ClinVar Miner

Variants studied for congenital hypogonadotropic hypogonadism

Included ClinVar conditions (97):
Minimum submission review status: Collection method:
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Gene type:
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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
971 418 2776 533 545 9 4942

Gene and significance breakdown #

Total genes and gene combinations: 113
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Gene or gene combination pathogenic likely pathogenic uncertain significance likely benign benign not provided total
CHD7 226 55 364 87 74 1 774
BBS10 61 73 125 35 17 0 271
BBS2 42 44 119 30 22 0 223
BBS9 26 4 130 32 40 0 211
BBS12 34 30 107 29 28 0 196
POLR3A 26 1 102 24 40 0 191
ASTN2, TRIM32 13 1 151 19 9 0 185
RAB3GAP2 2 3 125 37 21 1 179
BBS1, ZDHHC24 31 26 83 23 14 1 161
CEP290 12 3 115 6 19 0 155
BBS4 27 12 75 15 28 0 145
WDPCP 5 2 106 22 15 0 135
DCAF17 10 3 79 11 30 0 130
MKKS 23 3 82 9 18 0 129
BBS7 22 10 83 6 15 0 127
GNRHR 19 1 72 8 17 0 117
SDCCAG8 11 6 74 16 11 0 109
MKS1 4 23 68 8 8 0 105
SEMA3E 1 0 69 15 13 0 98
LOC101929710, PCSK1 5 2 77 6 4 0 94
BBS1 29 26 34 13 4 1 93
TTC8 4 2 63 14 12 0 84
LHX3 9 0 63 7 3 0 81
NR0B1 69 3 5 0 3 0 77
LEP 2 1 62 6 3 0 74
LEPR 4 0 56 6 7 0 73
PROP1 13 24 30 1 9 0 71
POLR3B 10 4 29 8 8 0 59
BBS5 18 7 16 5 9 0 55
ARL6 12 3 26 6 4 0 50
ACBD6, LHX4 5 0 14 7 11 1 38
HBB, LOC106099062, LOC107133510 30 1 7 0 2 1 38
POU1F1 17 3 15 0 1 1 36
POLR1C 30 1 4 0 0 0 32
OTX2 1 0 22 3 5 0 31
LOC100287944, POLR3B 0 1 23 0 5 0 29
HESX1 10 1 13 5 2 0 27
MAGEL2 17 0 5 1 0 1 24
LHX4 2 0 11 5 4 0 21
SMCHD1 20 0 0 0 0 0 20
HBB, LOC107133510, LOC110006319 10 2 6 0 0 0 17
DCAF17, METTL8 2 0 12 1 0 0 14
PNPLA6 10 2 2 0 0 0 14
RNF216 8 1 2 0 0 0 11
FGFR1 1 8 0 0 0 0 9
AKT3, SDCCAG8 0 0 8 0 1 0 8
C12orf29, CEP290 0 0 7 1 0 0 8
TMEM67 3 2 2 0 0 0 7
LEPR, LEPROT 0 0 4 1 1 0 6
BBS4, HIGD2B 0 0 2 0 3 0 5
C8orf37 2 2 1 0 0 0 5
CHMP2B, POU1F1 0 0 0 0 5 0 5
LZTFL1 3 1 1 0 0 0 5
SOX3 3 1 1 0 0 0 5
BBIP1 3 0 1 0 0 0 4
HS6ST1 0 1 1 3 0 0 4
SIM1 0 0 4 0 0 0 4
IFT74 2 1 0 0 0 1 3
RBM28 2 1 0 0 0 0 3
​intergenic 1 0 1 0 0 0 2
ATP10A, GABRA5, GABRB3, GABRG3, GOLGA6L2, HERC2, IPW, MAGEL2, MKRN3, NDN, NPAP1, OCA2, PWAR1, PWAR4, PWAR5, PWAR6, PWARSN, PWRN1, PWRN2, SNORD115-1, SNORD116-1, SNRPN, SNURF, UBE3A 2 0 0 0 0 0 2
ATP10A, GABRA5, GABRB3, GABRG3, HERC2, IPW, MAGEL2, MKRN3, NDN, NPAP1, OCA2, PWAR1, PWAR4, PWAR5, PWAR6, PWARSN, PWRN1, PWRN2, SNORD115-1, SNORD116-1, SNRPN, SNURF, UBE3A 2 0 0 0 0 0 2
IFT27, LOC105373021 2 0 0 0 0 0 2
POLR3A, RPS24 0 0 2 0 0 0 2
RALGAPB 0 2 0 0 0 0 2
WDR11 0 0 2 0 0 0 2
AKT3, CEP170, LINC01347, LOC110120698, MIR4677, PLD5, SDCCAG8 1 0 0 0 0 0 1
ALMS1 0 1 0 0 0 0 1
ANOS1 0 1 0 0 0 0 1
