ClinVar Miner

Variants studied for cerebral malformation

Included ClinVar conditions (176):
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
968 340 2461 805 606 16 5074

Gene and significance breakdown #

Total genes and gene combinations: 149
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Gene or gene combination pathogenic likely pathogenic uncertain significance likely benign benign not provided total
FLNA 41 23 206 76 92 3 435
RELN 8 0 171 56 49 1 280
ASPM 133 10 90 5 27 0 260
TSC1 5 1 93 82 21 0 200
FKTN 12 23 143 20 11 0 197
CDON 4 0 111 58 23 0 190
FKRP 22 6 83 25 12 0 146
COL4A1 17 2 41 47 26 1 134
COL4A2 3 1 40 58 32 0 134
GLI2 11 7 73 36 15 0 131
POMT1 18 6 63 18 21 0 124
POMT2 17 4 77 11 14 3 124
PTCH1 3 1 60 51 4 0 118
QARS1 10 1 65 28 12 0 116
RAB3GAP2 5 1 86 18 6 0 113
PAFAH1B1 89 17 4 0 2 1 112
DAG1 4 1 71 19 9 0 104
ARFGEF2 3 0 80 10 1 1 94
POMGNT1, TSPAN1 7 67 23 2 0 0 94
POMGNT2 4 1 63 14 10 0 92
CRPPA 24 6 34 6 12 0 82
RAB18 5 0 54 13 9 0 81
WDR62 19 8 32 4 16 0 76
LARGE1 5 1 49 16 2 0 73
LOC101927870, RELN 0 0 45 11 15 0 71
MCPH1 13 4 37 0 9 0 63
CDK5RAP2 15 1 29 0 19 2 62
B3GALNT2 12 9 32 10 4 0 60
GMPPB 12 5 33 8 3 0 60
ACTB 25 9 10 7 9 0 58
SHH 34 3 6 2 8 0 51
SLC9A6 12 3 16 9 12 0 50
TUBA1A 19 24 8 0 0 1 50
CEP152 9 4 36 0 0 1 47
RXYLT1 9 5 23 5 7 0 46
POMK 7 0 21 11 6 0 44
FOXH1 0 0 24 15 12 0 43
RAB3GAP1 19 0 17 4 2 0 42
TSC2 8 2 28 0 0 0 38
ADGRG1 20 3 14 0 0 0 37
B4GAT1 2 1 25 2 4 0 33
NODAL 0 0 20 9 4 0 33
STIL 5 1 17 0 8 0 31
LAMC3 4 0 9 2 13 0 28
RAB3GAP1, ZRANB3 3 0 17 6 2 0 28
CENPJ 6 2 16 0 7 0 27
TGIF1 7 1 6 9 7 0 27
ARX 21 2 2 0 0 0 25
TUBB2B 8 6 10 0 0 0 23
ACTG1 6 3 5 4 4 0 22
DCX 18 3 1 0 0 0 22
FLNA, LOC107988032 2 0 14 1 5 0 22
SIX3 12 0 6 0 4 0 22
ZIC2 14 4 1 1 2 0 22
LOC100507346, PTCH1 2 0 11 3 1 0 16
TUBB3 6 4 7 0 0 0 16
NDE1 7 0 8 0 0 0 15
CIT 8 0 5 0 0 0 13
FGF8 1 9 2 0 1 0 13
IER3IP1 3 0 6 3 1 0 13
POMGNT1 0 8 2 1 0 0 11
PSAT1 5 0 3 2 1 0 11
COL4A1, COL4A2 0 0 0 3 7 0 10
ZNF335 7 1 2 0 0 2 10
B3GALNT2, TBCE 1 1 7 0 0 0 9
LAMB1 4 2 3 0 0 0 9
CENPJ, RNF17 4 1 2 0 1 0 8
KNL1 3 4 2 0 0 0 8
MTOR 7 0 1 0 0 0 8
PHGDH 5 1 3 0 0 0 8
RTTN 6 0 2 0 0 0 8
ARX, LOC109610631 6 1 0 0 0 0 7
FOXH1, KIFC2 0 0 4 3 0 0 7
KIF14 7 0 0 0 0 0 7
NEDD4L 4 1 3 0 0 0 7
TUBB2A 3 4 2 0 0 0 7
