ClinVar Miner

Variants studied for non-syndromic X-linked intellectual disability

Included ClinVar conditions (53):
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
413 250 1297 1491 611 31 3994

Gene and significance breakdown #

Total genes and gene combinations: 78
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Gene or gene combination pathogenic likely pathogenic uncertain significance likely benign benign not provided total
HCFC1 6 1 115 672 255 0 1035
IQSEC2 105 34 316 362 126 2 918
ARX 28 11 171 266 21 1 493
RPS6KA3 27 10 40 60 50 0 185
DDX3X 83 70 24 4 1 16 174
BRWD3 12 12 89 8 50 0 169
ARX, LOC109610631 10 1 44 61 8 1 123
CLCN4 14 16 50 4 0 0 81
USP9X 4 14 47 5 1 3 73
FRMPD4 5 10 41 3 2 0 60
IL1RAPL1 7 8 26 1 16 0 57
ZNF711 5 3 30 2 13 3 55
PAK3 5 10 25 1 13 0 53
AFF2 4 2 36 3 5 0 50
RAB39B 3 1 23 0 10 0 37
ACSL4 5 6 22 2 2 0 36
OGT 7 4 24 0 0 1 35
DLG3 8 5 19 0 1 0 32
HCFC1, LOC130068842 0 0 4 14 12 0 30
KIF4A 5 1 13 1 5 0 25
RLIM 7 5 13 1 0 0 24
GDI1 7 4 7 2 1 0 21
SLC9A7 1 1 13 0 3 0 17
SYN1 6 1 8 0 1 1 17
SYP 4 1 11 0 0 0 16
USP27X 6 4 9 0 0 0 16
STEEP1 3 2 7 0 2 0 14
KLHL15 2 0 10 0 0 0 12
ARHGEF6 0 0 6 5 0 0 11
FTSJ1 5 0 5 0 0 1 11
LOC101928335, MID2 2 3 5 0 0 0 9
TSPAN7 3 0 2 2 2 2 9
POF1B, ZNF711 0 0 0 4 6 0 8
SLITRK2 6 0 2 0 0 0 8
LOC130068032, RPS6KA3 0 0 2 3 1 0 6
ZNF81 0 0 6 0 0 0 6
MID2 0 0 4 0 1 0 5
ZMYM3 3 2 1 0 0 0 5
ARX, PCYT1B, PDK3, POLA1 1 0 2 0 0 0 3
HUWE1 1 0 2 0 0 0 3
IQSEC2, SMC1A 0 0 2 1 0 0 3
LOC130068561, PAK3 0 0 2 0 1 0 3
LOC130068896, RAB39B 0 0 3 0 0 0 3
ADGRG2, BCLAF3, BEND2, CDKL5, EIF1AX, MAP3K15, MAP7D2, NHS, PDHA1, PHKA2, PPEF1, RAI2, RPS6KA3, RS1, SCML1, SCML2, SH3KBP1 1 0 1 0 0 0 2
ARHGEF6, LOC130068760 0 0 1 1 0 0 2
HSD17B10, IQSEC2, RIBC1, SMC1A 0 0 2 0 0 0 2
PTCHD1 1 1 0 0 0 0 2
SMARCA1 0 2 0 0 0 0 2
ZDHHC15 1 0 1 0 0 0 2
ZNF41 0 0 2 0 0 0 2
ZNF674 0 0 1 0 1 0 2
AFF2, FRAXE 1 0 0 0 0 0 1
AGTR2 0 0 0 1 0 0 1
ARHGAP6, FRMPD4, LOC113845784, LOC129391294, LOC130067941, LOC130067942, MSL3 0 0 1 0 0 0 1
ARX, LOC110120595, LOC110120597, POLA1 0 0 1 0 0 0 1
ARX, POLA1 0 1 0 0 0 0 1
ATP6AP1, ATP6AP1-DT, CTAG1A, DNASE1L1, EMD, FAM223A, FAM3A, FAM50A, FLNA, G6PD, GDI1, IKBKG, LAGE3, LOC107181288, LOC107988021, LOC107988022, LOC107988032, LOC107988033, LOC108281126, LOC121627985, LOC121853072, LOC129929052, LOC130068856, LOC130068857, LOC130068858, LOC130068859, LOC130068860, LOC130068861, LOC130068862, LOC130068863, LOC130068864, LOC130068865, LOC130068866, LOC130068867, LOC130068868, LOC130068869, LOC130068870, LOC130068871, LOC130068872, LOC130068873, LOC130068874, LOC130068875, LOC130068876, LOC130068877, LOC130068878, LOC130068879, LOC130068880, LOC130068881, MIR6858, PLXNA3, RPL10, SLC10A3, SNORA70, TAFAZZIN, UBL4A 1 0 0 0 0 0 1
ATP6AP1, FAM50A, GDI1 0 1 0 0 0 0 1
CASK, DDX3X, GPR34, GPR82, LOC113875025, LOC126863241, LOC130068160, LOC130068161, LOC130068162, LOC130068163, LOC130068164, LOC130068165, LOC130068166, LOC130068167, LOC130068168, LOC130068169, LOC130068170, LOC130068171, LOC130068172, LOC130068173, NYX 1 0 0 0 0 0 1