APBA2, ARHGAP11A, ARHGAP11B, ATP10A, CHRFAM7A, CHRNA7, CYFIP1, FAM189A1, FAN1, GABRA5, GABRB3, GABRG3, GOLGA6L1, GOLGA6L2, GOLGA8H, GOLGA8J, GOLGA8M, GOLGA8N, GOLGA8O, HERC2, IPW, KLF13, MAGEL2, MIR211, MKRN3, MTMR10, NDN, NIPA1, NIPA2, NPAP1, NSMCE3, OCA2, OR4M2, OR4N4, OTUD7A, POTEB, POTEB2, PWAR1, PWAR4, PWAR5, PWAR6, PWARSN, PWRN1, PWRN2, SNORD115-1, SNORD116-1, SNRPN, SNURF, TJP1, TRPM1, TUBGCP5, UBE3A 1 0 0 0 0 0 1
ARL6, CRYBG3 0 1 0 0 0 0 1
ATM 0 0 1 0 0 0 1
ATM, C11orf65 1 0 0 0 0 0 1
ATP10A, CYFIP1, GABRA5, GABRB3, GABRG3, GOLGA6L2, GOLGA8M, HERC2, IPW, MAGEL2, MKRN3, NDN, NIPA1, NIPA2, NPAP1, OCA2, PWAR1, PWAR4, PWAR5, PWAR6, PWARSN, PWRN1, PWRN2, SNORD115-1, SNORD116-1, SNRPN, SNURF, TUBGCP5, UBE3A 1 0 0 0 0 0 1
BBS1, DPP3, ZDHHC24 0 1 0 0 0 0 1
BBS9, RP9 0 0 1 0 0 0 1
CCDC141 0 0 1 0 0 0 1
CCDC28B 0 0 1 0 0 0 1
CEP19 1 0 0 0 0 0 1
CRB1 1 0 0 0 0 0 1
DMD, FTHL17, GK, IL1RAPL1, LOC108410393, LOC113875019, LOC116309149, LOC116309150, MAGEB1, MAGEB2, MAGEB3, MAGEB4, MIR3915, MIR4666B, MIR6134, NR0B1, TAB3, TASL 1 0 0 0 0 0 1
DMD, FTHL17, GK, LOC108410393, LOC113875019, LOC116309149, LOC116309150, MAGEB1, MAGEB2, MAGEB3, MAGEB4, NR0B1, TAB3, TASL 1 0 0 0 0 0 1
DMXL2 1 0 0 0 0 0 1
EML5, PTPN21, SPATA7, TTC8, ZC3H14 0 0 1 0 0 0 1
EP300 0 1 0 0 0 0 1
GLI1 0 0 1 0 0 0 1
HBB, LOC106099062, LOC107133510, LOC110006319 1 0 0 0 0 0 1
HERC2 0 0 1 0 0 0 1
HTR2B, PSMD1 0 0 1 0 0 0 1
IFT172 0 1 0 0 0 0 1
IFT27 1 0 0 0 0 0 1
IL1RAPL1, LOC108410393, LOC113875019, LOC116309149, LOC116309150, MAGEB1, MAGEB2, MAGEB3, MAGEB4, MIR4666B, NR0B1, TASL 1 0 0 0 0 0 1
IQSEC2 1 0 0 0 0 0 1
KCNAB2, NPHP4 0 1 0 0 0 0 1
KDM6A 0 1 0 0 0 0 1
KMT2D 0 1 0 0 0 0 1
LEP, LOC106728418 0 0 0 1 0 0 1
LOC108281134, SOX3 0 0 0 1 0 0 1
LOC108410393, NR0B1 1 0 0 0 0 0 1
MTOR 0 0 1 0 0 0 1
NDN 0 0 1 0 0 0 1
NPHP1 1 0 0 0 0 0 1
OPA1 0 0 1 0 0 0 1
PROKR2 0 1 0 0 0 0 1
PUF60 0 1 0 0 0 0 1
RAB3GAP1 1 0 0 0 0 0 1
RERE 0 1 0 0 0 0 1
RYR1 0 0 1 0 0 0 1
SYNE2 0 0 1 0 0 0 1
TAC3 0 1 0 0 0 0 1
TACR3 0 1 0 0 0 0 1
TNFRSF1A 1 0 0 0 0 0 1
TRAPPC3 0 1 0 0 0 0 1

Submitter and significance breakdown #

Total submitters: 117
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Submitter pathogenic likely pathogenic uncertain significance likely benign benign not provided total
Illumina Clinical Services Laboratory,Illumina 10 4 1605 193 337 0 2149
Invitae 325 56 1043 305 254 0 1983
Counsyl 25 194 111 9 1 0 340
OMIM 273 0 0 0 0 0 273
Fulgent Genetics,Fulgent Genetics 40 8 46 1 0 0 95
Baylor Genetics 56 3 4 0 0 0 63
GeneReviews 47 0 0 0 16 0 63
Genetic Services Laboratory, University of Chicago 41 7 13 0 0 0 61
Integrated Genetics/Laboratory Corporation of America 28 18 0 2 2 0 50
Laboratory of Medical Genetics, INSERM 48 0 0 0 0 0 48
Mendelics 15 2 8 13 9 0 47
Division of Genomic Diagnostics,The Children's Hospital of Philadelphia 26 3 6 0 6 0 41
