ClinVar Miner

Variants studied for holoprosencephaly

Included ClinVar conditions (30):
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
149 71 1236 672 381 3 2419

Gene and significance breakdown #

Total genes and gene combinations: 52
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Gene or gene combination pathogenic likely pathogenic uncertain significance likely benign benign not provided total
GLI2 23 19 270 218 82 0 579
CDON 4 0 265 93 101 0 446
ZIC2 23 9 111 97 12 1 250
PTCH1 6 2 117 43 50 2 211
SHH 40 14 76 57 17 0 196
FOXH1 0 0 85 39 21 0 141
LMBR1, SHH 0 0 95 18 24 0 137
SIX3 16 3 54 45 16 0 132
TGIF1 7 4 32 28 22 0 78
NODAL 0 0 30 6 12 0 48
LOC110008580, ZIC2 2 1 28 9 0 0 40
LOC100507346, PTCH1 3 0 18 10 6 0 36
CNOT1 2 2 7 0 7 0 17
FOXH1, KIFC2 0 0 11 1 3 0 15
FGF8 1 8 3 1 1 0 14
STAG2 5 1 2 4 1 0 13
DISP1 0 1 8 0 0 0 9
LOC130002133, PTCH1 0 0 7 1 1 0 9
​intergenic 2 0 0 0 2 0 4
FGFR1 1 3 0 0 0 0 4
LMBR1, SHH, ZRS 0 0 0 1 3 0 4
ACRV1, CCDC15, CDON, CHEK1, DDX25, EI24, ESAM, FAM118B, FEZ1, FOXRED1, HEPACAM, HEPN1, HYLS1, MSANTD2, NRGN, OR10G4, OR10G7, OR10G8, OR10G9, OR10S1, OR4D5, OR6M1, OR6T1, OR6X1, OR8A1, OR8B12, OR8B2, OR8B3, OR8B4, OR8B8, OR8D1, OR8D2, OR8D4, OR8G1, OR8G5, PANX3, PATE1, PATE2, PATE3, PATE4, PKNOX2, PUS3, ROBO3, ROBO4, RPUSD4, SCN3B, SIAE, SLC37A2, SPA17, SRPRA, STT3A, TBRG1, TIRAP, TMEM218, TMEM225, VSIG2, VWA5A, ZNF202 0 0 2 0 0 0 2
CDON, LOC130007022 0 0 2 0 0 0 2
GAS1 0 0 2 0 0 0 2
LAMA5 0 0 2 0 0 0 2
PLCH1 2 0 0 0 0 0 2
ABCC4, CLDN10, CLYBL, DCT, DNAJC3, DOCK9, DZIP1, FARP1, FGF14, GGACT, GPC5, GPC6, GPR18, GPR180, GPR183, HS6ST3, IPO5, ITGBL1, MBNL2, METTL21C, MIR17, MIR17HG, MIR18A, MIR19A, MIR19B1, MIR20A, MIR92A1, NALCN, OXGR1, PCCA, RAP2A, RNF113B, SLC15A1, SOX21, STK24, TGDS, TM9SF2, TMTC4, TPP2, UBAC2, UGGT2, ZIC2, ZIC5 1 0 0 0 0 0 1
ABCG5, ABCG8, CAMKMT, DYNC2LI1, LRPPRC, PPM1B, PREPL, SIX2, SIX3, SLC3A1 1 0 0 0 0 0 1
ABHD13, ANKRD10, ARGLU1, ARGLU1-DT, BIVM, BIVM-ERCC5, CARS2, CCDC168, CLYBL, COL4A1, COL4A2, DAOA, DOCK9, DOCK9-DT, EFNB2, ERCC5, FARP1, FGF14, FGF14-IT1, FKSG29, GGACT, GPR18, GPR183, ING1, IRS2, ITGBL1, LIG4, LINC00343, LINC00370, LINC00396, LINC00399, LINC00411, LINC00431, LINC00443, LINC00449, LINC00460, LINC00554, LINC00567, LINC00676, LINC01039, LINC01232, LINC01309, LINC03032, LINC03061, LINC03082, LOC105370349, LOC105370362, LOC107992391, LOC110008580, LOC110120930, LOC110121473, LOC112163637, LOC112163638, LOC112163639, LOC112163640, LOC112163643, LOC116268457, LOC121468004, LOC121468005, LOC121468006, LOC121468007, LOC121838582, LOC121838583, LOC124909516, LOC124909517, LOC124909518, LOC124909519, LOC124946325, LOC124946326, LOC124946327, LOC124946328, LOC124946329, LOC124946330, LOC124946331, LOC124946333, LOC124946334, LOC124946336, LOC124946337, LOC124946338, LOC124946339, LOC124946340, LOC126088081, LOC126861819, LOC126861820, LOC126861821, LOC126861822, LOC126861823, LOC126861824, LOC126861825, LOC126861826, LOC126861827, LOC126861828, LOC126861829, LOC126861830, LOC126861831, LOC126861832, LOC126861833, LOC126861834, LOC126861835, LOC126861836, LOC126861837, LOC126861838, LOC126861839, LOC126861840, LOC126861841, LOC126861842, LOC126861843, LOC126861844, LOC126861845, LOC126861846, LOC126861847, LOC126861848, LOC126861849, LOC126861850, LOC126861851, LOC126861852, LOC126861853, LOC126861854, LOC126861855, LOC126861856, LOC126861857, LOC126861858, LOC126861859, LOC126861860, LOC129390609, LOC130009997, LOC130009998, LOC130009999, LOC130010000, LOC130010001, LOC130010002, LOC130010003, LOC130010004, LOC130010005, LOC130010006, LOC130010007, LOC130010008, LOC130010009, LOC130010010, LOC130010011, LOC130010012, LOC130010013, LOC130010014, LOC130010015, LOC130010016, LOC130010017, LOC130010018, LOC130010019, LOC130010020, LOC130010021, LOC130010022, LOC130010023, LOC130010024, LOC130010025, LOC130010026, LOC130010027, LOC130010028, LOC130010029, LOC130010030, LOC130010031, LOC130010032, LOC130010033, LOC130010034, LOC130010035, LOC130010036, LOC130010037, LOC130010038, LOC130010039, LOC130010040, LOC130010041, LOC130010042, LOC130010043, LOC130010044, LOC130010045, LOC130010046, LOC130010047, LOC130010048, LOC130010049, LOC130010050, LOC130010051, LOC130010052, LOC130010053, LOC130010054, LOC130010055, LOC130010056, LOC130010057, LOC130010058, LOC130010059, LOC130010060, LOC130010061, LOC130010062, LOC130010063, LOC130010064, LOC130010065, LOC130010066, LOC130010067, LOC130010068, LOC130010069, LOC130010070, LOC130010071, LOC130010072, LOC130010073, LOC130010074, LOC130010075, LOC130010076, LOC130010077, LOC130010078, LOC130010079, LOC130010080, LOC130010081, LOC130010082, LOC130010083, LOC130010084, LOC130010085, LOC130010086, LOC130010087, LOC130010088, LOC130010089, LOC130010090, LOC130010091, LOC130010092, LOC130010093, LOC130010094, LOC130010095, LOC130010096, LOC130010097, LOC130010098, LOC130010099, LOC130010100, LOC130010101, LOC130010102, LOC130010103, LOC130010104, LOC130010105, LOC130010106, LOC130010107, LOC130010108, LOC130010109, LOC130010110, LOC130010111, LOC130010112, LOC130010113, LOC130010114, LOC130010115, LOC130010116, LOC130010117, LOC130010118, LOC130010119, LOC130010120, LOC130010121, LOC130010122, LOC130010123, LOC130010124, LOC130010125, LOC130010126, LOC130010127, LOC130010128, LOC130010129, LOC130010130, LOC130010131, LOC130010132, LOC130010133, LOC130010134, LOC130010135, LOC130010136, LOC130010137, LOC130010138, LOC130010139, LOC130010140, LOC130010141, LOC130010142, LOC130010143, LOC130010144, LOC130010145, LOC130010146, LOC130010147, LOC130494219, LOC132090155, LOC132090156, LOC132090157, LOC132090158, LOC132090159, LOC132090160, LOC132090161, LOC132090162, LOC132090163, LOC132090164, LOC132090165, LOC132090166, LOC132090167, LOC132090168, LOC132090169, LOC132090170, LOC132090171, LOC132090172, LOC132090173, LOC132090866, LOC132090867, METTL21C, MIR1267, MIR2681, MIR4306, MIR4705, MIR623, MIR8073, MYO16, NALCN, NALF1, NALF1-IT1, NAXD, PCCA, PCCA-DT, POGLUT2, PRECSIT, RAB20, SLC10A2, SLC15A1, SNORD31B, STK24, TEX30, TM9SF2, TMTC4, TNFSF13B, TPP2, UBAC2, ZIC2, ZIC5 1 0 0 0 0 0 1
