28 9 0 74
CC2D1A 3 12 45 3 3 1 66
KDM5B 13 20 24 1 5 2 61
ADK 2 5 24 6 8 0 44
FMN2 5 3 21 6 8 1 44
LINS1 5 17 21 1 0 0 42
MBOAT7 8 11 22 0 0 0 37
RUSC2 4 1 24 4 2 0 34
MED23 9 7 15 2 0 4 33
TRMT1 8 10 10 0 1 0 29
APC2 3 3 18 0 2 1 27
ELP2 8 7 14 0 0 3 27
NDST1 4 2 17 1 5 0 27
ALKBH8 4 4 12 1 5 0 24
PIDD1 9 3 10 2 0 0 23
CEP104 3 12 5 3 0 0 22
METTL23 6 4 9 1 0 0 20
WASHC4 6 6 9 0 1 0 20
ST3GAL3 6 1 7 2 3 0 18
C1orf105, PIGC 4 4 10 0 2 0 17
ZBTB11 11 0 5 0 1 0 17
ASCC3 13 2 1 0 0 0 16
EXOSC3, LOC130001814 2 1 3 10 1 0 16
GRIK2 2 0 13 1 0 0 16
LOC130003078, MAN1B1 0 0 6 9 1 0 16
LOC130003079, MAN1B1 2 2 6 5 2 0 15
TNIK 1 0 5 1 7 0 14
CRADD 5 4 6 0 0 1 13
LINGO1 3 0 6 0 4 0 13
METTL5 5 5 4 0 0 0 13
CRBN 3 1 4 0 3 0 11
EXOSC8 2 2 6 1 1 1 11
ZC3H14 2 0 5 2 2 0 10
CAMK2A 1 2 1 0 5 0 9
DCPS 2 1 4 0 2 0 9
LMAN2L 1 1 7 0 0 0 9
RSRC1 5 1 3 0 0 0 9
EIF3F 1 3 3 0 2 0 8
FBXO31 2 1 4 0 0 1 7
HNMT 2 2 4 0 0 0 7
C12orf4 2 5 0 0 0 0 6
DCPS, GSEC 1 2 4 1 0 0 6
FERRY3 4 2 1 0 0 0 6
WDR11 4 0 2 0 0 0 6
ADK, LOC102723439 1 2 0 1 2 0 5
DCPS, TIRAP 1 1 2 0 1 0 5
IMPA1 1 1 3 0 0 0 5
TAF13 2 1 1 0 1 0 5
CASP2 4 0 0 0 0 0 4
TECR 1 0 2 1 0 0 4
CRBN, TRNT1 2 1 1 0 0 0 3
EDC3 2 0 1 0 0 0 3
EIF3F, LOC126861132 1 0 2 0 0 0 3
EXOSC8, LOC130009581 0 0 3 0 0 0 3
KICS2 3 0 0 0 0 0 3
NSUN6 3 0 0 0 0 0 3
ANK3 0 0 2 0 0 0 2
APC2, LOC130062956 0 0 2 0 0 0 2
CEP104, LOC126805586 1 1 0 0 0 0 2
GRIA1 1 0 1 0 0 0 2
KDM5B, LOC129932249 0 0 2 0 0 0 2
KICS2, LOC130008196 2 0 0 0 0 0 2
NAA20 2 1 0 0 0 0 2
TPR 2 0 0 0 0 0 2
ABCA2, ABO, ADAMTS13, ADAMTSL2, AGPAT2, AJM1, AK8, BARHL1, BRD3, C8G, C9orf163, CACFD1, CAMSAP1, CARD9, CCDC183, CEL, CFAP77, CLIC3, COL5A1, DBH, DDX31, DIPK1B, DNLZ, DPP7, EDF1, EGFL7, ENTPD2, ENTR1, FAM163B, FBXW5, FCN1, FCN2, FUT7, GBGT1, GFI1B, GLT6D1, GPSM1, GRIN1, GTF3C4, GTF3C5, INPP5E, KCNT1, LCN1, LCN10, LCN12, LCN15, LCN6, LCN8, LCN9, LCNL1, LHX3, LINC02907, LINC02908, MAMDC4, MAN1B1, MED22, MIR126, MRPS2, MYMK, NACC2, NOTCH1, NPDC1, OBP2A, OBP2B, OLFM1, PAEP, PAXX, PHPT1, PIERCE1, PMPCA, PPP1R26, PTGDS, QSOX2, RABL6, RALGDS, REXO4, RNU6ATAC, RPL7A, RXRA, SAPCD2, SARDH, SEC16A, SETX, SLC2A6, SNAPC4, SNHG7, SOHLH1, SPACA9, STKLD1, SURF1, SURF2, SURF4, SURF6, TMEM141, TMEM250, TRAF2, TSC1, TTF1, UAP1L1, UBAC1, VAV2, WDR5 0 0 1 0 0 0 1
ABCA2, AGPAT2, AJM1, ANAPC2, ARRDC1, C8G, C9orf163, CACNA1B, CARD9, CCDC183, CIMIP2A, CLIC3, CYSRT1, DIPK1B, DNLZ, DPH7, DPP7, EDF1, EGFL7, EHMT1, ENTPD2, ENTPD8, ENTR1, EXD3, FBXW5, FUT7, GPSM1, GRIN1, INPP5E, LCN10, LCN12, LCN15, LCN6, LCN8, LCNL1, LHX3, LINC02908, LOC651337, LRRC26, MAMDC4, MAN1B1, MIR126, MRPL41, NDOR1, NELFB, NOTCH1, NOXA1, NPDC1, NRARP, NSMF, PAXX, PHPT1, PMPCA, PNPLA7, PTGDS, QSOX2, RABL6, RNF208, RNF224, SAPCD2, SEC16A, SLC34A3, SNAPC4, SNHG7, SSNA1, STPG3, TMEM141, TMEM203, TMEM210, TOR4A, TPRN, TRAF2, TUBB4B, UAP1L1, ZMYND19 1 0 0 0 0 0 1