Institute of Human Genetics,Klinikum rechts der Isar 38 3 0 0 0 0 41
DNA and Cytogenetics Diagnostics Unit,Erasmus Medical Center 1 1 1 9 27 0 39
MyeliNeuroGene Lab,McGill University Health Center Research Institute 35 0 0 0 0 0 35
Genome Diagnostics Laboratory,University Medical Center Utrecht 4 0 0 3 27 0 34
Diagnostic Laboratory, Department of Genetics,University Medical Center Groningen 1 0 0 2 25 0 28
Developmental Genetics Unit,King Faisal Specialist Hospital & Research Centre 16 7 1 1 0 0 25
Genomic Research Center, Shahid Beheshti University of Medical Sciences 6 5 13 1 0 0 25
Clinical Molecular Genetics Laboratory,Johns Hopkins All Children's Hospital 18 0 5 1 0 0 24
Harvard Reproductive Endocrine Science Center,Massachusetts General Hospital 20 0 0 0 0 0 20
University of Washington Center for Mendelian Genomics, University of Washington 0 20 0 0 0 0 20
Center for Human Genetics, Inc,Center for Human Genetics, Inc 5 6 5 2 1 0 19
Genome Diagnostics Laboratory,VU University Medical Center Amsterdam 1 0 0 4 13 0 18
Center for Human Disease Modeling,Duke University Medical Center 1 15 0 0 0 0 16
SBielas Lab, Department of Human Genetics,University of Michigan 15 0 0 0 0 0 15
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine 8 4 1 0 0 0 13
Chan Lab,Boston Children's Hospital 0 13 0 0 0 0 13
Centre for Mendelian Genomics,University Medical Centre Ljubljana 6 2 5 0 0 0 13
Sharon lab,Hadassah-Hebrew University Medical Center 9 4 0 0 0 0 13
HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology 11 0 1 0 0 0 12
MAGI'S LAB - Medical Genetics Laboratory, MAGI GROUP 6 3 3 0 0 0 12
Endocrinology Clinic, Seth G.S. Medical College 6 4 0 0 0 0 10
Biochemical Molecular Genetic Laboratory,King Abdulaziz Medical City 2 5 3 0 0 0 10
Department of Medical Genetics, Faculty of Medicine,Ege University 9 0 0 0 0 0 9
Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego 8 1 0 0 0 0 9
Athena Diagnostics Inc 0 0 0 0 8 0 8
Molecular Genetics Laboratory,Institute for Ophthalmic Research 8 0 0 0 0 0 8
GenomeConnect, ClinGen 0 0 0 0 0 8 8
Laboratoire de Genetique Biologique, CHU de Poitiers 7 1 0 0 0 0 8
Medical Genetics Laboratory, Kennedy Center,Juliane Marie Center, Rigshospitalet 3 3 1 0 0 0 7
Centre for Genomic Medicine, Manchester,Central Manchester University Hospitals 7 0 0 0 0 0 7
Department of Medical Genetics,Sanjay Gandhi Post Graduate Institute of Medical Sciences 2 5 0 0 0 0 7
Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago 0 0 7 0 0 0 7
Broad Institute Rare Disease Group,Broad Institute 3 3 1 0 0 0 7
Human Genetics - Radboudumc,Radboudumc 4 0 2 0 0 0 6
Tolun Lab, Human Genetics Laboratory,Bogazici University 1 0 5 0 0 0 6
Molecular Diagnostics Laboratory, M Health: University of Minnesota 4 2 0 0 0 0 6