ADCK5, BOP1, CCDC166, CPSF1, CYC1, CYP11B1, CYP11B2, DGAT1, EEF1D, EPPK1, EXOSC4, FAM83H, FBXL6, FOXH1, GFUS, GLI4, GML, GPAA1, GPIHBP1, GPT, GRINA, GSDMD, HGH1, HSF1, KIFC2, LY6D, LY6E, LY6H, LY6S, LYNX1, LYPD2, MAF1, MAFA, MAPK15, MFSD3, MIR1234, MIR661, MROH1, MROH6, NAPRT, NRBP2, OPLAH, PARP10, PLEC, PPP1R16A, PUF60, PYCR3, RECQL4, RHPN1, SCRIB, SCRT1, SCX, SHARPIN, SLC39A4, SLC52A2, SLURP1, SPATC1, TIGD5, TMEM249, TONSL, TOP1MT, VPS28, ZC3H3, ZFP41, ZFTRAF1, ZNF623, ZNF696, ZNF707 0 0 1 0 0 0 1
BIVM, BIVM-ERCC5, CCDC168, CLYBL, ERCC5, FGF14, GGACT, ITGBL1, METTL21C, NALCN, PCCA, POGLUT2, SLC10A2, TEX30, TM9SF2, TMTC4, TPP2, UBAC2, ZIC2, ZIC5 0 0 1 0 0 0 1
BLACE, CNPY1, DNAJB6, DPP6, DYNC2I1, EN2, EN2-DT, ESYT2, HTR5A, INSIG1, INSIG1-DT, LINC00244, LINC00689, LINC01022, LINC03010, LMBR1, LOC101927914, LOC105375589, LOC105375610, LOC106049962, LOC108254663, LOC110121044, LOC110121094, LOC110121203, LOC110599567, LOC113687207, LOC113687208, LOC114004407, LOC114255744, LOC116186918, LOC121201619, LOC121201620, LOC121201621, LOC121740705, LOC121740706, LOC121740707, LOC123956275, LOC123956276, LOC123956277, LOC123956278, LOC123956279, LOC123956280, LOC123956281, LOC123956282, LOC123956283, LOC123956284, LOC123956285, LOC126860237, LOC126860238, LOC126860239, LOC126860240, LOC126860241, LOC126860242, LOC126860243, LOC126860244, LOC126860245, LOC126860246, LOC126860247, LOC126860248, LOC126860249, LOC126860250, LOC126860251, LOC126860252, LOC126860253, LOC126860254, LOC126860255, LOC126860256, LOC126860257, LOC126860258, LOC126860259, LOC126860260, LOC126860261, LOC126860262, LOC126860263, LOC126860264, LOC126860265, LOC129389940, LOC129389941, LOC129389942, LOC129389943, LOC129389944, LOC129389945, LOC129389946, LOC129389947, LOC129389948, LOC129389949, LOC129389950, LOC129999690, LOC129999691, LOC129999692, LOC129999693, LOC129999694, LOC129999695, LOC129999696, LOC129999697, LOC129999698, LOC129999699, LOC129999700, LOC129999701, LOC129999702, LOC129999703, LOC129999704, LOC129999705, LOC129999706, LOC129999707, LOC129999708, LOC129999709, LOC129999710, LOC129999711, LOC129999712, LOC129999713, LOC129999714, LOC129999715, LOC129999716, LOC129999717, LOC129999718, LOC129999719, LOC129999720, LOC129999721, LOC129999722, LOC129999723, LOC129999724, LOC129999725, LOC129999726, LOC129999727, LOC129999728, LOC129999729, LOC129999730, LOC129999731, LOC129999732, LOC129999733, LOC129999734, LOC129999735, LOC129999736, LOC129999737, LOC129999738, LOC129999739, LOC129999740, LOC129999741, LOC129999742, LOC129999743, LOC129999744, LOC129999745, LOC129999746, LOC129999747, LOC