ClinVar Miner

Variants studied for common variable immunodeficiency

Included ClinVar conditions (23):
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 established risk allele likely risk allele risk factor not provided total
220 103 2100 1525 254 2 1 1 8 4109

Gene and significance breakdown #

Total genes and gene combinations: 53
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Gene or gene combination pathogenic likely pathogenic uncertain significance likely benign benign established risk allele likely risk allele risk factor not provided total
LRBA 77 39 911 683 100 0 0 0 4 1783
CR2 34 15 311 215 29 0 0 0 0 591
NFKB2 7 5 220 247 30 0 0 0 1 501
TNFRSF13B 30 11 168 86 16 2 0 1 3 297
TNFSF12, TNFSF12-TNFSF13 0 0 102 74 11 0 0 0 0 187
ICOS 9 3 78 54 21 0 0 0 0 158
LOC130067574, TNFRSF13C 1 1 59 43 8 0 0 0 0 101
LOC130004599, NFKB2 0 0 46 35 4 0 0 0 0 85
CR2, LOC126805994 5 0 40 32 3 0 0 0 0 77
NFKB1 20 16 14 4 7 0 0 0 0 57
CD19 6 1 41 5 4 0 0 0 0 56
TNFRSF13C 0 0 31 18 5 0 0 0 0 49
IKZF1 9 6 9 1 3 0 0 0 0 27
LOC130060153, TNFSF12, TNFSF12-TNFSF13 0 0 15 10 1 0 0 0 0 26
LOC121815964, NFKB2 0 0 9 6 1 0 0 0 0 16
IRF2BP2 1 1 7 1 3 0 0 0 0 13
LOC130004598, NFKB2 0 0 5 7 1 0 0 0 0 13
CD81 1 0 4 4 1 0 0 0 0 10
IRF2BP2, LOC129932812 1 2 4 0 3 0 0 0 0 10
MS4A1 1 0 5 0 1 0 0 0 0 7
LRBA, MAB21L2 4 0 1 0 0 0 0 0 0 5
ABI2, ALS2, BMPR2, C2CD6, CARF, CASP10, CASP8, CD28, CDK15, CFLAR, CTLA4, CYP20A1, FAM117B, FLACC1, FZD7, ICA1L, ICOS, MPP4, NBEAL1, NDUFB3, NOP58, RAPH1, STRADB, SUMO1, TMEM237, TRAK2, WDR12 1 0 1 0 0 0 0 0 0 2
BTK 0 0 1 0 0 0 1 0 0 2
CD40LG 1 0 1 0 0 0 0 0 0 2
IL21, LOC126807147 1 0 1 0 0 0 0 0 0 2
LOC123493218, LRBA 1 0 1 0 0 0 0 0 0 2
LOC126807127, NFKB1 0 1 1 0 0 0 0 0 0 2
NFKBID 0 0 2 0 0 0 0 0 0 2
RAG2 2 0 0 0 0 0 0 0 0 2
TTC7A 2 0 0 0 0 0 0 0 0 2
A4GALT, ACO2, ATP5MGL, CCDC134, CENPM, CHADL, CSDC2, CYB5R3, CYP2D6, DESI1, EP300, L3MBTL2, MEI1, MIR33A, NAGA, NDUFA6, NFAM1, PHETA2, PHF5A, PMM1, POLDIP3, POLR3H, RANGAP1, RBX1, RRP7A, SEPTIN3, SERHL2, SHISA8, SMDT1, SNU13, SREBF2, TCF20, TEF, TNFRSF13C, TOB2, WBP2NL, XPNPEP3, XRCC6, ZC3H7B 0 0 1 0 0 0 0 0 0 1
ACADVL, ACAP1, ALOX12, ALOX12B, ALOX15B, ALOXE3, ASGR1, ASGR2, ATP1B2, AURKB, BCL6B, BORCS6, C17orf49, CD68, CHD3, CHRNB1, CLDN7, CLEC10A, CNTROB, CTC1, CTDNEP1, CYB5D1, DLG4, DNAH2, DVL2, EFNB3, EIF4A1, EIF5A, ELP5, FBXO39, FGF11, FXR2, GABARAP, GPS2, GUCY2D, HES7, KCNAB3, KCTD11, KDM6B, MIR195, MIR497HG, MPDU1, NAA38, NEURL4, NLGN2, PER1, PHF23, PLSCR3, POLR2A, RNASEK, SAT2, SENP3, SHBG, SLC13A5, SLC16A11, SLC16A13, SLC2A4, SLC35G6, SOX15, SPEM1, SPEM2, TEKT1, TMEM102, TMEM107, TMEM256, TMEM88, TMEM95, TNFSF12, TNFSF12-TNFSF13, TNFSF13, TNK1, TP53, TRAPPC1, TRG-GCC2-6, TRK-TTT3-5, TRL-TAG1-1, TRQ-CTG1-5, TRR-TCT2-1, VAMP2, WRAP53, XAF1, YBX2, ZBTB4 0 0 1 0 0 0 0 0 0 1
ACADVL, ACAP1, ATP1B2, CD68, CHRNB1, CLDN7, CTDNEP1, DLG4, DVL2, EIF4A1, EIF5A, ELP5, FGF11, FXR2, GABARAP, GPS2, KCTD11, MPDU1, NEURL4, NLGN2, PHF23, PLSCR3, POLR2A, SAT2, SENP3, SHBG, SLC2A4, SLC35G6, SOX15, SPEM1, SPEM2, TMEM102, TMEM256, TMEM95, TNFSF12, TNFSF12-TNFSF13, TNFSF13, TNK1, TP53, WRAP53, YBX2, ZBTB4 0 0 1 0 0 0 0 0 0 1
