ClinVar Miner

Variants studied for cranial malformation

Included ClinVar conditions (76):
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 risk factor not provided total
455 121 2655 952 507 3 3 4581

Gene and significance breakdown #

Total genes and gene combinations: 63
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Gene or gene combination pathogenic likely pathogenic uncertain significance likely benign benign risk factor not provided total
RECQL4 133 32 1578 555 87 0 0 2374
SKI 14 7 160 86 22 0 0 277
WDR35 16 7 146 42 40 0 0 238
FGFR1 7 4 112 47 52 0 0 203
ALX4 9 0 75 19 70 2 0 175
FGFR2 52 16 52 19 44 0 0 164
MEGF8 7 2 80 40 33 0 0 161
IFT122 10 5 90 25 27 0 0 143
RUNX2 21 5 59 3 34 0 0 121
FGFR3 18 1 30 21 31 0 1 101
WDR19 4 1 70 12 12 0 0 99
RAB23 12 0 32 40 4 0 0 79
MSX2 9 1 39 8 27 0 0 78
TWIST1 35 8 21 5 3 0 0 69
KAT6A 24 10 13 5 0 0 1 52
ERF 16 4 14 11 6 0 0 50
BAG2, RAB23 0 0 27 5 6 0 0 38
TCF12 18 5 3 0 0 0 1 26
CD96 2 0 13 1 1 0 0 17
POR 11 0 3 1 1 0 0 14
LOC109611589, RUNX2 1 2 3 3 1 0 0 10
IL11RA 5 2 2 0 0 0 0 9
FREM1 2 0 6 0 0 0 0 8
IFT52 6 0 0 0 0 0 0 6
IRX5 3 0 3 0 0 0 0 6
CYP26B1 2 0 3 0 0 0 0 5
KIFBP 5 0 0 0 0 0 0 5
RUNX2, SUPT3H 1 0 2 1 1 0 0 5
ZNF462 3 1 0 0 0 0 0 4
​intergenic 1 0 1 0 0 0 0 2
IFT43 1 0 1 0 0 0 0 2
IFT43, TGFB3 0 0 0 2 0 0 0 2
LOC101928222, MATN3, WDR35 0 0 0 0 2 0 0 2
LOC109611593, RUNX2, SUPT3H 0 0 0 0 2 0 0 2
NPR2 0 2 0 0 0 0 0 2
PTCH1 0 0 2 0 0 0 0 2
SMAD6 0 1 1 0 0 0 0 2
SMO 1 0 1 0 0 0 0 2
SOST 2 0 0 0 0 0 0 2
SPECC1L, SPECC1L-ADORA2A 0 0 2 0 0 0 0 2
ZIC1 1 1 0 0 0 0 0 2
ACAP3, ACTRT2, AGRN, ANKRD65, ATAD3A, ATAD3B, ATAD3C, AURKAIP1, B3GALT6, C1QTNF12, C1orf159, CALML6, CCNL2, CDK11A, CDK11B, CFAP74, CPTP, DVL1, FAAP20, FNDC10, GABRD, GNB1, HES5, INTS11, MIB2, MIR200A, MIR200B, MIR429, MMEL1, MMP23B, MORN1, MRPL20, MXRA8, NADK, PANK4, PEX10, PLCH2, PRKCZ, PRXL2B, PUSL1, RER1, RNF223, SCNN1D, SDF4, SKI, SLC35E2A, SLC35E2B, SSU72, TAS1R3, TMEM240, TMEM52, TMEM88B, TNFRSF14, TNFRSF18, TNFRSF4, TTC34, TTLL10, UBE2J2, VWA1 0 0 1 0 0 0 0 1
ADAMTSL4 0 0 1 0 0 0 0 1
AGMO, AGR2, AGR3, AHR, ANKMY2, BZW2, CRPPA, DGKB, FERD3L, HDAC9, ITGB8, LRRC72, MACC1, MEOX2, POLR1F, PRPS1L1, SNX13, SOSTDC1, TMEM196, TSPAN13, TWIST1 1 0 0 0 0 0 0 1
ATP1A3, DEDD2, ERF, GRIK5, GSK3A, LOC111811970, MIR4323, POU2F2, RABAC1, ZNF526, ZNF574 1 0 0 0 0 0 0 1
BMP2 0 0 0 0 0 1 0 1
CIC, DEDD2, ERF, GRIK5, GSK3A, LOC111501767, LOC111811970, MIR4323, PAFAH1B3, POU2F2, ZNF526, ZNF574 1 0 0 0 0 0 0 1
FBN1 0 0 1 0 0 0 0 1
FBN2 0 0 1 0 0 0 0 1
GRIN2B 0 1 0 0 0 0 0 1
HUWE1 0 1 0 0 0 0 0 1
IGF1R 0 0 1 0 0 0 0 1
KAT6B 0 0 1 0 0 0 0 1
LOC112577524, SKI 0 0 1 0 0 0 0 1
LOC112939934, WDR19 0 0 1 0 0 0 0 1
MAN2B1 1 0 0 0 0 0 0 1
MATN3, WDR35 0 0 0 1 1 0 0 1
MSX1 0 0 1 0 0 0 0 1
MYH7 0 0 1 0 0 0 0 1
SPAG17 0 1 0 0 0 0 0 1
TCOF1 1 0 0 0 0 0 0 1
TGFBR1 0 0 1 0 0 0 0 1
TRPS1 0 1 0 0 0 0 0 1