129999748, LOC129999749, LOC129999750, LOC129999751, LOC129999752, LOC129999753, LOC129999754, LOC129999755, LOC129999756, LOC129999757, LOC129999758, LOC129999759, LOC129999760, LOC129999761, LOC129999762, LOC129999763, LOC129999764, LOC129999765, LOC129999766, LOC129999767, LOC129999768, LOC132089518, LOC132089519, LOC132089520, LOC285889, LOC389602, MIR153-2, MIR5707, MIR595, MNX1, NCAPG2, NOM1, PAXIP1, PAXIP1-DT, PTPRN2, RBM33, RBM33-DT, RNF32, RNF32-DT, SBE2, SHH, UBE3C, VIPR2, ZRS 1 0 0 0 0 0 1
BOC 0 0 1 0 0 0 1
CLYBL, DOCK9, FGF14, GGACT, GPR18, GPR183, ITGBL1, NALCN, PCCA, SLC15A1, TM9SF2, TMTC4, UBAC2, ZIC2, ZIC5 1 0 0 0 0 0 1
CLYBL, DOCK9, GGACT, GPR18, GPR183, PCCA, SLC15A1, STK24, TM9SF2, TMTC4, UBAC2, ZIC2, ZIC5 1 0 0 0 0 0 1
CLYBL, TM9SF2, UBAC2, ZIC2, ZIC5 1 0 0 0 0 0 1
CNIH3, CNIH4, DNAH14, NVL, WDR26 1 0 0 0 0 0 1
CNPY1, DNAJB6, EN2, HTR5A, INSIG1, LMBR1, MNX1, NCAPG2, NOM1, PAXIP1, PTPRN2, RBM33, RNF32, SHH, UBE3C 1 0 0 0 0 0 1
CNPY1, EN2, HTR5A, INSIG1, RBM33, SHH 1 0 0 0 0 0 1
DLGAP1, EMILIN2, LPIN2, MYL12A, MYL12B, MYOM1, TGIF1 1 0 0 0 0 0 1
DLL1 0 0 1 0 0 0 1
DLL1, LOC126859913 0 0 1 0 0 0 1
DNAJB6, LMBR1, MNX1, NOM1, RNF32, SHH, UBE3C 0 0 1 0 0 0 1
LOC130002132, PTCH1 0 1 0 0 0 0 1
LOC130062108, LOC130062109, LOC130062110, LOC130062111, TGIF1 1 0 0 0 0 0 1
LOC130065955, MATN4 0 0 1 0 0 0 1
MATN4 0 1 0 0 0 0 1
NSD1 0 1 0 0 0 0 1
SH2D1A 0 0 0 1 0 0 1
SIX2, SIX3 0 0 1 0 0 0 1
SUFU 0 0 1 0 0 0 1
ZRSR2 0 1 0 0 0 0 1

Submitter and significance breakdown #

Total submitters: 65
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Submitter pathogenic likely pathogenic uncertain significance likely benign benign not provided total
Labcorp Genetics (formerly Invitae), Labcorp 39 13 741 531 204 0 1528
Illumina Laboratory Services, Illumina 0 2 379 141 218 0 740
Fulgent Genetics, Fulgent Genetics 0 1 56 21 4 0 82
OMIM 60 0 3 0 0 0 63
GeneReviews 37 0 0 0 14 0 51
Genome-Nilou Lab 1 0 0 1 28 0 30
Muenke lab, National Institutes of Health 12 7 9 0 1 0 29
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories 1 0 1 1 16 0 19
Laboratory of Molecular Genetics, CHU Rennes 0 11 6 0 0 0 17
New York Genome Center 2 1 14 0 0 0 17
Baylor Genetics 7 3 2 0 0 0 12
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute 1 3 7 0 0 0 11
Centre for Mendelian Genomics, University Medical Centre Ljubljana 0 0 10 1 0 0 11
Revvity Omics, Revvity 0 0 10 0 0 0 10
Institute of Human Genetics, University of Leipzig Medical Center 0 2 6 0 0 0 8
Juno Genomics, Hangzhou Juno Genomics, Inc 3 5 0 0 0 0 8
Mendelics 2 0 1 1 3 0 7
Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein 1 1 5 0 0 0 7
Neuberg Centre For Genomic Medicine, NCGM 0 0 6 0 0 0 6
Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center 2 2 0 1 0 0 5
3billion 1 1 1 2 0 0 5
MVZ Medizinische Genetik Mainz 1 2 1 0 0 0 4
Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard 2 0 0 0 1 0 3
