ClinVar Miner

Variants studied for orofacial cleft

Included ClinVar conditions (68):
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 association total
70 28 461 116 46 3 705

Gene and significance breakdown #

Total genes and gene combinations: 77
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Gene or gene combination pathogenic likely pathogenic uncertain significance likely benign benign association total
BMP4 6 2 136 50 13 0 192
TP63 12 4 111 38 8 0 172
NECTIN1 4 2 130 9 7 0 151
TBX22 11 2 17 10 9 0 47
SUMO1 1 0 12 2 0 0 15
IRF6 1 0 4 0 6 0 11
​intergenic 5 0 4 0 0 0 9
GRHL3 6 2 0 0 0 0 8
LRP6 1 0 7 0 0 0 8
BMP4, LOC109433677 0 0 3 1 1 0 5
LOC111162620, TP63 0 0 4 0 1 0 5
MSX1 3 0 1 0 0 0 4
CDH1 0 0 2 1 0 0 3
PDGFRA 0 0 3 0 0 0 3
SATB2 3 0 0 0 0 0 3
ARHGAP29 0 0 2 0 0 0 2
DLX4 1 0 0 1 0 0 2
FLNA 1 0 1 0 0 0 2
LOC129992137, MSX1 1 0 0 1 0 0 2
MEIS2 1 1 0 0 0 0 2
NIPBL 1 0 1 0 0 0 2
PLOD2 0 2 0 0 0 0 2
ACBD3, AIDA, ANGEL2, ARF1, ATF3, BATF3, BPNT1, BROX, BTNL10, C1orf115, C1orf35, C1orf74, CAMK1G, CAPN2, CAPN8, CCDC185, CDC42BPA, CENPF, CNIH3, CNIH4, COQ8A, DEGS1, DISP1, DNAH14, DTL, DUSP10, ENAH, EPHX1, EPRS1, ESRRG, FAM177B, FBXO28, FLVCR1, FLVCR1-DT, G0S2, GARIN4, GJC2, GPATCH2, GUK1, H2AC25, H2BC26, H3-3A, H3-3A-DT, H3-4, HHAT, HHIPL2, HLX, HSD11B1, IARS2, IBA57, IBA57-DT, INTS7, IRF6, ITPKB, ITPKB-IT1, JMJD4, KCNH1, KCNH1-IT1, KCNK2, KCTD3, LAMB3, LBR, LEFTY1, LEFTY2, LIN9, LINC00210, LINC00467, LINC00538, LINC01352, LINC01641, LINC01653, LINC01655, LINC01696, LINC01698, LINC01703, LINC01710, LINC01717, LINC01740, LINC01774, LINC02257, LINC02474, LINC02602, LINC02608, LINC02765, LINC02769, LINC02771, LINC02773, LINC02779, LINC02809, LINC02817, LINC02869, LOC101927143, LOC101927164, LOC105373289, LOC107325941, LOC107325942, LOC107985355, LOC110120610, LOC110120807, LOC110121042, LOC110121057, LOC110121257, LOC110121306, LOC110121307, LOC111429604, LOC112577535, LOC112577536, LOC112577537, LOC112577538, LOC112577542, LOC112577543, LOC112577544, LOC112577545, LOC112577546, LOC112577547, LOC112577548, LOC113939983, LOC113939984, LOC115804245, LOC115804246, LOC115804247, LOC115804248, LOC120807606, LOC120807610, LOC120908903, LOC120908904, LOC120908905, LOC120908906, LOC120908907, LOC120908908, LOC120908909, LOC120908910, LOC120908911, LOC121725072, LOC121725073, LOC121725074, LOC121725075, LOC122149491, LOC122149492, LOC122149493, LOC122149494, LOC122149495, LOC122149496, LOC122149497, LOC122152293, LOC122152294, LOC122152295, LOC122152296, LOC122152297, LOC122152298, LOC122152299, LOC122152300, LOC122152301, LOC122152302, LOC122152303, LOC122152304, LOC122152305, LOC122152306, LOC122152307, LOC122152308, LOC122152309, LOC122152310, LOC122152311, LOC122152312, LOC122152313, LOC122152314, LOC122152315, LOC122152316, LOC122152317, LOC126805996, LOC126805997, LOC126805998, LOC126805999, LOC126806000, LOC126806001, LOC126806002