ClinVar Miner

Variants studied for Joubert syndrome 1

Included ClinVar conditions (11):
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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 total
1585 457 4220 5989 478 12600

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 total
CEP290 538 81 864 1521 89 3084
CC2D2A 197 56 530 944 42 1764
RPGRIP1L 214 60 522 806 45 1605
AHI1 165 40 434 616 53 1306
TMEM67 119 50 300 457 27 950
MKS1 95 34 224 435 16 800
INPP5E 53 42 372 272 43 731
OFD1 40 9 312 237 83 681
TCTN2 35 16 219 224 24 517
TCTN1 22 13 145 151 15 345
TMEM216 21 13 55 118 10 217
B9D1 8 3 58 73 6 147
CEP290, RLIG1 20 0 35 31 1 87
LOC130061271, MKS1 7 0 20 23 0 50
B9D2 4 1 16 14 8 42
LOC126863212, OFD1 2 0 25 10 2 39
CEP290, LOC129390514 2 2 11 21 1 37
B9D1, LOC130060455 1 0 10 9 1 21
CPLANE1 6 8 5 2 0 21
CEP41 0 0 9 3 1 13
TTC21B 0 0 9 1 3 13
ARMC9 0 10 0 0 0 10
AHI1, LOC128669075 0 0 0 9 0 9
TOGARAM1 8 8 1 0 0 9
TMEM237 1 1 4 1 1 8
CYB561A3, TMEM138 0 0 6 1 0 7
ARL13B 0 1 1 1 2 5
LOC130008755, TCTN1 0 0 0 4 1 5
ATP6V0A2, TCTN2 1 0 1 0 2 4
C2CD3 3 0 1 0 0 4
KIAA0753 3 1 0 0 0 4
TMEM138 0 0 4 0 0 4
NPHP1 0 0 2 0 1 3
OFD1, TRAPPC2 0 0 3 0 0 3
PIBF1 0 2 2 0 0 3
TMEM218 3 0 0 0 0 3
ATP6V0A2, LOC130009117, TCTN2 0 0 0 2 0 2
B9D2, TGFB1 0 0 1 0 1 2
C12orf50, CEP290, RLIG1 2 0 0 0 0 2
CBY1 2 0 0 0 0 2
CLUAP1 0 2 0 0 0 2
KATNIP 0 1 1 0 0 2
KIAA0586 1 1 0 0 0 2
USH2A 0 0 2 0 0 2
ABCA2, AGPAT2, AJM1, ANAPC2, ARRDC1, C8G, C9orf163, CACNA1B, CAMSAP1, CARD9, CCDC183, CIMIP2A, CLIC3, CYSRT1, DIPK1B, DNLZ, DPH7, DPP7, EDF1, EGFL7, EHMT1, ENTPD2, ENTPD8, ENTR1, EXD3, FBXW5, FUT7, GLT6D1, GPSM1, GRIN1, INPP5E, KCNT1, LCN1, LCN10, LCN12, LCN15, LCN6, LCN8, LCN9, LCNL1, LHX3, LINC02908, LOC651337, LRRC26, MAMDC4, MAN1B1, MIR126, MRPL41, MRPS2, NACC2, NDOR1, NELFB, NOTCH1, NOXA1, NPDC1, NRARP, NSMF, OBP2A, PAEP, PAXX, PHPT1, PMPCA, PNPLA7, PTGDS, QSOX2, RABL6, RNF208, RNF224, SAPCD2, SEC16A, SLC34A3, SNAPC4, SNHG7, SOHLH1, SSNA1, STPG3, TMEM141, TMEM203, TMEM210, TMEM250, TOR4A, TPRN, TRAF2, TUBB4B, UAP1L1, UBAC1, ZMYND19 1 0 0 0 0 1
AGPAT2, C9orf163, EGFL7, ENTR1, INPP5E, MIR126, NOTCH1, PMPCA, SEC16A 0 0 1 0 0 1
AHI1, LOC129389653, LOC129997223 1 0 0 0 0 1
AKAP1, APPBP2, BCAS3, BRIP1, C17orf47, C17orf67, CA4, CHCT1, CLTC, COIL, CUEDC1, DGKE, DHX40, DYNLL2, DYNLL2-DT, EPX, GDPD1, HEATR6, HSF5, LINC02875, LPO, MIR21, MKS1, MPO, MRPS23, MSI2, MTMR4, NACA2, NOG, OR4D1, OR4D2, PPM1D, PPM1E, PRR11, PTRH2, RAD51C, RNF43, RNFT1, RPS6KB1, SCPEP1, SEPTIN4, SKA2, SMG8, SRSF1, SUPT4H1, TBX2, TBX4, TEX14, TRIM25, TRIM37, TSPOAP1, TUBD1, USP32, VEZF1, VMP1, YPEL2 0 0 1 0 0 1
ALDH3A2, ALKBH5, ATPAF2, B9D1, COPS3, DRC3, DRG2, EPN2, EVPLL, FAM83G, FBXW10, FLCN, FLII, GID4, GRAP, GRAPL, LGALS9C, LLGL1, MAPK7, MED9, MFAP4, MIEF2, MIR33B, MPRIP, MYO15A, NT5M, PEMT, PLD6, PRPSAP2, RAI1, RASD1, RNF112, SHMT1, SLC47A1, SLC5A10, SMCR8, SNORD3A, SREBF1, TBC1D28, TNFRSF13B, TOM1L2, TOP3A, TRIM16L, TVP23B 0 0 1 0 0 1
ATXN3L, EGFL6, FAM9C, OFD1, RAB9A, TCEANC, TLR7, TLR8, TMSB4X, TRAPPC2 1 0 0 0 0 1
BST1, CC2D2A, CD38, FAM200B, FBXL5, FGFBP1, FGFBP2, PROM1, TAPT1 0 0 1 0 0 1
C12orf50, CEP290, KITLG, RLIG1, TMTC3 1 0 0 0 0 1
CARD9, ENTR1, INPP5E, PMPCA, SNAPC4 1 0 0 0 0 1
CEP104 0 0 1 0 0 1
CEP290, LOC129390514, LOC130008346, RLIG1 1 0 0 0 0 1
CPLANE1, LOC129993816 0 0 0 1 0 1
CPSF7, SDHAF2, TMEM216 0 0 1 0 0 1
EIF2B1, GTF2H3, TCTN2 0 0 1 0 0 1
EXOC8 0 0 1 0 0 1
FAM149B1 0 1 0 0 0 1
FTO, IRX3, IRX5, IRX6, MMP2, RPGRIP1L 1 0 0 0 0 1
FTO, IRX3, IRX5, RPGRIP1L 0 0 1 0 0 1
FTO, RPGRIP1L 0 0 0 1 0 1
IFT172 1 0 0 0 0 1
INPP5E, SEC16A 0 0 1 0 0 1
KIF7 0 0 1 0 0 1
LOC126863212, LOC130067975, LOC130067976, OFD1 1 0 0 0 0 1
LOC129935417, TMEM237 0 0 1 0 0 1
LRRC34 0 0 1 0 0 1
MICALL2 1 0 0 0 0 1
PDP1, TMEM67 1 0 0 0 0 1
PDPR 0 0 0 1 0 1
RCOR1 0 1 0 0 0 1
SLC30A7 1 0 0 0 0 1
TMEM17 0 0 1 0 0 1
TMEM231 0 0 1 0 0 1
WDPCP 0 0 1 0 0 1