KATNB1 6 0 0 0 0 0 6
TUBA8 1 0 5 0 0 0 6
​intergenic 2 0 1 0 2 0 5
ANKLE2 3 0 2 0 0 0 5
FGFR1 1 4 0 0 0 0 5
KIF2A 2 2 1 0 0 0 5
KIF5C 2 0 2 1 0 0 5
MFSD2A 3 1 1 0 0 0 5
TBC1D20 5 0 0 0 0 0 5
TMTC3 5 0 0 0 0 0 5
TUBB 4 0 1 0 0 0 5
CEP135 4 0 0 0 0 0 4
DISP1 0 1 3 0 0 0 4
EML1 4 0 0 0 0 0 4
EMX2 4 0 0 0 0 0 4
FIG4 3 0 1 0 0 0 4
MAP1B 0 4 0 0 0 0 4
NCAPD3 3 0 0 0 0 0 3
TUBG1 3 0 0 0 0 0 3
ANGPT2, MCPH1 1 0 2 0 0 0 2
ATP1A2 2 0 0 0 0 0 2
CENPE 2 1 0 0 0 0 2
DLL1 0 0 2 0 0 0 2
DNASE1L1, EMD, FLNA, RPL10, TAZ 0 0 2 0 0 0 2
EMD, FLNA 0 0 2 0 0 0 2
GAS1 0 0 2 0 0 0 2
LAMA2 0 0 2 0 0 0 2
LAMA5 0 0 2 0 0 0 2
LINGO4 0 0 2 0 0 0 2
LOC110008580, ZIC2 2 0 0 0 0 0 2
PHC1 1 0 1 0 0 0 2
PI4KA 2 0 0 0 0 0 2
PLOD1 2 0 0 0 0 0 2
TBC1D7, TBC1D7-LOC100130357 2 0 0 0 0 0 2
ABAT, ABCA3, ABCC1, ABCC6, ACSM1, ACSM2A, ACSM2B, ACSM3, ACSM5, ADCY9, AHSP, ALDOA, ALG1, AMDHD2, ANKS3, ANKS4B, APOBR, AQP8, ARHGAP17, ARL6IP1, ARMC5, ASPHD1, ATF7IP2, ATP2A1, ATP6V0C, ATXN2L, BAIAP3, BCAR4, BCKDK, BCL7C, BFAR, BICDL2, BMERB1, BOLA2, BOLA2B, BRICD5, C16orf54, C16orf58, C16orf71, C16orf72, C16orf82, C16orf89, C16orf90, C16orf91, C16orf92, C16orf96, CACNG3, CARHSP1, CASKIN1, CCDC154, CCDC189, CCNF, CCP110, CD19, CD2BP2, CDIP1, CDIPT, CDR2, CEMP1, CHP2, CIITA, CLCN7, CLDN6, CLDN9, CLEC16A, CLEC19A, CLN3, CLUAP1, COG7, COQ7, CORO1A, CORO7, CORO7-PAM16, COX6A2, CPPED1, CRAMP1, CREBBP, CRYM, CTF1, DCTN5, DCTPP1, DCUN1D3, DEXI, DNAH3, DNAJA3, DNASE1, DNASE1L2, DOC2A, E4F1, EARS2, ECI1, EEF2K, EEF2KMT, EIF3C, EIF3CL, ELOB, EME2, EMP2, ERCC4, ERI2, ERN2, FAHD1, FBRS, FBXL19, FLYWCH1, FLYWCH2, FOPNL, FUS, GDE1, GDPD3, GFER, GGA2, GLIS2, GLYR1, GNPTG, GP2, GPR139, GPRC5B, GRIN2A, GSG1L, GSPT1, GTF3C1, HAGH, HCFC1R1, HIRIP3, HMOX2, HS3ST2, HS3ST4, HS3ST6, HSD3B7, IFT140, IGFALS, IGSF6, IL21R, IL27, IL32, IL4R, INO80E, IQCK, ITGAD, ITGAL, ITGAM, ITGAX, ITPRIPL2, JPT2, KAT8, KCTD13, KCTD5, KDM8, KIAA0556, KIF22, KNOP1, KREMEN2, LAT, LCMT1, LITAF, LYRM1, MAPK3, MAPK8IP3, MARF1, MAZ, MEFV, MEIOB, METTL22, METTL9, MGRN1, MIR1225, MIR193B, MIR365A, MLST8, MMP25, MOSMO, MPV17L, MRPS34, MRTFB, MSRB1, MTRNR2L4, MVP, MYH11, MYLPF, NAA60, NAGPA, NDE1, NDUFAB1, NDUFB10, NFATC2IP, NLRC3, NME3, NMRAL1, NOMO1, NOMO2, NOMO3, NOXO1, NPIPA1, NPIPA2, NPIPA3, NPIPA5, NPIPB3, NPIPB4, NPIPB5, NPIPB6, NPW, NSMCE1, NTAN1, NTHL1, NTN3, NUBP1, NUBP2, NUDT16L1, NUPR1, OR1F1, OR2C1, ORAI3, OTOA, PAGR1, PALB2, PAM16, PAQR4, PARN, PDILT, PDPK1, PDXDC1, PDZD9, PGP, PHKG2, PKD1, PKMYT1, PLA2G10, PLK1, PMM2, POLR3E, PPL, PPP4C, PRKCB, PRM1, PRM2, PRM3, PRR14, PRRT2, PRSS21, PRSS22, PRSS27, PRSS33, PRSS36, PRSS41, PRSS53, PRSS8, PTX4, PYCARD, PYDC1, QPRT, RAB26, RABEP2, RBBP6, RBFOX1, RMI2, RNF151, RNF40, RNPS1, ROGDI, RPL3L, RPS15A, RPS2, RRN3, RSL1D1, SBK1, SCNN1B, SCNN1G, SDR42E2, SEC14L5, SEPHS2, SEPTIN1, SEPTIN12, SETD1A, SEZ6L2, SGF29, SH2B1, SHISA9, SLC5A11, SLC5A2, SLC9A3R2, SLX1A, SLX1B, SLX4, SMG1, SMIM22, SNHG9, SNN, SNX29, SOCS1, SPN, SPNS1, SPSB3, SRCAP, SRL, SRRM2, STX1B, STX4, SULT1A1, SULT1A2, SULT1A3, SULT1A4, SYNGR3, SYT17, TAOK2, TBC1D10B, TBC1D24, TBL3, TBX6, TEDC2, TEKT5, TELO2, TFAP4, TGFB1I1, THOC6, THUMPD1, TIGD7, TLCD3B, TMC5, TMC7, TMEM114, TMEM159, TMEM186, TMEM204, TMEM219, TNFRSF12A, TNFRSF17, TNP2, TNRC6A, TP53TG3, TP53TG3B, TP53TG3C, TP53TG3D, TPSAB1, TPSB2, TPSD1, TRAF7, TRAP1, TRIM72, TSC2, TSR3, TUFM, TVP23A, TXNDC11, UBALD1, UBE2I, UBFD1, UBN1, UMOD, UNKL, UQCRC2, USP31, USP7, VASN, VKORC1, VPS35L, VWA3A, XPO6, XYLT1, YPEL3, ZC3H7A, ZG16, ZG16B, ZKSCAN2, ZNF174, ZNF200, ZNF205, ZNF213, ZNF263, ZNF267, ZNF48, ZNF500, ZNF597, ZNF598, ZNF629, ZNF646, ZNF668, ZNF688, ZNF689, ZNF720, ZNF747, ZNF75A, ZNF764, ZNF768, ZNF771, ZNF785, ZNF843, ZP2, ZSCAN10, ZSCAN32 1 0 0 0 0 0 1
AKT3 0 1 0 0 0 0 1
ANKMY2, BZW2, CRPPA, LRRC72, SOSTDC1 1 0 0 0 0 0 1
ASPA, CLUH, LOC100288728, METTL16, OR1A1, OR1A2, OR1D2, OR1D5, OR1E1, OR1E2, OR1G1, OR3A1, OR3A2, OR3A3, PAFAH1B1, RAP1GAP2, SPATA22, TRPV3 1 0 0 0 0 0 1
BAG6 0 0 1 0 0 0 1
BOC 0 0 1 0 0 0 1
BORCS5 0 1 0 0 0 0 1
CDK5 1 0 0 0 0 0 1
CDK6 1 0 0 0 0 0 1
CEP85L 0 0 1 0 0 0 1
CLUH, METTL16, PAFAH1B1, RAP1GAP2 1 0 0 0 0 0 1
CNOT1 0 0 1 0 0 0 1
COPB2 1 0 0 0 0 0 1
DPH1, HIC1, INPP5K, METTL16, MIR132, MIR212, MIR22, MNT, MYO1C, OVCA2, PAFAH1B1, PITPNA, PRPF8, RILP, RPA1, RTN4RL1, SCARF1, SERPINF1, SERPINF2, SGSM2, SLC43A2, SMG6, SMYD4, SRR, TLCD2, TSR1, WDR81 1 0 0 0 0 0 1
DYNC1H1 0 1 0 0 0 0 1
EHMT1 1 0 0 0 0 0 1
ENTPD1 0 0 1 0 0 0 1
ERMARD 1 0 0 0 0 0 1
FKTN, FSD1L 1 0 0 0 0 0 1
FNTA, HOOK3, MIR4469, POMK, RNF170, THAP1 0 0 1 0 0 0 1
GRIN1 0 0 1 0 0 0 1
LOC100287015, MCPH1 1 0 0 0 0 0 1