, LOC126806003, LOC126806004, LOC126806005, LOC126806006, LOC126806007, LOC126806008, LOC126806009, LOC126806010, LOC126806011, LOC126806012, LOC126806013, LOC126806014, LOC126806015, LOC126806016, LOC126806017, LOC126806018, LOC126806019, LOC126806020, LOC126806021, LOC126806022, LOC126806023, LOC126806024, LOC126806025, LOC126806026, LOC126806027, LOC126806028, LOC126806029, LOC126806030, LOC126806031, LOC126806032, LOC126806033, LOC126806034, LOC126806035, LOC126806036, LOC126806037, LOC126806038, LOC126806039, LOC128772240, LOC128772241, LOC128772242, LOC128772243, LOC128772244, LOC128772245, LOC129388734, LOC129388735, LOC129388736, LOC129388737, LOC129388738, LOC129388739, LOC129388740, LOC129388741, LOC129388742, LOC129388743, LOC129388744, LOC129388745, LOC129388746, LOC129388747, LOC129388748, LOC129388749, LOC129388750, LOC129388751, LOC129388752, LOC129388753, LOC129388754, LOC129388755, LOC129388756, LOC129388757, LOC129388758, LOC129388759, LOC129388760, LOC129388761, LOC129388762, LOC129388763, LOC129388764, LOC129388765, LOC129388766, LOC129388767, LOC129388768, LOC129388769, LOC129388770, LOC129388771, LOC129932422, LOC129932423, LOC129932424, LOC129932425, LOC129932426, LOC129932427, LOC129932428, LOC129932429, LOC129932430, LOC129932431, LOC129932432, LOC129932433, LOC129932434, LOC129932435, LOC129932436, LOC129932437, LOC129932438, LOC129932439, LOC129932440, LOC129932441, LOC129932442, LOC129932443, LOC129932444, LOC129932445, LOC129932446, LOC129932447, LOC129932448, LOC129932449, LOC129932450, LOC129932451, LOC129932452, LOC129932453, LOC129932454, LOC129932455, LOC129932456, LOC129932457, LOC129932458, LOC129932459, LOC129932460, LOC129932461, LOC129932462, LOC129932463, LOC129932464, LOC129932465, LOC129932466, LOC129932467, LOC129932468, LOC129932469, LOC129932470, LOC129932471, LOC129932472, LOC129932473, LOC129932474, LOC129932475, LOC129932476, LOC129932477, LOC129932478, LOC129932479, LOC129932480, LOC129932481, LOC129932482, LOC129932483, LOC129932484, LOC129932485, LOC129932486, LOC129932487, LOC129932488, LOC129932489, LOC129932490, LOC129932491, LOC129932492, LOC129932493, LOC129932494, LOC129932495, LOC129932496, LOC129932497, LOC129932498, LOC129932499, LOC129932500, LOC129932501, LOC129932502, LOC129932503, LOC129932504, LOC129932505, LOC129932506, LOC129932507, LOC129932508, LOC129932509, LOC129932510, LOC129932511, LOC129932512, LOC129932513, LOC129932514, LOC129932515, LOC129932516, LOC129932517, LOC129932518, LOC129932519, LOC129932520, LOC129932521, LOC129932522, LOC129932523, LOC129932524, LOC129932525, LOC129932526, LOC129932527, LOC129932528, LOC129932529, LOC129932530, LOC129932531, LOC129932532, LOC129932533, LOC129932534, LOC129932535, LOC129932536, LOC129932537, LOC129932538, LOC129932539, LOC129932540, LOC129932541, LOC129932542, LOC129932543, LOC129932544, LOC129932545, LOC129932546, LOC129