Submitter and significance breakdown #

Total submitters: 81
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Submitter pathogenic likely pathogenic uncertain significance likely benign benign risk factor not provided total
Invitae 207 43 1947 817 232 0 0 3246
Illumina Clinical Services Laboratory,Illumina 0 0 604 128 295 0 0 1001
OMIM 178 0 0 0 0 3 0 181
Baylor Genetics 15 3 50 0 0 0 0 68
Fulgent Genetics,Fulgent Genetics 16 2 49 0 0 0 0 67
Genomic Diagnostic Laboratory, Division of Genomic Diagnostics,Children's Hospital of Philadelphia 33 7 1 0 0 0 0 41
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories 0 0 0 10 13 0 0 23
Department of Medical Genetics, Oslo University Hospital 12 11 0 0 0 0 0 23
Mendelics 2 2 4 8 6 0 0 22
Centre for Mendelian Genomics,University Medical Centre Ljubljana 4 8 8 0 0 0 0 20
Klinisk genetik och genomik Research,Gothenburg University 2 3 15 0 0 0 0 20
GeneReviews 19 0 0 0 0 0 0 19
Baylor-Hopkins Center for Mendelian Genomics,Johns Hopkins University 9 0 1 0 0 0 0 10
Department of Medical Genetics,Faculty of Medicine, Istanbul University 5 4 1 0 0 0 0 10
Natera, Inc. 2 0 3 3 1 0 0 9
Genomic Research Center, Shahid Beheshti University of Medical Sciences 0 0 8 1 0 0 0 9
Centre de Biologie Pathologie Génétique, Centre Hospitalier Universitaire de Lille 6 1 0 1 0 0 0 8
Equipe Genetique des Anomalies du Developpement, Université de Bourgogne 3 4 0 0 0 0 0 7
Johns Hopkins Genomics, Johns Hopkins University 4 2 0 1 0 0 0 7
Genetic Services Laboratory, University of Chicago 5 1 0 0 0 0 0 6
Institute of Human Genetics, University of Leipzig Medical Center 0 3 3 0 0 0 0 6
Biochemical Molecular Genetic Laboratory,King Abdulaziz Medical City 2 3 1 0 0 0 0 6
Bioscientia Institut fuer Medizinische Diagnostik GmbH,Sonic Healthcare 4 1 0 0 0 0 0 5
Database of Curated Mutations (DoCM) 0 5 0 0 0 0 0 5
Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn 5 0 0 0 0 0 0 5
Institute of Human Genetics, Klinikum rechts der Isar 4 0 0 0 0 0 0 4
UF de Génétique Moléculaire,Hôpital Lariboisière 4 0 0 0 0 0 0 4
Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego 4 0 0 0 0 0 0 4
SIB Swiss Institute of Bioinformatics 1 1 0 0 2 0 0 4
Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago 0 0 4 0 0 0 0 4
Genomic Medicine Lab, University of California San Francisco 2 0 2 0 0 0 0 4
Human Genetics - Radboudumc,Radboudumc 1 1 1 0 0 0 0 3
Muenke lab,National Institutes of Health 3 0 0 0 0 0 0 3
Rare Disease Group, Clinical Genetics,Karolinska Institutet 1 0 2 0 0 0 0 3
Clinical Genomics Program, Stanford Medicine 0 2 1 0 0 0 0 3
Clinical Molecular Genetics Laboratory,Johns Hopkins All Children's Hospital 1 0 1 0 0 0 0 2
Developmental Genetics Unit,King Faisal Specialist Hospital & Research Centre 1 1 0 0 0 0 0 2
UCLA Clinical Genomics Center, UCLA 2 0 0 0 0 0 0 2
Service de Génétique Moléculaire,Hôpital Robert Debré 0 2 0 0 0 0 0 2
Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia,Universidade Católica de Brasília 2 0 0 0 0 0 0 2
Soonchunhyang University Bucheon Hospital,Soonchunhyang University Medical Center 0 1 1 0 0 0 0 2
Talkowski Laboratory, Center for Human Genetic Research,Massachusetts General Hospital 1 0 1 0 0 0 0 2