ARG1, MED23 0 0 0 0 1 0 1
BRME1, CC2D1A 1 0 0 0 0 0 1
C8orf17, TRAPPC9 1 0 0 0 0 0 1
CC2D1A, LOC129391070 1 0 0 0 0 0 1
CHMP1A 0 1 0 0 0 0 1
EEF1D 1 0 0 0 0 0 1
EEFSEC 0 1 0 0 0 0 1
FMN2, LOC126806069 0 0 1 0 0 0 1
GPI 0 0 1 0 0 0 1
LHFPL5 1 0 0 0 0 0 1
LOC130003078, LOC130003079, MAN1B1 0 0 1 0 0 0 1
LOC130003080, MAN1B1 1 0 0 0 0 0 1
LOC130008643, WASHC4 0 0 1 0 0 0 1
LOC130056407, VRK1 0 0 1 0 0 0 1
LOC130063689, TRMT1 0 1 0 0 0 0 1
MBOAT7, TSEN34 0 0 0 1 0 0 1
MROH6 0 0 1 0 0 0 1
SYNGAP1 0 1 0 0 0 0 1
TMEM276, TMEM276-ZFTRAF1, ZFTRAF1 0 0 1 0 0 0 1

Submitter and significance breakdown #

Total submitters: 139
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Submitter pathogenic likely pathogenic uncertain significance likely benign benign not provided total
Labcorp Genetics (formerly Invitae), Labcorp 121 26 395 695 98 0 1335
Illumina Laboratory Services, Illumina 1 2 263 41 69 0 376
Baylor Genetics 17 10 236 0 0 0 263
OMIM 194 0 0 0 0 0 194
Fulgent Genetics, Fulgent Genetics 7 58 63 21 3 0 152
Revvity Omics, Revvity 6 13 77 1 0 0 97
Genome-Nilou Lab 0 0 0 0 80 0 80
Genomic Medicine Center of Excellence, King Faisal Specialist Hospital and Research Centre 14 17 35 1 0 0 67
Natera, Inc. 1 1 48 7 3 0 60
New York Genome Center 2 6 45 0 0 0 53
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute 16 11 16 2 0 0 45
Women's Health and Genetics/Laboratory Corporation of America, LabCorp 25 16 0 0 0 0 41
Institute of Human Genetics, University of Leipzig Medical Center 15 6 9 0 1 0 31
3billion, Medical Genetics 5 7 1 15 0 0 28
Neuberg Centre For Genomic Medicine, NCGM 3 10 15 0 0 0 28
Genomic Research Center, Shahid Beheshti University of Medical Sciences 3 3 11 1 0 0 18
Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard 2 5 9 0 0 0 16
Mendelics 6 4 0 3 2 0 15
Pittsburgh Clinical Genomics Laboratory, University of Pittsburgh Medical Center 0 8 6 0 0 0 14
GenomeConnect - Brain Gene Registry 0 0 0 0 0 13 13
Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center 3 9 0 0 0 0 12
Genetic Services Laboratory, University of Chicago 9 3 0 0 0 0 12
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories 0 1 6 2 2 0 11
Centogene AG - the Rare Disease Company 2 2 6 0 0 0 10
Center For Human Genetics And Laboratory Diagnostics, Dr. Klein, Dr. Rost And Colleagues 1 7 2 0 0 0 10
Daryl Scott Lab, Baylor College of Medicine 2 1 5 1 0 0 9
Equipe Genetique des Anomalies du Developpement, Université de Bourgogne 2 7 0 0 0 0 9
SIB Swiss Institute of Bioinformatics 0 8 0 0 0 0 8
Biochemical Molecular Genetic Laboratory, King Abdulaziz Medical City 3 4 1 0 0 0 8
MGZ Medical Genetics Center 3 2 2 0 0 0 7
Mayo Clinic Laboratories, Mayo Clinic 0 0 7 0 0 0 7