932547, LOC129932548, LOC129932549, LOC129932550, LOC129932551, LOC129932552, LOC129932553, LOC129932554, LOC129932555, LOC129932556, LOC129932557, LOC129932558, LOC129932559, LOC129932560, LOC129932561, LOC129932562, LOC129932563, LOC129932564, LOC129932565, LOC129932566, LOC129932567, LOC129932568, LOC129932569, LOC129932570, LOC129932571, LOC129932572, LOC129932573, LOC129932574, LOC129932575, LOC129932576, LOC129932577, LOC129932578, LOC129932579, LOC129932580, LOC129932581, LOC129932582, LOC129932583, LOC129932584, LOC129932585, LOC129932586, LOC129932587, LOC129932588, LOC129932589, LOC129932590, LOC129932591, LOC129932592, LOC129932593, LOC129932594, LOC129932595, LOC129932596, LOC129932597, LOC129932598, LOC129932599, LOC129932600, LOC129932601, LOC129932602, LOC129932603, LOC129932604, LOC129932605, LOC129932606, LOC129932607, LOC129932608, LOC129932609, LOC129932610, LOC129932611, LOC129932612, LOC129932613, LOC129932614, LOC129932615, LOC129932616, LOC129932617, LOC129932618, LOC129932619, LOC129932620, LOC129932621, LOC129932622, LOC129932623, LOC129932624, LOC129932625, LOC129932626, LOC129932627, LOC129932628, LOC129932629, LOC129932630, LOC129932631, LOC129932632, LOC129932633, LOC129932634, LOC129932635, LOC129932636, LOC129932637, LOC129932638, LOC129932639, LOC129932640, LOC129932641, LOC129932642, LOC129932643, LOC129932644, LOC129932645, LOC129932646, LOC129932647, LOC129932648, LOC129932649, LOC129932650, LOC129932651, LOC129932652, LOC129932653, LOC129932654, LOC129932655, LOC129932656, LOC129932657, LOC129932658, LOC129932659, LOC129932660, LOC129932661, LOC129932662, LOC129932663, LOC129932664, LOC129932665, LOC129932666, LOC129932667, LOC129932668, LOC129932669, LOC129932670, LOC129932671, LOC129932672, LOC129932673, LOC129932674, LOC129932675, LOC129932676, LOC129932677, LOC129932678, LOC129932679, LOC129932680, LOC129932681, LOC129932682, LOC129932683, LOC129932684, LOC129932685, LOC129932686, LOC129932687, LOC129932688, LOC129932689, LOC129932690, LOC129932691, LOC129932692, LOC129932693, LOC129932694, LOC129932695, LOC129932696, LOC129932697, LOC129932698, LOC129932699, LOC129932700, LOC129932701, LOC129932702, LOC129932703, LOC129932704, LOC129932705, LOC129932706, LOC129932707, LOC129932708, LOC129932709, LOC129932710, LOC129932711, LOC129932712, LOC129932713, LOC129932714, LOC129932715, LOC129932716, LOC129932717, LOC129932718, LOC129932719, LOC129932720, LOC129932721, LOC129932722, LOC129932723, LOC132088617, LOC132088618, LOC132088619, LOC132088620, LOC132088621, LOC132088622, LOC132088623, LOC132088627, LOC132088628, LOC132088629, LOC132088630, LOC132088631, LOC132088632, LOC132088633, LOC132088634, LOC132088635, LOC132088636, LOC132088637, LOC132088638, LOC132088639, LOC132088640, LOC132088641, LOC132088644, LOC132088646, LOC132088647, LOC132088648, LOC132088649, LOC132088650, LOC132088651, LOC132088652