Center for Human Genetics and Laboratory Diagnostics, Dr. Klein, Dr. Rost and Colleagues 2 0 0 0 0 0 0 2
Geisinger Autism and Developmental Medicine Institute,Geisinger Health System 0 0 2 0 0 0 0 2
GenomeConnect, ClinGen 0 0 0 0 0 0 2 2
Laboratorio de Citogenómica y Microarreglos,Universidad Autonoma de Nuevo Leon 0 2 0 0 0 0 0 2
Génétique des Maladies du Développement, Hospices Civils de Lyon 2 0 0 0 0 0 0 2
Molecular Biology Laboratory, Fundació Puigvert 0 2 0 0 0 0 0 2
Laboratory for Molecular Medicine,Partners HealthCare Personalized Medicine 0 1 0 0 0 0 0 1
Molecular Genetics Laboratory,BC Children's and BC Women's Hospitals 1 0 0 0 0 0 0 1
Integrated Genetics/Laboratory Corporation of America 0 1 0 0 0 0 0 1
Victorian Clinical Genetics Services,Murdoch Childrens Research Institute 1 0 0 0 0 0 0 1
Laboratory for Genetics of Human Development Center for Human Genetics, Catholic University of Leuven 1 0 0 0 0 0 0 1
ClinVar Staff, National Center for Biotechnology Information (NCBI) 1 0 0 0 0 0 0 1
Blueprint Genetics 0 1 0 0 0 0 0 1
HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology 0 0 1 0 0 0 0 1
Knight Diagnostic Laboratories, Oregon Health and Sciences University 1 0 0 0 0 0 0 1
Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics 1 0 0 0 0 0 0 1
Lupski Lab, Baylor-Hopkins CMG, Baylor College of Medicine 0 0 1 0 0 0 0 1
Hadassah Hebrew University Medical Center 0 1 0 0 0 0 0 1
Laboratory of Molecular Genetics,CHU RENNES 0 0 1 0 0 0 0 1
Daryl Scott Lab,Baylor College of Medicine 0 1 0 0 0 0 0 1
Undiagnosed Diseases Network,NIH 1 0 0 0 0 0 0 1
CHLA Center for Personalized Medicine,Children's Hospital, Los Angeles 1 0 0 0 0 0 0 1
Biologia e Medicina Molecolare, Sapienza University of Rome 1 0 0 0 0 0 0 1
MAGI'S LAB - Medical Genetics Laboratory, MAGI GROUP 0 1 0 0 0 0 0 1
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen 0 0 0 0 1 0 0 1
Broad Institute Rare Disease Group, Broad Institute 0 1 0 0 0 0 0 1
Molecular Diagnostics Laboratory, M Health Fairview: University of Minnesota 1 0 0 0 0 0 0 1
Laboratory of Medical Genetics, National & Kapodistrian University of Athens 0 0 1 0 0 0 0 1
Cavalleri Lab, Royal College of Surgeons in Ireland 0 1 0 0 0 0 0 1
Institute of Bioinformatics 0 1 0 0 0 0 0 1
Clinical Genetics Laboratory,Federal University of Health Sciences of Porto Alegre 1 0 0 0 0 0 0 1
Department of Genetics, Rouen University Hospital, Normandy Center for Genomic and Personalized Medicine 1 0 0 0 0 0 0 1
Cytogenetics and Genomics Lab,Cyprus Institute Of Neurology and Genetics 1 0 0 0 0 0 0 1
GenomeConnect-Association for Creatine Deficiencies, Association for Creatine Deficiencies 0 0 0 0 0 0 1 1
Genetics Institute, Tel Aviv Sourasky Medical Center 1 0 0 0 0 0 0 1
NYU Undiagnosed Diseases Program,NYU School of Medicine 0 1 0 0 0 0 0 1
Department of Clinical Biochemistry,University General Hospital Attikon, Medical School, National & Kapodistrian University of Athens 1 0 0 0 0 0 0 1
Medical Genetics Lab, Xi'an Fourth Hospital 0 1 0 0 0 0 0 1
Wilkie Group, Clinical Genetics Lab, WIMM,University of Oxford 1 0 0 0 0 0 0 1

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