SIB Swiss Institute of Bioinformatics 0 1 1 1 2 0 5
Institute for Genomic Medicine (IGM) Clinical Laboratory,Nationwide Children's Hospital 2 3 0 0 0 0 5
Myriad Women's Health, Inc. 5 0 0 0 0 0 5
Institute of Human Genetics,University of Goettingen 2 2 0 0 0 0 4
Victorian Clinical Genetics Services,Murdoch Childrens Research Institute 2 2 0 0 0 0 4
SN ONGC Dept of Genetics and Molecular biology Vision Research Foundation 4 0 0 0 0 0 4
UCLA Clinical Genomics Center, UCLA 2 2 0 0 0 0 4
Division of Human Genetics,Children's Hospital of Philadelphia 2 1 1 0 0 0 4
Lupski Lab, Baylor-Hopkins CMG, Baylor College of Medicine 3 0 1 0 0 0 4
Hadassah Hebrew University Medical Center 0 4 0 0 0 0 4
Department of Pediatrics and Neonatology,Nagoya City University Graduate School of Medical Sciences 4 0 0 0 0 0 4
Soonchunhyang University Bucheon Hospital,Soonchunhyang University Medical Center 0 2 2 0 0 0 4
Bioscientia Institut fuer Medizinische Diagnostik GmbH,Sonic Healthcare 2 2 0 0 0 0 4
Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn 4 0 0 0 0 0 4
Institute of Human Genetics,Cologne University 2 0 1 0 0 0 3
Mayo Clinic Genetic Testing Laboratories,Mayo Clinic 0 0 3 0 0 0 3
Shenzhen Institute of Pediatrics,Shenzhen Children's Hospital 1 2 0 0 0 0 3
Center for Human Genetics and Laboratory Diagnostics, Dr. Klein, Dr. Rost and Colleagues 2 0 1 0 0 0 3
Undiagnosed Diseases Network,NIH 1 0 2 0 0 0 3
Myelin Disorders Clinic-Children's Medical Center/Medical Genetics Lab-Tarbiat Modares University, Children's Medical Center, Pediatrics Center of Excellence, 0 0 3 0 0 0 3
Shaikh Laboratory, University of Colorado 0 2 0 0 0 0 2
Laboratory of Molecular Oncology,N.N. Petrov Institute of Oncology 1 0 1 0 0 0 2
Center of Genomic medicine, Geneva,University Hospital of Geneva 2 0 0 0 0 0 2
Talkowski Laboratory, Center for Human Genetic Research,Massachusetts General Hospital 1 0 1 0 0 0 2
GenePathDx,Causeway Health Care Private Ltd 0 2 0 0 0 0 2
Equipe Genetique des Anomalies du Developpement, Université de Bourgogne 2 0 0 0 0 0 2
CHLA Center for Personalized Medicine,Children's Hospital, Los Angeles 0 0 2 0 0 0 2
The Translational Medicine Center of Children Development and Disease,Fudan University 2 0 0 0 0 0 2
Department of Genetics,Sultan Qaboos University Hospital, Oman 2 0 0 0 0 0 2
UNC Molecular Genetics Laboratory,University of North Carolina at Chapel Hill 2 0 0 0 0 0 2
Laboratory of Medical Genetics, National & Kapodistrian University of Athens 2 0 0 0 0 0 2
Genomic Medicine Lab, University of California San Francisco 2 0 0 0 0 0 2
Reproductive Health Research and Development,BGI Genomics 2 0 0 0 0 0 2
Reproductive Endocrine Unit, Massachusetts General Hospital 0 2 0 0 0 0 2
Biesecker Lab/Clinical Genomics Section,National Institutes of Health 0 1 0 0 0 0 1