Centre for Mendelian Genomics, University Medical Centre Ljubljana 1 3 2 0 1 0 7
Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India 4 2 1 0 0 0 7
GenomeConnect, ClinGen 0 0 0 0 0 7 7
Juno Genomics, Hangzhou Juno Genomics, Inc 2 3 2 0 0 0 7
Breda Genetics srl 1 1 5 0 0 0 7
Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein 2 3 2 0 0 0 7
Clinical Genomics Laboratory, Washington University in St. Louis 1 1 4 0 0 0 6
Geisinger Autism and Developmental Medicine Institute, Geisinger Health System 1 1 4 0 0 0 6
Institute of Human Genetics, University of Goettingen 0 4 1 0 0 0 5
Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München 5 0 0 0 0 0 5
Service de Génétique Moléculaire, Hôpital Robert Debré 0 3 0 2 0 0 5
Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics 1 3 1 0 0 0 5
Institute of Human Genetics, University Hospital of Duesseldorf 2 1 2 0 0 0 5
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen 0 0 1 0 4 0 5
Johns Hopkins Genomics, Johns Hopkins University 0 3 1 1 0 0 5
Department of Human Genetics, Hannover Medical School 0 0 5 0 0 0 5
Undiagnosed Diseases Network, NIH 2 2 0 0 0 0 4
Department Of Genetics, Sultan Qaboos University Hospital, Sultan Qaboos University 1 0 3 0 0 0 4
Provincial Medical Genetics Program of British Columbia, University of British Columbia 1 1 2 0 0 0 4
Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet 0 3 0 0 0 0 3
GeneReviews 1 0 0 0 0 2 3
Duke University Health System Sequencing Clinic, Duke University Health System 2 1 0 0 0 0 3
Knight Diagnostic Laboratories, Oregon Health and Sciences University 0 0 3 0 0 0 3
Lupski Lab, Baylor-Hopkins CMG, Baylor College of Medicine 3 0 0 0 0 0 3
Genetics and Molecular Pathology, SA Pathology 0 0 3 0 0 0 3
Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago 1 0 2 0 0 0 3
Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen 1 2 0 0 0 0 3
Génétique des Maladies du Développement, Hospices Civils de Lyon 1 2 0 0 0 0 3
Bezmialem Vakif University, Medical Faculty 1 0 2 0 0 0 3
Reproductive Health Research and Development, BGI Genomics 0 2 0 0 1 0 3
Zotz-Klimas Genetics Lab, MVZ Zotz Klimas 0 0 3 0 0 0 3
Lifecell International Pvt. Ltd 1 2 0 0 0 0 3
Clinical Genetics Laboratory, University Hospital Schleswig-Holstein 2 1 0 0 0 0 3
Developmental and Behavioral Pediatrics, First Affiliated Hospital of Jilin University 1 0 2 0 0 0 3
Institute of Human Genetics, Cologne University 1 0 1 0 0 0 2
Institute of Human Genetics, University of Ulm 2 0 0 0 0 0 2
Division of Human Genetics, Children's Hospital of Philadelphia 2 0 0 0 0 0 2
University of Washington Center for Mendelian Genomics, University of Washington 0 2 0 0 0 0 2
HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology 0 0 2 0 0 0 2