LOC102724058, SCN1A 1 0 0 0 0 0 1
MACF1 1 0 0 0 0 0 1
MATN4 0 1 0 0 0 0 1
MYH11, NDE1 0 0 1 0 0 0 1
NBN 1 0 0 0 0 0 1
NCAPD2 1 0 0 0 0 0 1
NCAPH 1 0 0 0 0 0 1
NR2F1 0 0 1 0 0 0 1
NSDHL 0 0 1 0 0 0 1
PIK3CA 0 0 1 0 0 0 1
RHEB 0 1 0 0 0 0 1
SASS6 1 0 0 0 0 0 1
SCN3A 0 1 0 0 0 0 1
SUFU 0 0 1 0 0 0 1
TUBA3E 0 1 0 0 0 0 1
WDFY3 1 0 0 0 0 0 1
WDR81 0 1 0 0 0 0 1

Submitter and significance breakdown #

Total submitters: 86
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Submitter pathogenic likely pathogenic uncertain significance likely benign benign not provided total
Invitae 114 45 1161 350 342 0 2012
Illumina Clinical Services Laboratory,Illumina 1 0 780 434 135 0 1350
Genetic Services Laboratory, University of Chicago 227 64 259 0 0 0 550
OMIM 444 0 4 0 0 0 448
GeneReviews 174 0 0 0 71 0 245
Fulgent Genetics,Fulgent Genetics 22 8 183 1 0 0 214
Counsyl 7 67 31 3 0 0 108
Diagnostic Laboratory, Department of Genetics,University Medical Center Groningen 1 0 1 9 65 0 76
Genomic Research Center,Shahid Beheshti University of Medical Sciences 6 9 23 2 0 0 40
Juha Muilu Group; Institute for Molecular Medicine Finland (FIMM) 1 36 0 0 0 0 37
Baylor Miraca Genetics Laboratories, 15 5 15 0 0 0 35
DNA and Cytogenetics Diagnostics Unit,Erasmus Medical Center 0 1 0 3 30 0 34
Claritas Genomics 8 15 6 0 0 0 29
Muenke lab,National Institutes of Health 12 7 9 0 1 0 29
Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago 4 2 17 0 0 0 23
Athena Diagnostics Inc 0 0 0 0 20 0 20
Lupski Lab, Baylor-Hopkins CMG,Baylor College of Medicine 2 7 11 0 0 0 20
Laboratory of Molecular Genetics,CHU RENNES 0 14 6 0 0 0 20
GenomeConnect, ClinGen 0 0 0 0 0 16 16
Department of Genetics,Robert DEBRE University Hospital 15 0 0 0 0 0 15
Centre for Mendelian Genomics,University Medical Centre Ljubljana 7 3 4 0 0 0 14
Mayo Clinic Genetic Testing Laboratories,Mayo Clinic 1 2 9 0 0 0 12
NeuroMeGen,Hospital Clinico Santiago de Compostela 0 7 1 0 0 0 8
Laboratory for Molecular Medicine,Partners HealthCare Personalized Medicine 1 6 0 0 0 0 7
Hehr Laboratory,Center for Human Genetics - University of Regensburg 0 5 2 0 0 0 7
Foundation for Research in Genetics and Endocrinology,Institute of Human Genetics 3 1 3 0 0 0 7