, LOC132088653, LOC132088654, LOC132088656, LOC132088657, LOC132088658, LOC132088659, LOC132088660, LOC132088661, LOC132088662, LOC132088663, LOC132088664, LOC132088666, LOC132088667, LOC132088670, LOC132088671, LOC132088673, LOC132088674, LOC132090673, LOC132090674, LOC132090675, LOC132090676, LOC132205953, LPGAT1, LYPLAL1, LYPLAL1-DT, MARK1, MIA3, MIR194-1, MIR205, MIR205HG, MIR215, MIR3122, MIR320B2, MIR3620, MIR4260, MIR4666A, MIR4742, MIR5008, MIR664A, MIR6741, MIR6742, MIXL1, MRPL55, MTARC1, MTARC2, NEK2, NEK2-DT, NENF, NSL1, NTRAS, NVL, OBSCN, PACC1, PARP1, PPP2R5A, PROX1, PRSS38, PSEN2, PTPN14, PYCR2, RAB3GAP2, RCOR3, RD3, RHOU, RNA5S1, RNA5S10, RNA5S11, RNA5S12, RNA5S13, RNA5S14, RNA5S15, RNA5S16, RNA5S17, RNA5S2, RNA5S3, RNA5S4, RNA5S5, RNA5S6, RNA5S7, RNA5S8, RNA5S9, RNF187, RPS6KC1, RRP15, SDE2, SERTAD4, SLC30A1, SLC30A10, SMYD2, SNAP47, SNORA16B, SNORA36B, SPATA17, SPATA45, SRP9, STUM, SUSD4, SYT14, TAF1A, TATDN3, TGFB2, TGFB2-OT1, TLR5, TMEM63A, TP53BP2, TRAF3IP3, TRAF5, TRIM11, TRIM17, TRT-TGT2-1, USH2A, UTP25, VASH2, WDR26, WNT3A, WNT9A, ZC3H11B, ZNF678 0 0 0 0 0 1 1
ADAMTSL1 0 0 1 0 0 0 1
ADRA2B, ANKRD23, ANKRD36, ANKRD39, ARID5A, ASTL, CIAO1, CNNM3, CNNM4, DUSP2, FAHD2B, FAM178B, FER1L5, ITPRIPL1, KANSL3, LMAN2L, NCAPH, SEMA4C, SNRNP200, STARD7, TMEM127 1 0 0 0 0 0 1
AGBL4, AGBL4-IT1, BEND5, BTF3L4, C1orf185, CC2D1B, CDKN2C, COA7, DMRTA2, ELAVL4, EPS15, FAF1, GPX7, KTI12, LINC01562, LINC02808, LOC107992392, LOC110120607, LOC110120609, LOC112590801, LOC112590802, LOC112590803, LOC112590804, LOC115801428, LOC121725022, LOC122056869, LOC122056870, LOC122056871, LOC122056872, LOC122056873, LOC122056874, LOC126805730, LOC126805731, LOC126805732, LOC126805733, LOC129388513, LOC129388514, LOC129388515, LOC129388516, LOC129388517, LOC129388518, LOC129388519, LOC129388520, LOC129388521, LOC129388522, LOC129388523, LOC129388524, LOC129930503, LOC129930504, LOC129930505, LOC129930506, LOC129930507, LOC129930508, LOC129930509, LOC129930510, LOC129930511, LOC129930512, LOC129930513, LOC129930514, LOC129930515, LOC129930516, LOC129930517, LOC129930518, LOC129930519, LOC129930520, LOC129930521, LOC129930522, LOC129930523, LOC129930524, LOC129930525, LOC129930526, LOC129930527, LOC129930528, LOC129930529, LOC129930530, LOC129930531, LOC129930532, LOC129930533, LOC129930534, LOC129930535, LOC129930536, LOC129930537, LOC129930538, LOC129930539, LOC129930540, LOC129930541, LOC129930542, LOC129930543, LOC129930544, LOC129930545, LOC129930546, LOC129930547, LOC129930548, LOC129930549, LOC129930550, LOC129930551, LOC129930552, LOC129930553, LOC129930554, LOC129930555, LOC129930556, MIR4421, MIR6500, MIR761, NRDC, ORC1, OSBPL9, PRPF38A, RAB3B, RNF11, SHISAL2A, TTC39A, TUT4, TXNDC12, ZFYVE9, ZYG11B 0 0 0 0 0 1 1
AMER1 1 0 0 0 0 0 1
AMOTL1 0 1 0 0 0 0 1
ARF3 0 1 0 0 0 0 1
ARID1B, CLDN20, NOX3, SNX9, TFB1M, TIAM2, TMEM242, ZDHHC14 1 0 0 0 0 0 1