Undiagnosed Diseases Program Translational Research Laboratory, National Institutes of Health 2 0 0 0 0 0 2
Institute for Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin 2 0 0 0 0 0 2
Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego 0 2 0 0 0 0 2
Wangler Lab, Baylor College of Medicine 0 0 2 0 0 0 2
Genomic Medicine Lab, University of California San Francisco 0 1 1 0 0 0 2
Clinical Genetics, University of Leipzig 1 1 0 0 0 0 2
Medical Genetics Laboratory, Tarbiat Modares University 0 2 0 0 0 0 2
Clinical Genomics Laboratory, Stanford Medicine 0 1 1 0 0 0 2
Molecular Genetics Lab, CHRU Brest 1 1 0 0 0 0 2
Comprehensive Medical Genetic Center, Shiraz University of Medical Sciences 2 0 0 0 0 0 2
GenomeConnect - Invitae Patient Insights Network 0 0 0 0 0 2 2
Pediatric Genetics Clinic, Sheba Medical Center 1 1 0 0 0 0 2
DASA 2 0 0 0 0 0 2
Genomics England Pilot Project, Genomics England 0 2 0 0 0 0 2
Pediatric/Medical Genetics, Ministry of Health, Qatif Central Hospital 0 2 0 0 0 0 2
Clinical Laboratory Sciences Program (CLSP), King Saud bin Abdulaziz University for Health Sciences (KSAU-HS) 1 1 0 0 0 0 2
Solve-RD Consortium 0 2 0 0 0 0 2
Dr.Nikuei Genetic Center 1 1 0 0 0 0 2
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine 0 1 0 0 0 0 1
North West Genomic Laboratory Hub, Manchester University NHS Foundation Trust 0 1 0 0 0 0 1
Centre for Inherited Metabolic Diseases, Karolinska University Hospital 1 0 0 0 0 0 1
Counsyl 0 0 1 0 0 0 1
Sema4, Sema4 0 1 0 0 0 0 1
Department of Molecular and Human Genetics, Baylor College of Medicine 1 0 0 0 0 0 1
Institute for Human Genetics and Genomic Medicine, Uniklinik RWTH Aachen 1 0 0 0 0 0 1
Hadassah Hebrew University Medical Center 0 1 0 0 0 0 1
Centre de Biologie Pathologie Génétique, Centre Hospitalier Universitaire de Lille 1 0 0 0 0 0 1
Soonchunhyang University Bucheon Hospital, Soonchunhyang University Medical Center 0 0 1 0 0 0 1
Department of Medical Genetics, National Institute of Health 1 0 0 0 0 0 1
Department of Medical Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences 1 0 0 0 0 0 1
Groupe Hospitalier Pitie Salpetriere, UF Genomique du Developpement, Assistance Publique Hopitaux de Paris 0 1 0 0 0 0 1
Leeds Institute of Biomedical and Clinical Sciences, University of Leeds 1 0 0 0 0 0 1
Centre for Arab Genomic Studies, Sheikh Hamdan Award for Medical Sciences 0 1 0 0 0 0 1
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center 0 0 1 0 0 0 1
Molecular Genetics Laboratory, Faculty of Medicine, Prince of Songkla University, Thailand 0 1 0 0 0 0 1
Molecular Diagnostics Laboratory, M Health Fairview: University of Minnesota 0 1 0 0 0 0 1
Laboratory of Medical Genetics, National & Kapodistrian University of Athens 0 1 0 0 0 0 1
