ClinVar Miner

Variants studied for non-syndromic polydactyly

Included ClinVar conditions (43):
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
101 39 420 254 171 12 977

Gene and significance breakdown #

Total genes and gene combinations: 47
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Gene or gene combination pathogenic likely pathogenic uncertain significance likely benign benign not provided total
GLI3 22 8 193 48 10 0 281
PIK3R2 4 4 88 120 55 2 269
AKT3 5 7 31 52 14 3 108
LMBR1 0 0 47 4 52 0 103
LOC130063979, PIK3R2 0 1 19 23 8 0 51
HOXD13 18 1 6 0 1 0 25
IQCE 5 2 1 0 16 0 24
CCND2 8 4 5 1 2 7 19
GLI1 5 2 3 0 3 0 12
LMBR1, ZRS 11 1 0 0 0 0 12
KIAA0825 5 0 2 0 2 0 9
FBLN1 0 0 5 1 2 0 8
LMBR1, LOC129999727 0 0 4 1 3 0 8
LOC130063980, PIK3R2 0 0 1 4 1 0 6
CIBAR1 2 2 0 0 0 0 3
​intergenic 0 0 2 0 0 0 2
AKT3, SDCCAG8 1 0 1 0 0 0 2
CC2D2A 2 0 0 0 0 0 2
EFCAB7 0 0 2 0 0 0 2
KIAA0825, LOC126807453 0 1 1 0 0 0 2
PIGL 0 0 2 0 0 0 2
ZNF141 1 1 0 0 1 0 2
ACTN2, AGT, AKT3, ARID4B, ARV1, B3GALNT2, BECN2, C1orf131, C1orf198, CAPN9, CEP170, CHML, CHRM3, COA6, COG2, DISC1, DISC1-IT1, DISC2, EDARADD, EGLN1, ERO1B, EXO1, EXOC8, FAM89A, FH, FMN2, GALNT2, GGPS1, GNG4, GNPAT, GPR137B, GREM2, HEATR1, IRF2BP2, KCNK1, KMO, LGALS8, LINC00184, LINC00582, LINC01132, LINC01139, LINC01347, LINC01348, LINC01354, LINC01737, LINC01744, LINC01745, LINC02768, LINC02961, LINC02971, LINC03108, LNCATV, LOC100506929, LOC101927604, LOC101927787, LOC105373209, LOC107546745, LOC107546746, LOC107546747, LOC107546778, LOC107546780, LOC107548103, LOC108004528, LOC110121205, LOC110121263, LOC110121264, LOC110121265, LOC110121266, LOC111365197, LOC111365208, LOC112577554, LOC112577555, LOC112577556, LOC112577557, LOC112577558, LOC112577559, LOC112577560, LOC112577561, LOC112577565, LOC115804249, LOC115804250, LOC115804251, LOC115804252, LOC115804253, LOC120908915, LOC120908916, LOC120908917, LOC120908918, LOC120908919, LOC120908920, LOC120908921, LOC120908922, LOC120908923, LOC121725076, LOC122152333, LOC122152334, LOC122152335, LOC122152336, LOC122152337, LOC122152338, LOC122152339, LOC122152340, LOC122152341, LOC122152342, LOC122152343, LOC122152344, LOC122152345, LOC122152346, LOC122152347, LOC122152348, LOC122152349, LOC122152350, LOC122152351, LOC122152352, LOC122152353, LOC122526782, LOC126264117, LOC126806042, LOC126806043, LOC126806044, LOC126806045, LOC126806046, LOC126806047, LOC