ACO2, CCDC134, CENPM, CSDC2, DESI1, LOC105373044, LOC108348030, LOC110740341, LOC111562373, LOC112695098, LOC121627945, LOC121627946, LOC125446244, LOC126863159, LOC126863160, LOC130067537, LOC130067538, LOC130067539, LOC130067540, LOC130067541, LOC130067542, LOC130067543, LOC130067544, LOC130067545, LOC130067546, LOC130067547, LOC130067548, LOC130067549, LOC130067550, LOC130067551, LOC130067552, LOC130067553, LOC130067554, LOC130067555, LOC130067556, LOC130067557, LOC130067558, LOC130067559, LOC130067560, LOC130067561, LOC130067562, LOC130067563, LOC130067564, LOC130067565, LOC130067566, LOC130067567, LOC130067568, LOC130067569, LOC130067570, LOC130067571, LOC130067572, LOC130067573, LOC130067574, LOC130067575, LOC130067576, LOC130067577, LOC130067578, LOC130067579, LOC130067580, LOC130067581, MEI1, MIR33A, MIR378I, NAGA, PHF5A, PMM1, POLR3H, RANGAP1, SEPTIN3, SHISA8, SMIM45, SNU13, SREBF2, TEF, TNFRSF13C, TOB2, WBP2NL, XRCC6, ZC3H7B 0 0 1 0 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 0 0 0 1
ARID4B, B3GALNT2, COA6, GGPS1, GNG4, IRF2BP2, KCNK1, LINC00184, LINC01132, LINC01348, LINC01354, LINC02768, LINC02961, LINC02971, LINC03108, LNCATV, LOC101927787, LOC105373209, LOC107546745, LOC107546746, LOC107546747, LOC107548103, LOC111365197, LOC111365208, LOC112577555, LOC112577556, LOC112577557, LOC112577558, LOC112577559, LOC112577560, LOC120908915, LOC120908916, LOC120908917, LOC120908918, LOC120908919, LOC120908920, LOC120908921, LOC120908922, LOC120908923, LOC122152340, LOC122152341, LOC122152342, LOC122152343, LOC122152344, LOC122152345, LOC126264117, LOC126806052, LOC126806053, LOC126806054, LOC126806055, LOC126806056, LOC126806057, LOC126806058, LOC126806059, LOC126806060, LOC126806061, LOC126806062, LOC126806063, LOC126806064, LOC126806065, LOC129388781, LOC129388782, LOC129388783, LOC129388784, LOC129388785, LOC129388786, LOC129869688, 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, LOC132088683, LOC132088684, LYST, MIR1537, MIR4427, MIR4671, MIR4753, NID1, RBM34, SLC35F3, SNORA14B, TARBP1, TBCE, TOMM20 1 0 0 0 0 0 0 0 0 1
BANK1, BDH2, CENPE, CISD2, MANBA, NFKB1, SLC39A8, SLC9B1, SLC9B2, TACR3, UBE2D3 0 1 0 0 0 0 0 0 0 1
C1orf116, C4BPA, C4BPB, CD34, CD46, CD55, CR1, CR1L, CR2, FCAMR, FCMR, IL10, IL19, IL20, IL24, MIR29B2CHG, MIR29C, PFKFB2, PIGR, PLXNA2, YOD1 0 0 1 0 0 0 0 0 0 1
CR2, LOC129932399 0 0 0 0 1 0 0 0 0 1
CTLA4 0 1 0 0 0 0 0 0 0 1
CTLA4, ICOS 1 0 0 0 0 0 0 0 0 1
IKBKG 0 0 1 0 0 0 0 0 0 1
IL21 0 0 0 0 1 0 0 0 0 1
LOC108281188, LOC123493218, LOC129993220, LRBA 0 0 1 0 0 0 0 0 0 1
LOC108281188, LOC129993220, LRBA 0 0 1 0 0 0 0 0 0 1
LOC108281188, LOC129993221, LOC129993222, LOC129993223, LRBA 1 0 0 0 0 0 0 0 0 1
LOC121815964, LOC130004598, LOC130004599, NFKB2 0 0 1 0 0 0 0 0 0 1
LOC123493216, LOC129993219, LRBA 1 0 0 0 0 0 0 0 0 1
LOC129993220, LRBA 0 0 1 0 0 0 0 0 0 1
MANBA, NFKB1 1 0 0 0 0 0 0 0 0 1
RUVBL1, SEC61A1 1 0 0 0 0 0 0 0 0 1
SEC61A1 1 0 0 0 0 0 0 0 0 1
STIM1 0 0 1 0 0 0 0 0 0 1