CENPT, THAP11 0 1 0 0 0 0 1
CSTF2 1 0 0 0 0 0 1
FAM120C, FGD1, HSD17B10, HUWE1, IQSEC2, KDM5C, MIR98, MIRLET7F2, PHF8, RIBC1, SMC1A, TSR2, WNK3 0 0 1 0 0 0 1
FGF13 1 0 0 0 0 0 1
FLNA, HCFC1, IRAK1, MECP2, NAA10, OPN1LW, OPN1MW, OPN1MW2, RENBP, TEX28, TKTL1, TMEM187 0 0 1 0 0 0 1
GPR173, HSD17B10, HUWE1, IQSEC2, KDM5C, MIR98, MIRLET7F2, PHF8, RIBC1, SMC1A, TSPYL2 1 0 0 0 0 0 1
HSD17B10, HUWE1, IQSEC2, KDM5C, MIR98, MIRLET7F2, RIBC1, SMC1A 0 0 1 0 0 0 1
HSD17B10, HUWE1, IQSEC2, RIBC1, SMC1A 0 0 0 1 0 0 1
IL1RAPL1, ZNF611 1 0 0 0 0 0 1
IQSEC2, KDM5C 1 0 0 0 0 0 1
KLHL15, LOC114022706 0 0 1 0 0 0 1
LOC130068281, SYP 0 1 0 0 0 0 1
MECP2 1 0 0 0 0 0 1
NPHP1 0 0 0 0 1 0 1
NTF4 0 0 0 1 0 0 1
PHIP 0 0 1 0 0 0 1
REN 0 0 1 0 0 0 1
SERPINA1 1 0 0 0 0 0 1
SLC25A43, SLC25A5, STEEP1 0 1 0 0 0 0 1

Submitter and significance breakdown #

Total submitters: 156
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Submitter pathogenic likely pathogenic uncertain significance likely benign benign not provided total
Labcorp Genetics (formerly Invitae), Labcorp 129 18 587 1415 470 0 2619
Illumina Laboratory Services, Illumina 1 5 131 13 104 0 252
OMIM 134 0 5 0 0 0 139
Revvity Omics, Revvity 5 8 105 0 0 0 118
Baylor Genetics 12 15 86 0 0 0 113
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute 14 6 48 2 0 0 70
Institute of Human Genetics, University of Leipzig Medical Center 8 18 30 2 0 0 58
Fulgent Genetics, Fulgent Genetics 0 3 20 26 1 0 50
PreventionGenetics, part of Exact Sciences 0 0 18 17 3 0 38
Genome-Nilou Lab 0 0 0 0 38 0 38
New York Genome Center 0 2 29 0 0 0 31
Gene2Care/ Palmer Lab, University of New South Wales 3 6 22 0 0 0 31
3billion 6 12 7 4 0 0 29
Mendelics 14 1 7 4 1 0 27
Centre for Mendelian Genomics, University Medical Centre Ljubljana 1 2 18 2 1 0 24
Neuberg Centre For Genomic Medicine, NCGM 3 4 15 0 0 0 22
Center For Human Genetics And Laboratory Diagnostics, Dr. Klein, Dr. Rost And Colleagues 5 2 14 0 0 0 21
Juno Genomics, Hangzhou Juno Genomics, Inc 3 3 13 0 0 0 19
Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center 5 11 1 0 0 0 17
Equipe Genetique des Anomalies du Developpement, Université de Bourgogne 4 9 2 2 0 0 17
Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein 1 1 15 0 0 0 17
Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center 0 2 12 1 0 0 15
Women's Health and Genetics/Laboratory Corporation of America, LabCorp 5 9 0 0 0 0 14
HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology 3 2 8 1 0 0 14
Pittsburgh Clinical Genomics Laboratory, University of Pittsburgh Medical Center 0 2 12 0 0 0 14
MGZ Medical Genetics Center 0 5 8 0 0 0 13
Génétique des Maladies du Développement, Hospices Civils de Lyon 8 4 1 0 0 0 13
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories 0 1 2 2 7 0 12
GeneReviews 0 0 0 0 0 11 11
Institute for Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin 2 2 7 0 0 0 11
Institute of Human Genetics, Clinical Exome/Genome Diagnostics Group, University Hospital Bonn 0 2 9 0 0 0 11
GenomeConnect - Brain Gene Registry 0 0 0 0 0 11 11