Laboratory of Medical Genetics, National & Kapodistrian University of Athens 1 1 1 0 0 0 3
Center for Reproductive Medicine, Peking University Third Hospital 0 1 2 0 0 0 3
Institute of Human Genetics, Clinical Exome/Genome Diagnostics Group, University Hospital Bonn 0 0 3 0 0 0 3
MGZ Medical Genetics Center 0 0 2 0 0 0 2
Centogene AG - the Rare Disease Company 0 0 2 0 0 0 2
Center For Human Genetics And Laboratory Diagnostics, Dr. Klein, Dr. Rost And Colleagues 0 1 1 0 0 0 2
Genetics and Molecular Pathology, SA Pathology 0 1 1 0 0 0 2
Seattle Children's Hospital Molecular Genetics Laboratory, Seattle Children's Hospital 2 0 0 0 0 0 2
Johns Hopkins Genomics, Johns Hopkins University 0 0 2 0 0 0 2
GenomeConnect - Brain Gene Registry 0 0 0 0 0 2 2
Solve-RD Consortium 0 2 0 0 0 0 2
Genetic Services Laboratory, University of Chicago 1 0 0 0 0 0 1
Institute of Human Genetics, University of Goettingen 1 0 0 0 0 0 1
Hehr Laboratory, Center for Human Genetics Regensburg 0 1 0 0 0 0 1
Molecular Genetics Laboratory, BC Children's and BC Women's Hospitals 0 0 1 0 0 0 1
Women's Health and Genetics/Laboratory Corporation of America, LabCorp 0 1 0 0 0 0 1
Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München 1 0 0 0 0 0 1
Genomic Research Center, Shahid Beheshti University of Medical Sciences 0 0 1 0 0 0 1
Clinical Genomics Laboratory, Washington University in St. Louis 0 1 0 0 0 0 1
CSER _CC_NCGL, University of Washington 0 0 0 1 0 0 1
Division of Human Genetics, Children's Hospital of Philadelphia 0 1 0 0 0 0 1
HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology 1 0 0 0 0 0 1
NeuroMeGen, Hospital Clinico Santiago de Compostela 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
Bioinformatics dept., Datar Cancer Genetics Limited, India 0 0 1 0 0 0 1
Institute of Human Genetics, University of Wuerzburg 0 1 0 0 0 0 1
Wangler Lab, Baylor College 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
Rare Disease Group, Clinical Genetics, Karolinska Institutet 0 1 0 0 0 0 1
Genetics Department, University Hospital of Toulouse 0 0 1 0 0 0 1
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen 0 0 0 0 1 0 1
UNC Molecular Genetics Laboratory, University of North Carolina at Chapel Hill 0 0 1 0 0 0 1
Clinical Genetics Laboratory, Federal University of Health Sciences of Porto Alegre 0 1 0 0 0 0 1
Human Genetics Section, Sidra Medicine 0 1 0 0 0 0 1
Institute of Human Genetics, University Hospital Muenster 0 0 1 0 0 0 1
Pittsburgh Clinical Genomics Laboratory, University of Pittsburgh Medical Center 0 1 0 0 0 0 1
GenomeConnect - Invitae Patient Insights Network 0 0 0 0 0 1 1
Suma Genomics 1 0 0 0 0 0 1
Clinical Genetics Laboratory, University Hospital Schleswig-Holstein 0 0 1 0 0 0 1
Molecular Genetics and NGS Laboratory, Hospital Fundacion Valle Del Lili 1 0 0 0 0 0 1
Dr.Nikuei Genetic Center 0 0 0 1 0 0 1

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