126806048, LOC126806049, LOC126806050, LOC126806051, LOC126806052, LOC126806053, LOC126806054, LOC126806055, LOC126806056, LOC126806057, LOC126806058, LOC126806059, LOC126806060, LOC126806061, LOC126806062, LOC126806063, LOC126806064, LOC126806065, LOC126806066, LOC126806067, LOC126806068, LOC126806069, LOC126806070, LOC126806071, LOC126806072, LOC126806073, LOC126806074, LOC129388775, LOC129388776, LOC129388777, LOC129388778, LOC129388779, LOC129388780, LOC129388781, LOC129388782, LOC129388783, LOC129388784, LOC129388785, LOC129388786, LOC129388787, LOC129388788, LOC129388789, LOC129388790, LOC129388791, LOC129388792, LOC129388793, LOC129388794, LOC129388795, LOC129388796, LOC129388797, LOC129388798, LOC129388799, LOC129869688, LOC129929020, LOC129932752, LOC129932753, LOC129932754, LOC129932755, LOC129932756, LOC129932757, LOC129932758, LOC129932759, LOC129932760, LOC129932761, LOC129932762, LOC129932763, LOC129932764, LOC129932765, LOC129932766, LOC129932767, LOC129932768, LOC129932769, LOC129932770, LOC129932771, LOC129932772, LOC129932773, LOC129932774, LOC129932775, LOC129932776, LOC129932777, LOC129932778, LOC129932779, LOC129932780, LOC129932781, LOC129932782, LOC129932783, LOC129932784, LOC129932785, LOC129932786, LOC129932787, LOC129932788, LOC129932789, LOC129932790, LOC129932791, LOC129932792, LOC129932793, LOC129932794, LOC129932795, LOC129932796, LOC129932797, LOC129932798, LOC129932799, LOC129932800, LOC129932801, LOC129932802, LOC129932803, LOC129932804, LOC129932805, LOC129932806, LOC129932807, LOC129932808, LOC129932809, LOC129932810, LOC129932811, LOC129932812, LOC129932813, LOC129932814, LOC129932815, LOC129932816, LOC129932817, LOC129932818, LOC129932819, LOC129932820, LOC129932821, LOC129932822, LOC129932823, LOC129932824, LOC129932825, LOC129932826, LOC129932827, LOC129932828, LOC129932829, LOC129932830, LOC129932831, LOC129932832, LOC129932833, LOC129932834, LOC129932835, LOC129932836, LOC129932837, LOC129932838, LOC129932839, LOC129932840, LOC129932841, LOC129932842, LOC129932843, LOC129932844, LOC129932845, LOC129932846, LOC129932847, LOC129932848, LOC129932849, LOC129932850, LOC129932851, LOC129932852, LOC129932853, LOC129932854, LOC129932855, LOC129932856, LOC129932857, LOC129932858, LOC129932859, LOC129932860, LOC129932861, LOC129932862, LOC129932863, LOC129932864, LOC129932865, LOC129932866, LOC129932867, LOC129932868, LOC129932869, LOC129932870, LOC129932871, LOC129932872, LOC129932873, LOC129932874, LOC129932875, LOC129932876, LOC129932877, LOC129932878, LOC129932879, LOC129932880, LOC129932881, LOC129932882, LOC129932883, LOC129932884, LOC129932885, LOC129932886, LOC129932887, LOC129932888, LOC129932889, LOC129932890, LOC129932891, LOC132088676, LOC132088677, LOC132088678, LOC132088679, LOC132088680, LOC132088681, LOC132088683, LOC132088684, LOC132088685, LOC132088686, LOC132090677, LYST, MAP10, MAP1LC3C, MAP3K21, MIR1182, MIR1537, MIR3123, MIR4427, MIR4428, MIR4671, MIR4677, MIR4753, MT1HL1, MTR, NID1, NTPCR, OPN3, PCNX2, PGBD5, PLD5, RBM34, RGS7, RYR2, SDCCAG8, SIPA1L2, SLC35F3, SNORA14B, SPRTN, TARBP1, TBCE, TOMM20, TRIM67, TSNAX, TSNAX-DISC1, TTC13, WDR64, ZP4 1 0 0 0 0 0 1
ADSS2, AKT3, CATSPERE, CEP170, CHML, COX20, DESI2, EXO1, FH, HNRNPU, KMO, MAP1LC3C, OPN3, PLD5, SDCCAG8, SPMIP3, WDR64, ZBTB18 0 0 1 0 0 0 1
AKT3, AKT3-IT1, CEP170, LINC01347, LINC02774, LOC110120698, LOC111828504, LOC112577566, LOC122152350, LOC122152351, LOC122152352, LOC122152353, LOC122152354, LOC126806071, LOC126806072, LOC126806073, LOC126806074, LOC126806075, LOC129388799, LOC129932891, LOC129932892, LOC129932893, LOC129932894, LOC129932895, LOC129932896, LOC129932897, LOC129932898, LOC129932899, LOC129932900, LOC440742, MIR4677, PLD5, SDCCAG8, SPMIP3, ZBTB18 1 0 0 0 0 0 1
AKT3, CEP170, SDCCAG8 0 0 1 0 0 0 1
ARMC6, ARRDC2, BORCS8, CCDC124, CERS1, COMP, COPE, CRLF1, CRTC1, DDX49, ELL, FKBP8, GDF1, GDF15, HOMER3, IFI30, IL12RB1, INSL3, IQCN, ISYNA1, JAK3, JUND, KCNN1, KLHL26, KXD1, LRRC25, LSM4, MAST3, MEF2B, MPV17L2, NR2C2AP, PDE4C, PGPEP1, PIK3R2, RAB3A, REX1BD, RFXANK, RPL18A, SLC25A42, SLC5A5, SSBP4, SUGP2, TMEM161A, TMEM59L, UBA52, UPF1 0 0 1 0 0 0 1
ATP6V1B1 1 0 0 0 0 0 1
BBIP1 1 0 0 0 0 0 1
BBS10 1 0 0 0 0 0 1
BBS12 1 0 0 0 0 0 1
BCL11A 1 0 0 0 0 0 1
CHST11 0 0 1 0 0 0 1
DHX34 0 1 0 0 0 0 1
EP300, LOC126863158 1 0 0 0 0 0 1
EVX2, LOC110120627 0 1 0 0 0 0 1
IQCE, LOC126859928 0 0 0 0 1 0 1
IQCE, LOC129997827 0 1 0 0 0 0 1
KIF7 0 1 0 0 0 0 1
LMBR1, SHH, ZRS 1 0 0 0 0 0 1
LOC100507346, PTCH1 1 0 0 0 0 0 1
LSM1 0 0 1 0 0 0 1
MT-ATP6, MT-ATP8, MT-CO1, MT-CO2, MT-CO3, MT-ND1, MT-ND2, MT-ND3, MT-ND4, MT-ND4L, MT-ND5, MT-TA, MT-TC, MT-TD, MT-TG, MT-TH, MT-TI, MT-TK, MT-TM, MT-TN, MT-TQ, MT-TR, MT-TS1, MT-TS2, MT-TW, MT-TY 1 0 0 0 0 0 1
OFD1 0 0 1 0 0 0 1
PTCH1 0 1 0 0 0 0 1
TULP1 1 0 0 0 0 0 1
ZEB2 0 0 1 0 0 0 1