Centogene AG - the Rare Disease Company 0 1 9 0 0 0 10
Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München 7 3 0 0 0 0 10
Genomic Research Center, Shahid Beheshti University of Medical Sciences 1 2 7 0 0 0 10
Centre de Biologie Pathologie Génétique, Centre Hospitalier Universitaire de Lille 7 3 0 0 0 0 10
Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard 4 3 1 1 1 0 10
Molecular Genetics Lab, CHRU Brest 3 3 4 0 0 0 10
Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen 2 6 1 0 0 0 9
Laboratory of Medical Genetics, University of Torino 2 2 5 0 0 0 9
MVZ Medizinische Genetik Mainz 0 3 6 0 0 0 9
Hadassah Hebrew University Medical Center 1 3 4 0 0 0 8
Laboratory of Medical Genetics, National & Kapodistrian University of Athens 3 1 3 1 0 0 8
Institute for Genomic Medicine (IGM) Clinical Laboratory, Nationwide Children's Hospital 4 2 1 0 0 0 7
GenomeConnect, ClinGen 0 0 0 0 0 7 7
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen 0 0 0 5 1 0 6
Department of Genetics, Rouen University Hospital, Normandy Center for Genomic and Personalized Medicine 1 5 0 0 0 0 6
Daan van Aalten Lab, University of Dundee 5 0 1 0 0 0 6
Institute of Human Genetics, University of Goettingen 0 3 2 0 0 0 5
Molecular Genetics Laboratory, BC Children's and BC Women's Hospitals 3 2 0 0 0 0 5
Mayo Clinic Laboratories, Mayo Clinic 0 1 4 0 0 0 5
Service de Génétique Moléculaire, Hôpital Robert Debré 0 1 3 1 0 0 5
Medical Genetic Institute of Henan Province, Henan Provincial People’s Hospital 1 0 3 0 1 0 5
Genomic Medicine Lab, University of California San Francisco 2 0 3 0 0 0 5
Institute of Immunology and Genetics Kaiserslautern 1 3 1 0 0 0 5
Genetic Services Laboratory, University of Chicago 4 0 0 0 0 0 4
Clinical Genomics Laboratory, Washington University in St. Louis 0 0 4 0 0 0 4
Lupski Lab, Baylor-Hopkins CMG, Baylor College of Medicine 3 0 1 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
Daryl Scott Lab, Baylor College of Medicine 2 1 1 0 0 0 4
Genetics and Molecular Pathology, SA Pathology 1 1 2 0 0 0 4
Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego 2 2 0 0 0 0 4
Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago 0 0 4 0 0 0 4
Biochemical Molecular Genetic Laboratory, King Abdulaziz Medical City 0 1 3 0 0 0 4
Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn 2 1 1 0 0 0 4
Institute for Human Genetics, University Hospital Essen 2 1 1 0 0 0 4
Zotz-Klimas Genetics Lab, MVZ Zotz Klimas 0 0 4 0 0 0 4
Clinical Genomics Laboratory, Stanford Medicine 0 2 2 0 0 0 4
Clinical Genetics Laboratory, University Hospital Schleswig-Holstein 1 0 3 0 0 0 4
Solve-RD Consortium 0 4 0 0 0 0 4
Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet 1 0 2 0 0 0 3
Institute of Human Genetics, FAU Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg 1 1 0 1 0 0 3
Institute for Human Genetics and Genomic Medicine, Uniklinik RWTH Aachen 0 2 1 0 0 0 3
Duke University Health System Sequencing Clinic, Duke University Health System 0 2 1 0 0 0 3
Laboratory of Human Genetics, Universidade de São Paulo 2 0 1 0 0 0 3
