ClinVar Miner

Variants studied for Meckel syndrome

Included ClinVar conditions (40):
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
1256 521 3747 4661 345 2 10101

Gene and significance breakdown #

Total genes and gene combinations: 57
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Gene or gene combination pathogenic likely pathogenic uncertain significance likely benign benign not provided total
CEP290 511 112 943 1478 90 2 3026
CC2D2A 181 82 618 878 52 0 1722
RPGRIP1L 206 77 567 772 49 0 1605
TMEM67 111 79 353 429 26 0 946
MKS1 83 77 289 417 18 0 824
TCTN2 28 20 260 194 26 0 508
TMEM231 30 7 157 126 16 0 334
TCTN1 20 12 140 140 14 0 326
NPHP3, NPHP3-ACAD11 14 12 150 40 4 0 219
B9D1 3 4 72 67 10 0 149
CEP290, RLIG1 20 6 38 30 1 0 88
TMEM216 5 14 39 4 7 0 66
LOC130061271, MKS1 9 3 27 22 1 0 56
B9D2 3 2 15 13 11 0 42
CEP290, LOC129390514 2 2 12 19 1 0 36
LOC129937586, NPHP3, NPHP3-ACAD11 0 0 20 4 0 0 24
B9D1, LOC130060455 0 0 13 7 2 0 21
LOC130059440, TMEM231 3 1 7 6 1 0 18
KIF14 2 1 6 2 3 0 14
TSHB 6 1 3 2 1 0 12
ATP6V0A2, TCTN2 0 0 1 3 6 0 8
TXNDC15 6 2 1 0 0 0 7
LOC105371520, TMEM107 3 0 0 0 2 0 5
LOC130008755, TCTN1 0 0 0 4 1 0 5
LOC130059035, RPGRIP1L 0 0 3 0 0 0 3
ADAT1, GABARAPL2, KARS1, TERF2IP, TMEM231 1 0 1 0 0 0 2
ATP6V0A2, LOC130009117, TCTN2 0 0 0 2 0 0 2
B9D2, TGFB1 0 0 1 0 1 0 2
LOC129937587, NPHP3, NPHP3-ACAD11 0 0 1 0 1 0 2
TMEM218 2 0 0 0 0 0 2
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 0 1
AKAP10, ALDH3A1, ALDH3A2, B9D1, EPN2, EPN2-IT1, FAM83G, GRAP, GRAPL, LINC02094, LOC102724624, LOC105371574, LOC121852925, LOC121852926, LOC125177436, LOC125177437, LOC125177438, LOC125177439, LOC126862517, LOC130060435, LOC130060436, LOC130060437, LOC130060438, LOC130060439, LOC130060440, LOC130060441, LOC130060442, LOC130060443, LOC130060444, LOC130060445, LOC130060446, LOC130060447, LOC130060448, LOC130060449, LOC130060450, LOC130060451, LOC130060452, LOC130060453, LOC130060454, LOC130060455, LOC130060456, LOC130060457, LOC130060458, LOC130060459, LOC130060460, LOC130060461, LOC130060462, LOC130060463, LOC130060464, LOC130060465, LOC130060466, LOC130060467, LOC130060468, LOC130060469, LOC130060470, LOC130060471, LOC130060472, LOC130060473, LOC130060474, LOC130060475, LOC130060476, LOC130060477, LOC130060478, LOC130060479, LOC130060480, LOC130060481, LOC132090459, LOC388436, MAPK7, MFAP4, MIR1180, PRPSAP2, RNF112, SLC47A1, SLC47A2, SLC5A10, SNORA59B, SNORD3A, SNORD3B-1, SNORD3B-2, SNORD3C, SNORD3D, SPECC1, SPECC1-DT, TRG-CCC3-1, TRW-CCA2-1, ULK2 1 0 0 0 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 0 1
BST1, CC2D2A, CD38, FAM200B, FBXL5, FGFBP1, FGFBP2, PROM1, TAPT1 0 0 1 0 0 0 1
C12orf50, CEP290, KITLG, RLIG1, TMTC3 1 0 0 0 0 0 1
CCDC172 0 0 1 0 0 0 1
CEP290, LOC129390514, LOC130008346, RLIG1 1 0 0 0 0 0 1
CEP295 0 0 1 0 0 0 1
CHST5, CHST6, TMEM170A, TMEM231 1 0 0 0 0 0 1
CHST5, CHST6, TMEM231 1 0 0 0 0 0 1
CIMIP2B 0 0 1 0 0 0 1
CSPP1 0 1 0 0 0 0 1
DUOX2 0 0 0 1 0 0 1
EIF2B1, GTF2H3, TCTN2 0 0 1 0 0 0 1
EVC2 0 1 0 0 0 0 1
EXOC3L2 0 1 0 0 0 0 1
EXOC4, LOC101928861 0 1 0 0 0 0 1
FTO, IRX3, IRX5, IRX6, MMP2, RPGRIP1L 1 0 0 0 0 0 1
FTO, IRX3, IRX5, RPGRIP1L 0 0 1 0 0 0 1
FTO, RPGRIP1L 0 0 0 1 0 0 1
KIAA0586 0 1 0 0 0 0 1
PDP1, TMEM67 1 0 0 0 0 0 1
SNORD118, TMEM107 0 0 1 0 0 0 1
TGFB1 0 0 0 0 1 0 1
TMEM138 0 1 0 0 0 0 1
TMEM237 0 1 0 0 0 0 1
TTC6 0 0 1 0 0 0 1