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories 1 0 0 0 0 0 1
Hehr Laboratory,Center for Human Genetics - University of Regensburg 0 0 1 0 0 0 1
Laboratory for Genetics of Human Development Center for Human Genetics, Catholic University of Leuven 1 0 0 0 0 0 1
Quest Diagnostics Nichols Institute San Juan Capistrano 1 0 0 0 0 0 1
State Key Lab of Medical Genetics, Central South University 1 0 0 0 0 0 1
Department of Molecular Endocrinology,National Research Institute for Child Health and Development 1 0 0 0 0 0 1
Centre for Translational Omics - GOSgene,University College London 1 0 0 0 0 0 1
Human Molecular Genetics Lab,Quaid-I-Azam University 1 0 0 0 0 0 1
Knight Diagnostic Laboratories, Oregon Health and Sciences University 0 1 0 0 0 0 1
Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics 0 1 0 0 0 0 1
Research Centre for Medical Genetics 0 1 0 0 0 0 1
Baylor-Hopkins Center for Mendelian Genomics,Johns Hopkins University 0 0 1 0 0 0 1
Centre de Biologie Pathologie Génétique, Centre Hospitalier Universitaire de Lille 1 0 0 0 0 0 1
IUMS Hospital Medical Genetics Lab,Iran University of Medical Sciences (IUMS) 1 0 0 0 0 0 1
The Molecular Genetic Diagnosis Center, Children’s Hospital of Fudan University 1 0 0 0 0 0 1
Santos-Cortez Lab,University of Colorado School of Medicine 0 1 0 0 0 0 1
Geisinger Autism and Developmental Medicine Institute,Geisinger Health System 0 0 1 0 0 0 1
Kariminejad - Najmabadi Pathology & Genetics Center 0 0 1 0 0 0 1
Gujarat Genomics Initiative,Gujarat State Biotechnology Mission 1 0 0 0 0 0 1
Fukami Lab, Dept of Molecular Endocrinology,National Research Institute for Child Health and Development 1 0 0 0 0 0 1
Dpt. of Clinical Genetics, Molecular Genetics Lab 4062,University Hospital of Copenhagen, Rigshospitalet 0 1 0 0 0 0 1
Hacettepe Genetic Diseases Diagnosis Center,Hacettepe University Faculty of Medicine 0 1 0 0 0 0 1
InterGenetics 1 0 0 0 0 0 1
Génétique des Maladies du Développement, Hospices Civils de Lyon 1 0 0 0 0 0 1
Department of Pediatrics and Developmental Biology,Tokyo Medical and Dental University 0 0 1 0 0 0 1
Johns Hopkins Genomics,Johns Hopkins University 1 0 0 0 0 0 1
Genetic Outpatient Clinic,Children's Memorial Health Institute 0 1 0 0 0 0 1
Genetics Department,Polish Mother's Memorial Hospital Research Institute 0 0 1 0 0 0 1
Istituto Neurologico Mediterraneo,Istituto di Ricovero e Cura a Carattere Scientifico 1 0 0 0 0 0 1
Genetics,Children's Hospital New Orleans 0 0 1 0 0 0 1
GenomeConnect - CFC International 0 0 0 0 0 1 1
Diagnostics Lab (ASPIRE), CSIR - Centre for Cellular and Molecular Biology 0 1 0 0 0 0 1
Section for Clinical Neurogenetics,University of Tübingen 1 0 0 0 0 0 1
MedGen Diagnostic Laboratory,MedGen Medical Centre 1 0 0 0 0 0 1

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