Dobyns Lab, Seattle Children's Research Institute 2 1 0 0 0 0 3
Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics 0 0 3 0 0 0 3
Undiagnosed Diseases Network, NIH 1 2 0 0 0 0 3
Johns Hopkins Genomics, Johns Hopkins University 0 2 1 0 0 0 3
Pediatric Genetics Clinic, Sheba Medical Center 2 1 0 0 0 0 3
Suma Genomics 1 2 0 0 0 0 3
Genomics England Pilot Project, Genomics England 0 3 0 0 0 0 3
Athena Diagnostics 0 0 0 0 2 0 2
Center for Human Genetics, Inc, Center for Human Genetics, Inc 0 0 2 0 0 0 2
Institute of Human Genetics, Cologne University 0 2 0 0 0 0 2
Strand Center for Genomics and Personalized Medicine, Strand Life Sciences Pvt Ltd 0 0 2 0 0 0 2
Center for Human Genetics, University of Leuven 0 2 0 0 0 0 2
Institute of Human Genetics, University Hospital of Duesseldorf 1 0 1 0 0 0 2
Hunter Genetics General Clinical Genetics Service, Hunter Genetics 0 1 1 0 0 0 2
Neurogenetics Research Program, University of Adelaide 1 0 0 0 1 0 2
Geisinger Autism and Developmental Medicine Institute, Geisinger Health System 1 1 0 0 0 0 2
Seattle Children's Hospital Molecular Genetics Laboratory, Seattle Children's Hospital 2 0 0 0 0 0 2
Molecular Diagnostics Laboratory, M Health Fairview: University of Minnesota 1 1 0 0 0 0 2
UNC Molecular Genetics Laboratory, University of North Carolina at Chapel Hill 0 0 2 0 0 0 2
Diagnostics Services (NGS), CSIR - Centre For Cellular And Molecular Biology 0 1 1 0 0 0 2
Center of Excellence for Medical Genomics, Chulalongkorn University 1 1 0 0 0 0 2
Diagnostic Genetics, Severance Hospital, Yonsei University College of Medicine 1 1 0 0 0 0 2
Dr. med. U. Finckh, Human Genetics, Eurofins MVZ 0 0 2 0 0 0 2
GenomeConnect - Simons Searchlight 1 1 0 0 0 0 2
Developmental and Behavioral Pediatrics, First Affiliated Hospital of Jilin University 1 0 1 0 0 0 2
DECIPHERD-UDD, Universidad del Desarrollo 0 1 1 0 0 0 2
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine 1 0 0 0 0 0 1
Hehr Laboratory, Center for Human Genetics Regensburg 0 0 1 0 0 0 1
Randwick Genomics Laboratory, Prince of Wales Hospital Sydney, Australia, New South Wales Health Pathology 0 1 0 0 0 0 1
Intergen, Intergen Genetics and Rare Diseases Diagnosis Center 0 1 0 0 0 0 1
Institute of Human Genetics, University of Ulm 0 1 0 0 0 0 1
Department of Clinical Science, University of Bergen 0 1 0 0 0 0 1
UCLA Clinical Genomics Center, UCLA 0 1 0 0 0 0 1
Shaikh Laboratory, University of Colorado 0 1 0 0 0 0 1
Serv. Biochemistry and Molecular genetics, Hospital Clinic de Barcelona, Hospital Clínic de Barcelona 1 0 0 0 0 0 1
Knight Diagnostic Laboratories, Oregon Health and Sciences University 1 0 0 0 0 0 1
Center of Genomic medicine, Geneva, University Hospital of Geneva 1 0 0 0 0 0 1
NeuroMeGen, Hospital Clinico Santiago de Compostela 0 1 0 0 0 0 1
Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics 1 0 0 0 0 0 1
Molecular Genetics Department, Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology 0 1 0 0 0 0 1
Bioscientia Institut fuer Medizinische Diagnostik GmbH, Sonic Healthcare 0 0 1 0 0 0 1