Laboratory of Medical Genetics, University of Torino 1 0 0 0 0 0 1
Genetics and Genomic Medicine Centre, NeuroGen Healthcare, NeuroGen Healthcare 1 0 0 0 0 0 1
Pathology and Clinical Laboratory Medicine, King Fahad Medical City 0 0 0 0 1 0 1
Institute of Human Genetics, Heidelberg University 1 0 0 0 0 0 1
Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn 0 1 0 0 0 0 1
Myelin Disorders Clinic-Children's Medical Center/Medical Genetics Lab-Tarbiat Modares University, Children's Medical Center, Pediatrics Center of Excellence, 0 0 1 0 0 0 1
Molecular Medicine for Neurodegenerative and Neuromuscular Diseases Unit, IRCCS Fondazione Stella Maris 1 0 0 0 0 0 1
Institut de Recherche Interdisciplinaire en Biologie Humaine et Moleculaire, Universite Libre de Bruxelles 0 1 0 0 0 0 1
Institute of Pediatric Research, Children's Hospital of Soochow University, Soochow University 0 1 0 0 0 0 1
Laboratorio de Genética Hospitales Universitarios Virgen de las Nieves y Clínico San Cecilio (Granada, Spain), Hospitales Universitarios Virgen de las Nieves y Clínico San Cecilio (Granada, Spain) 0 1 0 0 0 0 1
Genetics Institute, Tel Aviv Sourasky Medical Center 1 0 0 0 0 0 1
Institute of Human Genetics, University Hospital Muenster 0 1 0 0 0 0 1
Dr. med. U. Finckh, Human Genetics, Eurofins MVZ 0 0 1 0 0 0 1
Medical Genetics Laboratory, Gulhane Training and Research Hospital 0 0 1 0 0 0 1
Paris Brain Institute, Inserm - ICM 1 0 0 0 0 0 1
Kids Neuroscience Centre, Sydney Children's Hospitals Network 1 0 0 0 0 0 1
Institute of Human Genetics, Clinical Exome/Genome Diagnostics Group, University Hospital Bonn 0 0 1 0 0 0 1
Suma Genomics 0 0 1 0 0 0 1
Service de Biologie Medicale, CIUSSS du Saguenay-Lac-Saint-Jean 1 0 0 0 0 0 1
Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax 1 0 0 0 0 0 1
Molecular Genetics, Royal Melbourne Hospital 0 0 0 0 1 0 1
Department of Laboratory Medicine and Genetics, Samsung Medical Center 0 1 0 0 0 0 1
Department of Biochemistry and Molecular Biology, Faculty of Medicine, Al-Neelain University 1 0 0 0 0 0 1
Laboratory Cellgenetics, GMDL Cellgenetics 1 0 0 0 0 0 1
Institute of Immunology and Genetics Kaiserslautern 0 1 0 0 0 0 1
Molecular Genetics and NGS Laboratory, Hospital Fundacion Valle Del Lili 1 0 0 0 0 0 1
Department Of Human Genetics, Institute Of Clinical And Translational Research, Biomedical Research Center, Slovak Academy Of Sciences 1 0 0 0 0 0 1
Jpch, Dept Of Neurology, Jiangxi Provincial Children’s Hospital 1 0 0 0 0 0 1
MVZ Medizinische Genetik Mainz 0 0 1 0 0 0 1
Diagnostics Centre, Carl Von Ossietzky University Oldenburg 0 1 0 0 0 0 1
SC Genetica Medica, ASST Santi Paolo e Carlo 0 1 0 0 0 0 1
Clinical Genetics, University Hospital Uppsala 0 1 0 0 0 0 1

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