Submitter and significance breakdown #

Total submitters: 77
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Submitter pathogenic likely pathogenic uncertain significance likely benign benign established risk allele likely risk allele risk factor not provided total
Invitae 150 31 1888 1487 214 0 0 0 0 3770
Illumina Laboratory Services, Illumina 0 0 88 9 21 0 0 0 0 118
Genome-Nilou Lab 3 3 45 11 35 0 0 0 0 97
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories 1 1 9 21 36 0 0 0 0 68
Baylor Genetics 2 3 47 0 0 0 0 0 0 52
OMIM 50 0 0 0 0 0 0 0 0 50
Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago 1 3 34 3 0 0 0 0 0 41
Fulgent Genetics, Fulgent Genetics 0 2 23 11 0 0 0 0 0 36
Revvity Omics, Revvity 1 4 25 0 0 0 0 0 0 30
Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein 0 10 16 0 0 0 0 0 0 26
Neuberg Centre For Genomic Medicine, NCGM 1 3 15 0 0 0 0 0 0 19
Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center 2 3 8 1 1 0 0 0 0 15
3billion 6 5 2 0 0 0 0 0 0 13
NIHR Bioresource Rare Diseases, University of Cambridge 10 1 1 0 0 0 0 0 0 12
Institute of Human Genetics, University of Leipzig Medical Center 5 5 1 0 0 0 0 0 0 11
UOSD Laboratory of Genetics & Genomics of Rare Diseases, Istituto Giannina Gaslini 1 0 7 3 0 0 0 0 0 11
New York Genome Center 0 1 10 0 0 0 0 0 0 11
Mendelics 4 3 3 0 0 0 0 0 0 10
Genetics and Molecular Pathology, SA Pathology 0 2 4 2 0 0 0 0 0 8
Women's Health and Genetics/Laboratory Corporation of America, LabCorp 3 2 0 1 1 0 0 0 0 7
Centogene AG - the Rare Disease Company 0 2 4 0 0 0 0 0 0 6
Johns Hopkins Genomics, Johns Hopkins University 1 1 3 0 0 0 0 0 0 5
Clinic of Clinical Immunology with Stem Cell Bank, Expert Centre for Rare Diseases - PID, University Hospital "Alexandrovska" 3 3 0 0 0 0 0 0 0 5
Pediatric Infectious Diseases and Immunodeficiencies Unit (UPIIP)- HUVH-VHIR, Vall d'Hebron University Hospital 1 1 2 0 0 0 1 0 0 5
Genome Diagnostics Laboratory, University Medical Center Utrecht 0 1 0 1 2 0 0 0 0 4
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute 1 1 2 0 0 0 0 0 0 4
Samuels research lab, Centre de Recherche du CHU Ste-Justine 4 0 0 0 0 0 0 0 0 4
GenomeConnect, ClinGen 0 0 0 0 0 0 0 0 4 4
GenomeConnect - Invitae Patient Insights Network 0 0 0 0 0 0 0 0 4 4
Healthincode, Healthincode group 2 2 0 0 0 0 0 0 0 4
Mayo Clinic Laboratories, Mayo Clinic 0 0 3 0 0 0 0 0 0 3
Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego 2 1 0 0 0 0 0 0 0 3
Immunogenetics Laboratory, Johns Hopkins All Children's Hospital 1 2 0 0 0 0 0 0 0 3
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center 0 0 0 2 1 0 0 0 0 3
Biochemical Molecular Genetic Laboratory, King Abdulaziz Medical City 1 2 0 0 0 0 0 0 0 3
Al Jalila Children's Genomics Center, Al Jalila Childrens Speciality Hospital 0 0 1 2 0 0 0 0 0 3
Diagnostics Services (NGS), CSIR - Centre For Cellular And Molecular Biology 0 1 2 0 0 0 0 0 0 3
Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center 1 1 0 0 0 0 0 0 0 2
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine 0 2 0 0 0 0 0 0 0 2