BAG2, BEND6, BMP5, COL21A1, DST, ELOVL5, FAM83B, GCLC, GFRAL, HCRTR2, HMGCLL1, KIAA1586, KILH, KLHL31, LINC00680, LINC01564, LINC03001, LOC101927189, LOC101927293, LOC113175007, LOC121132689, LOC121740652, LOC121740653, LOC123744825, LOC123744826, LOC123744827, LOC123744828, LOC123744829, LOC123744830, LOC123744831, LOC126088080, LOC126859694, LOC126859695, LOC126859696, LOC126859697, LOC126859698, LOC129389544, LOC129389545, LOC129996644, LOC129996645, LOC129996646, LOC129996647, LOC129996648, LOC129996649, LOC129996650, LOC129996651, LOC129996652, LOC129996653, LOC129996654, LOC129996655, LOC129996656, LOC129996657, LOC129996658, LOC129996659, LOC129996660, LOC129996661, LOC129996662, LOC129996663, LOC129996664, LOC129996665, LOC129996666, LOC129996667, LOC129996668, LOC129996669, LOC132089408, LOC132089409, LOC132089410, LOC132089411, LOC132089412, LOC132089413, LOC132090757, LRRC1, MIR548U, MIR5685, MLIP, MLIP-IT1, PRIM2, RAB23, TINAG, TRA-AGC12-3, TRA-AGC13-2, TRA-AGC16-1, TRA-AGC24-1, TRI-AAT1-1, TRM-CAT7-1, ZNF451 0 0 1 0 0 0 1
BMP4, CDKN3, CGRRF1, CNIH1, GCH1, GMFB, SAMD4A 1 0 0 0 0 0 1
C2CD3, LOC121392929 0 0 1 0 0 0 1
CDH11 0 0 1 0 0 0 1
CECR2 0 0 1 0 0 0 1
COL11A1 0 1 0 0 0 0 1
COL2A1 0 0 1 0 0 0 1
CPLANE1 0 0 1 0 0 0 1
DEPDC5 0 0 1 0 0 0 1
DNAH11 0 0 1 0 0 0 1
FANCD2, FANCD2OS 0 0 1 0 0 0 1
FGF10 0 1 0 0 0 0 1
FGF14 0 1 0 0 0 0 1
FST 0 1 0 0 0 0 1
GDF11 0 1 0 0 0 0 1
GJA1 0 1 0 0 0 0 1
GNB1 1 0 0 0 0 0 1
INPP1, LOC129935252 0 0 1 0 0 0 1
INPP5E 1 0 0 0 0 0 1
IRAK1 0 0 1 0 0 0 1
KIF1A 0 0 1 0 0 0 1
LEMD3, LOC124629392, LOC130008224, LOC130008225, LOC130008226 0 0 0 0 0 1 1
LOC109286564, TBX22 0 0 0 0 1 0 1
LRRC32 0 1 0 0 0 0 1
MAFB 0 1 0 0 0 0 1
MYO15A 0 0 0 1 0 0 1
MYO19, PIGW 0 1 0 0 0 0 1
NDC1 0 0 1 0 0 0 1
NDST1 0 0 1 0 0 0 1
NEK9 0 0 0 1 0 0 1
NFIA 0 1 0 0 0 0 1
NTN1 0 0 1 0 0 0 1
PPP1R13L 1 0 0 0 0 0 1
RAB3GAP1 1 0 0 0 0 0 1
ROR2 0 0 1 0 0 0 1
RUNX2 0 0 1 0 0 0 1
RYK 0 0 1 0 0 0 1
SETD5 1 0 0 0 0 0 1
SHANK1 1 0 0 0 0 0 1
SMARCA4 0 1 0 0 0 0 1
TAF1B 0 0 1 0 0 0 1
TENM4 0 0 0 1 0 0 1
TNFRSF13B 0 0 1 0 0 0 1
TTN 1 0 0 0 0 0 1
VANGL1 0 0 1 0 0 0 1
WFS1 1 0 0 0 0 0 1
ZNF462 0 0 1 0 0 0 1

Submitter and significance breakdown #

Total submitters: 48
Download table as spreadsheet
Submitter pathogenic likely pathogenic uncertain significance likely benign benign association total
Illumina Laboratory Services, Illumina 0 0 249 45 24 0 317
Fulgent Genetics, Fulgent Genetics 2 4 99 29 0 0 134
Labcorp Genetics (formerly Invitae), Labcorp 3 0 77 42 11 0 133
OMIM 32 0 3 0 0 0 35
Centre for Mendelian Genomics, University Medical Centre Ljubljana 4 4 2 0 0 0 10
Center for Personalized Medicine, Children's Hospital Los Angeles 2 1 6 1 0 0 10
Pharmacology and Genetics Laboratory, Bauru School of Dentistry, University of Sao Paulo 0 0 4 0 6 0 10
Grupo de Genetica Humana, Facultad de Medicina - Universidad de La Sabana 1 2 7 0 0 0 10