Geisinger Autism and Developmental Medicine Institute,Geisinger Health System 1 1 5 0 0 0 7
Laboratoire de Cytogenetique,Hospices Civils de Lyon 3 2 2 0 0 0 7
UCLA Clinical Genomics Center, UCLA 1 5 0 0 0 0 6
Molecular Genetics Laboratory,BC Children's and BC Women's Hospitals 4 1 0 0 0 0 5
Integrated Genetics/Laboratory Corporation of America 2 3 0 0 0 0 5
Division of Human Genetics,Children's Hospital of Philadelphia 0 2 3 0 0 0 5
Center of Genomic medicine, Geneva,University Hospital of Geneva 4 1 0 0 0 0 5
Soonchunhyang University Bucheon Hospital,Soonchunhyang University Medical Center 1 1 2 1 0 0 5
Equipe Genetique des Anomalies du Developpement,Université de Bourgogne 2 3 0 0 0 0 5
Human Molecular Genetics and Metabolic Disorders,Pakistan Institute for Engineering and Applied Science (PIEAS) 5 0 0 0 0 0 5
Broad Institute Rare Disease Group,Broad Institute 1 3 1 0 0 0 5
ClinVar Staff, National Center for Biotechnology Information (NCBI) 0 4 0 0 0 0 4
Developmental Genetics Unit,King Faisal Specialist Hospital & Research Centre 0 4 0 0 0 0 4
Institute of Human Genetics,Klinikum rechts der Isar 3 1 0 0 0 0 4
HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology 1 0 1 2 0 0 4
Dobyns Lab,Seattle Children's Research Institute 2 1 1 0 0 0 4
Center for Human Genetics and Laboratory Diagnostics, Dr. Klein, Dr. Rost and Colleagues 1 2 1 0 0 0 4
Undiagnosed Diseases Network,NIH 1 1 2 0 0 0 4
SBielas Lab, Department of Human Genetics,University of Michigan 4 0 0 0 0 0 4
Clinical Genetics Group,University of Otago 4 0 0 0 0 0 4
Epi4K Consortium 0 4 0 0 0 0 4
Institute of Human Genetics,Cologne University 0 0 2 1 0 0 3
SIB Swiss Institute of Bioinformatics 1 0 0 0 2 0 3
Biochemical Molecular Genetic Laboratory,King Abdulaziz Medical City 0 0 3 0 0 0 3
Department of Genetics,Sultan Qaboos University Hospital, Oman 3 0 0 0 0 0 3
Institute of Human Genetics,University of Goettingen 0 0 2 0 0 0 2
Courtagen Diagnostics Laboratory,Courtagen Life Sciences 2 0 0 0 0 0 2
Mendelics 1 1 0 0 0 0 2
Institute of Human Genetics,Friedrich-Alexander-Universität Erlangen-Nürnberg 2 0 0 0 0 0 2
Department of Clinical Genetics,Oxford University Hospitals NHS Trust 2 0 0 0 0 0 2
Knight Diagnostic Laboratories,Oregon Health and Sciences University 1 1 0 0 0 0 2