Submitter and significance breakdown #

Total submitters: 67
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Submitter pathogenic likely pathogenic uncertain significance likely benign benign not provided total
Labcorp Genetics (formerly Invitae), Labcorp 4 2 126 198 78 0 408
Fulgent Genetics, Fulgent Genetics 5 1 193 51 7 0 257
Illumina Laboratory Services, Illumina 0 0 51 5 55 0 111
OMIM 50 0 0 0 0 0 50
Genome-Nilou Lab 0 0 0 0 34 0 34
Centre for Mendelian Genomics, University Medical Centre Ljubljana 7 1 8 0 0 0 16
GeneReviews 0 0 0 0 0 11 11
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute 9 0 2 0 0 0 11
Baylor Genetics 4 2 4 0 0 0 10
Revvity Omics, Revvity 2 0 8 0 0 0 10
Institute for Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin 9 1 0 0 0 0 10
3billion, Medical Genetics 5 2 3 0 0 0 10
Institute of Human Genetics, University of Leipzig Medical Center 3 4 1 0 0 0 8
Genomic Medicine Center of Excellence, King Faisal Specialist Hospital and Research Centre 3 2 2 0 0 0 7
Neuberg Centre For Genomic Medicine, NCGM 1 0 6 0 0 0 7
Juno Genomics, Hangzhou Juno Genomics, Inc 3 1 2 0 0 0 6
Equipe Genetique des Anomalies du Developpement, Université de Bourgogne 3 2 0 0 0 0 5
Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen 3 2 0 0 0 0 5
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center 1 0 0 0 4 0 5
MGZ Medical Genetics Center 1 1 2 0 0 0 4
Lupski Lab, Baylor-Hopkins CMG, Baylor College of Medicine 2 1 1 0 0 0 4
Center for Statistical Genetics, Columbia University 2 0 2 0 0 0 4
Laboratory of Medical Genetics (UMR_S 1112), INSERM/Strasbourg University 4 0 0 0 0 0 4
Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München 0 3 0 0 0 0 3
Laboratory of Medical Genetics, National & Kapodistrian University of Athens 1 2 0 0 0 0 3
Human Molecular Lab, Hazara University 3 0 0 0 0 0 3
Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet 0 1 1 0 0 0 2
Institute for Genomic Medicine (IGM) Clinical Laboratory, Nationwide Children's Hospital 2 0 0 0 0 0 2
Intergen, Intergen Genetics and Rare Diseases Diagnosis Center 1 0 1 0 0 0 2
Clinical Genomics Laboratory, Washington University in St. Louis 0 0 2 0 0 0 2
HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology 0 1 1 0 0 0 2
Molecular Genetics Department, Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology 0 2 0 0 0 0 2
Talkowski Laboratory, Center for Human Genetic Research, Massachusetts General Hospital 0 0 2 0 0 0 2
Department of Medical Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences 1 1 0 0 0 0 2
Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India 2 0 0 0 0 0 2
Institute for Genomic Medicine, Nationwide Children's Hospital 2 0 0 0 0 0 2
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen 0 0 0 0 2 0 2
Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard 2 0 0 0 0 0 2
New York Genome Center 0 0 2 0 0 0 2
MVZ Medizinische Genetik Mainz 0 0 2 0 0 0 2
Genome Diagnostics Laboratory, University Medical Center Utrecht 1 0 0 0 0 0 1
Women's Health and Genetics/Laboratory Corporation of America, LabCorp 1 0 0 0 0 0 1
Mendelics 0 0 0 0 1 0 1
ClinVar Staff, National Center for Biotechnology Information (NCBI) 0 1 0 0 0 0 1
Genomic Research Center, Shahid Beheshti University of Medical Sciences 0 0 0 0 1 0 1
Institute of Human Genetics, FAU Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg 1 0 0 0 0 0 1
Institute for Human Genetics and Genomic Medicine, Uniklinik RWTH Aachen 1 0 0 0 0 0 1
University of Washington Center for Mendelian Genomics, University of Washington 0 1 0 0 0 0 1
Hadassah Hebrew University Medical Center 0 1 0 0 0 0 1
NeuroMeGen, Hospital Clinico Santiago de Compostela 0 1 0 0 0 0 1
Center For Human Genetics And Laboratory Diagnostics, Dr. Klein, Dr. Rost And Colleagues 0 1 0 0 0 0 1
MVZ Praenatalmedizin und Genetik Nuernberg 0 1 0 0 0 0 1
Department of Animal Sciences, Quaid-i-Azam University 1 0 0 0 0 0 1
SIB Swiss Institute of Bioinformatics 0 0 1 0 0 0 1
TIDEX, University of British Columbia 0 1 0 0 0 0 1
GenomeConnect, ClinGen 0 0 0 0 0 1 1
Tolun Lab, Human Genetics Laboratory, Bogazici University 0 0 1 0 0 0 1
Wendy Chung Laboratory, Columbia University Medical Center 0 0 1 0 0 0 1
Genomic Medicine Lab, University of California San Francisco 1 0 0 0 0 0 1
Johns Hopkins Genomics, Johns Hopkins University 0 0 1 0 0 0 1
Department of Genetics, Rouen University Hospital, Normandy Center for Genomic and Personalized Medicine 1 0 0 0 0 0 1
Zotz-Klimas Genetics Lab, MVZ Zotz Klimas 1 0 0 0 0 0 1
Department of Pediatrics, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University 0 1 0 0 0 0 1
Kids Neuroscience Centre, Sydney Children's Hospitals Network 1 0 0 0 0 0 1
Institute of Human Genetics, Clinical Exome/Genome Diagnostics Group, University Hospital Bonn 0 1 0 0 0 0 1
Human Genome Lab, NIMHANS, National Institute of Mental Health and Neuro Sciences 0 1 0 0 0 0 1
Molecular Genetics and NGS Laboratory, Hospital Fundacion Valle Del Lili 0 1 0 0 0 0 1

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