Lupski Lab, Baylor-Hopkins CMG, Baylor College of Medicine 1 0 7 0 0 0 8
Talkowski Laboratory, Center for Human Genetic Research, Massachusetts General Hospital 4 0 4 0 0 0 8
Hadassah Hebrew University Medical Center 0 2 2 2 0 0 6
Genomic Medicine Center of Excellence, King Faisal Specialist Hospital and Research Centre 0 3 1 0 0 0 4
University of Washington Center for Mendelian Genomics, University of Washington 0 2 2 0 0 0 4
Ludwig Lab, Institute of Human Genetics, University Hospital Bonn 4 0 0 0 0 0 4
Orthodontics Department, Peking University School and Hospital of Stomatology 2 2 0 0 0 0 4
Craniofacial science Laboratory, School of Dental Sciences, universiti sains malaysia 0 0 1 0 0 3 4
Mendelics 0 0 0 0 3 0 3
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute 0 1 2 0 0 0 3
Institute of Human Genetics, University of Leipzig Medical Center 0 1 2 0 0 0 3
Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard 0 0 3 0 0 0 3
Autoinflammatory diseases unit, CHU de Montpellier 2 1 0 0 0 0 3
HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology 1 0 1 0 0 0 2
Knight Diagnostic Laboratories, Oregon Health and Sciences University 0 1 1 0 0 0 2
Al Jalila Children’s Genomics Center, Al Jalila Childrens Speciality Hospital 1 1 0 0 0 0 2
Medical Genetics Laboratory, CHRU Nancy 2 0 0 0 0 0 2
Clinical Genetics Laboratory, University Hospital Schleswig-Holstein 2 0 0 0 0 0 2
Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein 0 0 2 0 0 0 2
Baylor Genetics 0 0 1 0 0 0 1
Genome Diagnostics Laboratory, University Medical Center Utrecht 1 0 0 0 0 0 1
Centogene AG - the Rare Disease Company 0 1 0 0 0 0 1
ClinVar Staff, National Center for Biotechnology Information (NCBI) 1 0 0 0 0 0 1
Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München 1 0 0 0 0 0 1
CSER _CC_NCGL, University of Washington 0 0 0 1 0 0 1
Laboratory of Molecular Genetics (Pr. Bezieau's lab), CHU de Nantes 1 0 0 0 0 0 1
Soonchunhyang University Bucheon Hospital, Soonchunhyang University Medical Center 0 0 1 0 0 0 1
Laboratory of Molecular Genetics, CHU Rennes 0 1 0 0 0 0 1
Equipe Genetique des Anomalies du Developpement, Université de Bourgogne 1 0 0 0 0 0 1
Genetics and Molecular Pathology, SA Pathology 0 0 1 0 0 0 1
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen 0 0 0 0 1 0 1
Genome Diagnostics Laboratory, Amsterdam University Medical Center 1 0 0 0 0 0 1
Laboratory of Medical Genetics, University of Torino 0 0 1 0 0 0 1
Human Genetics Department, Tarbiat Modares University 1 0 0 0 0 0 1
New York Genome Center 0 0 1 0 0 0 1
Genome-Nilou Lab 0 0 0 0 1 0 1
Clinical Genomics and Bioinformatics Laboratory, Pirogov Russian National Research Medical University 1 0 0 0 0 0 1
Shieh Lab, University of California, San Francisco 0 1 0 0 0 0 1
3billion, Medical Genetics 1 0 0 0 0 0 1
Dr.Nikuei Genetic Center 0 0 0 0 1 0 1

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