Molecular Genetics Pathology Laboratory, University Of Arkansas for Medical Sciences 1 0 1 0 0 0 2
Diagnostics Division,Centre for DNA Fingerprinting and Diagnostics 0 2 0 0 0 0 2
Centre de Biologie Pathologie Génétique,Centre Hospitalier Universitaire de Lille 2 0 0 0 0 0 2
Bioscientia Institut fuer Medizinische Diagnostik GmbH,Sonic Healthcare 1 0 1 0 0 0 2
Heinzen Lab,Columbia University 2 0 0 0 0 0 2
Ege University Pediatric Genetics,Ege University 2 0 0 0 0 0 2
CHLA Center for Personalized Medicine,Children's Hospital, Los Angeles 1 0 1 0 0 0 2
Genome Diagnostics Laboratory,VU University Medical Center Amsterdam 2 0 0 0 0 0 2
Molecular Diagnostics Laboratory,M Health: University of Minnesota 0 2 0 0 0 0 2
Department of Rehabilitation Medicine, Incheon St. Mary’s Hospital,College of Medicine, The Catholic University of Korea 0 2 0 0 0 0 2
Clinical Molecular Genetics Laboratory,Johns Hopkins All Children's Hospital 1 0 0 0 0 0 1
Quest Diagnostics Nichols Institute San Juan Capistrano 1 0 0 0 0 0 1
CSER_CC_NCGL; University of Washington Medical Center 0 0 0 1 0 0 1
Hadassah Hebrew University Medical Center 0 1 0 0 0 0 1
Prenatal Medicine Munich,Prenatal Medicine Munich 0 1 0 0 0 0 1
Center for Human Genetics,University of Leuven 1 0 0 0 0 0 1
Genetic Diagnostic Laboratory,University of Szeged 0 1 0 0 0 0 1
Medical Research Institute,Tokyo Medical and Dental University 1 0 0 0 0 0 1
Laboratory Genomica,Gynecology and Assisted Reproduction Hospital Malinov DM 1 0 0 0 0 0 1
Bioinformatics dept.,Datar Cancer Genetics Limited, India 0 0 1 0 0 0 1
Reutter Lab, Institute of Human Genetics,University Hospital Bonn 1 0 0 0 0 0 1
Research Group Niklas Dahl,Uppsala University 1 0 0 0 0 0 1
Talkowski Laboratory, Center for Human Genetic Research,Massachusetts General Hospital 0 0 1 0 0 0 1
Department of Medical Genetics,Sanjay Gandhi Post Graduate Institute of Medical Sciences 1 0 0 0 0 0 1
Phosphorus, Inc. 0 0 1 0 0 0 1
Genetics Division,Universidade Federal de Sao Paulo 0 1 0 0 0 0 1
Consultorio y Laboratorio de Neurogenética,Hospital JM Ramos Mejia 0 1 0 0 0 0 1
Laboratory of Medical Genetics,National & Kapodistrian University of Athens 1 0 0 0 0 0 1
Department of Pediatrics,Driscoll Children's Hospital 1 0 0 0 0 0 1

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