Submitter and significance breakdown #

Total submitters: 58
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Submitter pathogenic likely pathogenic uncertain significance likely benign benign not provided total
Invitae 1180 291 3031 4556 287 0 9345
Illumina Laboratory Services, Illumina 0 2 637 50 59 0 747
Fulgent Genetics, Fulgent Genetics 89 76 428 148 2 0 743
Natera, Inc. 5 2 84 11 7 0 109
Juha Muilu Group; Institute for Molecular Medicine Finland (FIMM) 1 82 0 0 0 0 83
Counsyl 1 31 33 5 0 0 70
Genome-Nilou Lab 0 0 14 0 55 0 69
OMIM 48 0 0 0 0 0 48
New York Genome Center 1 1 34 0 0 0 36
Baylor Genetics 9 2 18 0 0 0 29
Department Of Translational Genomics (developmental Genetics Section), King Faisal Specialist Hospital & Research Centre 9 13 4 0 0 0 26
Genetic Services Laboratory, University of Chicago 14 7 3 0 0 0 24
Women's Health and Genetics/Laboratory Corporation of America, LabCorp 15 8 0 0 0 0 23
Myriad Genetics, Inc. 1 18 0 0 0 0 19
Pathology and Clinical Laboratory Medicine, King Fahad Medical City 6 9 0 0 0 0 15
Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India 2 6 0 0 0 0 8
Neuberg Supratech Reference Laboratories Pvt Ltd, Neuberg Centre for Genomic Medicine 3 1 4 0 0 0 8
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen 0 0 0 0 7 0 7
3billion 3 1 3 0 0 0 7
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center 0 0 0 1 5 0 6
Institute of Human Genetics, University of Leipzig Medical Center 1 0 4 0 0 0 5
Johns Hopkins Genomics, Johns Hopkins University 3 2 0 0 0 0 5
Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center 1 3 0 0 0 0 4
Genomic Research Center, Shahid Beheshti University of Medical Sciences 1 1 2 0 0 0 4
Centre for Mendelian Genomics, University Medical Centre Ljubljana 2 1 1 0 0 0 4
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute 2 0 1 0 0 0 3
Center For Human Genetics And Laboratory Diagnostics, Dr. Klein, Dr. Rost And Colleagues 1 2 0 0 0 0 3
Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard 1 0 1 1 0 0 3
Suma Genomics 2 0 1 0 0 0 3
Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center 2 0 1 0 0 0 3
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine 0 2 0 0 0 0 2
Revvity Omics, Revvity 2 0 0 0 0 0 2
MGZ Medical Genetics Center 1 0 0 1 0 0 2
Institute Of Human Genetics Munich, Klinikum Rechts Der Isar, Tu München 2 0 0 0 0 0 2
Knight Diagnostic Laboratories, Oregon Health and Sciences University 1 1 0 0 0 0 2
Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics 1 0 1 0 0 0 2
UW Hindbrain Malformation Research Program, University of Washington 2 0 0 0 0 0 2
Diagnostics Division, CENTRE FOR DNA FINGERPRINTING AND DIAGNOSTICS 0 2 0 0 0 0 2
Medical Genetic Institute of Henan Province, Henan Provincial People’s Hospital 2 0 0 0 0 0 2
Center for Molecular Medicine, Children’s Hospital of Fudan University 0 2 0 0 0 0 2
Geisinger Autism and Developmental Medicine Institute, Geisinger Health System 0 0 2 0 0 0 2
GenomeConnect, ClinGen 0 0 0 0 0 2 2
Biochemical Molecular Genetic Laboratory, King Abdulaziz Medical City 0 1 1 0 0 0 2
Laboratory of Medical Genetics, National & Kapodistrian University of Athens 2 0 0 0 0 0 2
Sydney Genome Diagnostics, Children's Hospital Westmead 2 0 0 0 0 0 2
Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein 1 0 1 0 0 0 2
Medical Genetics Center, Maternal and Child Health Hospital of Hubei Province 0 1 1 0 0 0 2
Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital 1 0 0 0 0 0 1
Genome Diagnostics Laboratory, University Medical Center Utrecht 0 0 0 1 0 0 1
Blueprint Genetics 0 1 0 0 0 0 1
Hadassah Hebrew University Medical Center 0 1 0 0 0 0 1
Institute of Human Genetics, University Hospital of Duesseldorf 1 0 0 0 0 0 1
Rare Disease Group, Clinical Genetics, Karolinska Institutet 1 0 0 0 0 0 1
Department Of Genetics, Sultan Qaboos University Hospital, Sultan Qaboos University 1 0 0 0 0 0 1
Institute of Human Genetics, Heidelberg University 0 1 0 0 0 0 1
Diagnostics Services (NGS), CSIR - Centre For Cellular And Molecular Biology 1 0 0 0 0 0 1
Department of Clinical Genetics and Genetic Counseling, Mediscan Systems 1 0 0 0 0 0 1
DASA 0 1 0 0 0 0 1

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