Reutter Lab, Institute of Human Genetics, University Hospital Bonn 0 0 1 0 0 0 1
Center for Molecular Medicine, Children’s Hospital of Fudan University 0 1 0 0 0 0 1
KK Women’s and Children’s Hospital 0 0 0 1 0 0 1
SIB Swiss Institute of Bioinformatics 0 1 0 0 0 0 1
TIDEX, University of British Columbia 0 0 1 0 0 0 1
Laboratoire de Génétique Moléculaire, CHU Bordeaux 0 1 0 0 0 0 1
Institute for Genomic Medicine, Nationwide Children's Hospital 0 1 0 0 0 0 1
Genetics Division, Universidade Federal de Sao Paulo 1 0 0 0 0 0 1
Laboratory of Functional Genomics, Research Centre for Medical Genetics 0 1 0 0 0 0 1
Tehran Medical Genetics Laboratory 0 1 0 0 0 0 1
Department Of Genetics, Sultan Qaboos University Hospital, Sultan Qaboos University 1 0 0 0 0 0 1
HUSP Clinical Genetics Laboratory, Hospital Universitario San Pedro De Logroño (HUSP) 0 1 0 0 0 0 1
Kids Research, The Children's Hospital at Westmead 0 1 0 0 0 0 1
Institute of Human Genetics, Heidelberg University 1 0 0 0 0 0 1
Biochemistry Laboratory of CDMU, Chengde Medical University 0 1 0 0 0 0 1
Medical Genome Center, National Center of Neurology and Psychiatry 0 1 0 0 0 0 1
Al Jalila Children’s Genomics Center, Al Jalila Childrens Speciality Hospital 0 0 1 0 0 0 1
GenomeConnect-Association for Creatine Deficiencies, Association for Creatine Deficiencies 0 0 0 0 0 1 1
Service de Biochimie Médicale et Biologie Moléculaire, CHU Clermont-Ferrand 1 0 0 0 0 0 1
Institute of Human Genetics, University Hospital Muenster 1 0 0 0 0 0 1
Medicover Genetics GmbH, Medicover Humangenetik Berlin-Lichtenberg MVZ 0 1 0 0 0 0 1
Molecular Genetics Laboratory, Motol Hospital 0 1 0 0 0 0 1
Biological Sciences, International Islamic University, Islamabad 1 0 0 0 0 0 1
Pars Genome Lab 0 0 0 0 1 0 1
Lifecell International Pvt. Ltd 0 1 0 0 0 0 1
National Institute of Neuroscience, National Center of Neurology and Psychiatry 1 0 0 0 0 0 1
Kids Neuroscience Centre, Sydney Children's Hospitals Network 0 0 1 0 0 0 1
GenomeConnect - Invitae Patient Insights Network 0 0 0 0 0 1 1
DASA 1 0 0 0 0 0 1
Department of Human Genetics, Hannover Medical School 0 0 1 0 0 0 1
Spanish Undiagnosed Rare Disease Program-IIER, Instituto de Salud Carlos III 1 0 0 0 0 0 1
Laboratory of genome editing, Research Centre for Medical Genetics 1 0 0 0 0 0 1
Clinical Laboratory Sciences Program (CLSP), King Saud bin Abdulaziz University for Health Sciences (KSAU-HS) 1 0 0 0 0 0 1
Rare Genetic Disease Lab, Dept of Zoology, Government Postgraduate College Dargai Malakand, Higher Education Govt. of Khyber Pakhtunkhwa 0 0 1 0 0 0 1
Payam Genetics Center, General Welfare Department of North Khorasan Province 1 0 0 0 0 0 1
Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL) 0 0 1 0 0 0 1
Breakthrough Genomics, Breakthrough Genomics 1 0 0 0 0 0 1
Pediatric Lab, Suzhou Municipal Hospital 0 0 1 0 0 0 1
Dr.Nikuei Genetic Center 0 0 0 0 1 0 1
Research Institute of Medical Genetics, Tomsk National Research Medical Center of Russian Academy of Sciences 1 0 0 0 0 0 1

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