Submitter and significance breakdown #

Total submitters: 37
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Submitter pathogenic likely pathogenic uncertain significance likely benign benign total
Labcorp Genetics (formerly Invitae), Labcorp 1517 380 4004 5959 462 12321
Natera, Inc. 9 5 177 15 15 221
Illumina Laboratory Services, Illumina 0 0 115 22 27 164
Fulgent Genetics, Fulgent Genetics 1 20 84 4 0 109
UW Hindbrain Malformation Research Program, University of Washington 53 4 0 0 0 57
Mendelics 14 8 6 3 15 46
University of Washington Center for Mendelian Genomics, University of Washington 0 18 1 0 0 19
Genomic Medicine Center of Excellence, King Faisal Specialist Hospital and Research Centre 1 4 5 1 0 11
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine 3 7 0 0 0 10
Centre for Mendelian Genomics, University Medical Centre Ljubljana 2 3 5 0 0 10
OMIM 4 0 2 0 0 6
Genome-Nilou Lab 0 0 0 0 6 6
Baylor Genetics 0 0 5 0 0 5
Genomic Research Center, Shahid Beheshti University of Medical Sciences 0 1 2 1 0 4
Rare Disease Group, Clinical Genetics, Karolinska Institutet 3 1 0 0 0 4
Institute of Human Genetics, University Hospital of Duesseldorf 1 2 0 0 0 3
Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard 0 0 3 0 0 3
Molecular and Clinical Genetics, Institute of Human Genetics P.A.S. 3 0 0 0 0 3
Al Jalila Children’s Genomics Center, Al Jalila Childrens Speciality Hospital 1 2 0 0 0 3
Biesecker Lab/Clinical Genomics Section, National Institutes of Health 0 2 0 0 0 2
GeneReviews 2 0 0 0 0 2
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute 1 1 0 0 0 2
Department of Medical Genetics, Oslo University Hospital 2 0 0 0 0 2
Lupski Lab, Baylor-Hopkins CMG, Baylor College of Medicine 2 0 0 0 0 2
Universitätsklinikum Salzburg, Universitätskinderklinik 1 1 0 0 0 2
Biochemical Molecular Genetic Laboratory, King Abdulaziz Medical City 1 1 0 0 0 2
Reproductive Health Research and Development, BGI Genomics 1 0 1 0 0 2
Clinical Genomics Laboratory, Stanford Medicine 0 0 2 0 0 2
Pittsburgh Clinical Genomics Laboratory, University of Pittsburgh Medical Center 0 2 0 0 0 2
Department of Neurology, Linyi People’s Hospital, The Eleventh Clinical Medical College of Qingdao University 2 0 0 0 0 2
Neuberg Centre For Genomic Medicine, NCGM 0 0 2 0 0 2
Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India 0 0 1 0 0 1
Yale Center for Mendelian Genomics, Yale University 0 1 0 0 0 1
Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen 0 1 0 0 0 1
Prenatal Diagnosis Center, The Sixth Medical Center of PLA General Hospital 1 0 0 0 0 1
DASA 1 0 0 0 0 1
Payam Genetics Center, General Welfare Department of North Khorasan Province 0 1 0 0 0 1

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