Institute of Human Genetics, Cologne University 0 2 0 0 0 0 0 0 0 2
Genomic Research Center, Shahid Beheshti University of Medical Sciences 1 0 1 0 0 0 0 0 0 2
Department of Molecular and Human Genetics, Baylor College of Medicine 2 0 0 0 0 0 0 0 0 2
Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics 0 2 0 0 0 0 0 0 0 2
Hadassah Hebrew University Medical Center 0 2 0 0 0 0 0 0 0 2
Bioscientia Institut fuer Medizinische Diagnostik GmbH, Sonic Healthcare 0 1 1 0 0 0 0 0 0 2
Centre for Mendelian Genomics, University Medical Centre Ljubljana 0 1 1 0 0 0 0 0 0 2
Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India 0 0 2 0 0 0 0 0 0 2
Department of Pathology and Laboratory Medicine, Sinai Health System 0 0 0 0 0 2 0 0 0 2
Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen 0 2 0 0 0 0 0 0 0 2
Molecular Diagnostics Laboratory, M Health Fairview: University of Minnesota 0 2 0 0 0 0 0 0 0 2
Clinical Genomics Program, Stanford Medicine 0 0 2 0 0 0 0 0 0 2
Beijing Key Laboratry for Genetics of Birth Defects, Beijing Children's Hospital 0 2 0 0 0 0 0 0 0 2
Genetic Services Laboratory, University of Chicago 0 1 0 0 0 0 0 0 0 1
Molecular Genetics Laboratory - Diagnostics Genetics, LabPLUS - Auckland City Hospital 1 0 0 0 0 0 0 0 0 1
MGZ Medical Genetics Center 0 1 0 0 0 0 0 0 0 1
Intergen, Intergen Genetics and Rare Diseases Diagnosis Center 0 1 0 0 0 0 0 0 0 1
Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München 1 0 0 0 0 0 0 0 0 1
UCLA Clinical Genomics Center, UCLA 0 1 0 0 0 0 0 0 0 1
Division of Human Genetics, Children's Hospital of Philadelphia 1 0 0 0 0 0 0 0 0 1
Knight Diagnostic Laboratories, Oregon Health and Sciences University 0 1 0 0 0 0 0 0 0 1
Center of Genomic medicine, Geneva, University Hospital of Geneva 0 0 0 0 0 0 0 1 0 1
Genetech, Genetech Research Institute 0 0 1 0 0 0 0 0 0 1
Undiagnosed Diseases Network, NIH 0 0 1 0 0 0 0 0 0 1
Department of Immunology, University Hospital Southampton NHSFT 1 0 0 0 0 0 0 0 0 1
Institute for Genomic Medicine, Nationwide Children's Hospital 0 1 0 0 0 0 0 0 0 1
Seattle Children's Hospital Molecular Genetics Laboratory, Seattle Children's Hospital 0 1 0 0 0 0 0 0 0 1
Laboratory of Medical Genetics, National & Kapodistrian University of Athens 0 1 0 0 0 0 0 0 0 1
St. Jude Molecular Pathology, St. Jude Children's Research Hospital 0 0 1 0 0 0 0 0 0 1
Immunology Clinic, Ucla 1 0 0 0 0 0 0 0 0 1
Breda Genetics srl 0 0 1 0 0 0 0 0 0 1
University of Washington Department of Laboratory Medicine, University of Washington 0 1 0 0 0 0 0 0 0 1
Clinical Immunology, Karolinska University Hospital 1 0 0 0 0 0 0 0 0 1
Suma Genomics 0 0 1 0 0 0 0 0 0 1
Bioinformatics Unit, Institut Pasteur de Montevideo 1 0 0 0 0 0 0 0 0 1
Servicio de Inmunologia, Hospital Universitario Virgen del Rocio 1 0 0 0 0 0 0 0 0 1
Department of Human Genetics, Hannover Medical School 0 0 1 0 0 0 0 0 0 1
Medizinische Genetik Mainz, Limbach Genetics GmbH 0 1 0 0 0 0 0 0 0 1

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