Common variable immunodeficiency

disease
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Also known as common variable hypogamma-globulinemiaCommon Variable Immune Deficiencyhypogamma-globulinemia, acquiredImmunoglobulin deficiency, late-onsetprimary antibody deficiencyprimary hypogammaglobulinemiasecondary hypogammaglobulinemia

Summary

Common variable immunodeficiency (MONDO:0015517) is a disease (an umbrella term covering 16 Mondo subtypes) with 65 cohort genes (52 GWAS associations across 3 studies) and 42 clinical trials. The dominant Reactome pathway is Interleukin-23 signaling (4 cohort genes). Top therapeutic interventions include human immunoglobulin g, dextrose, and leniolisib.

At a glance

  • Umbrella term: 16 Mondo subtypes
  • Cohort genes: 65
  • GWAS associations: 52
  • ClinVar variants: 294
  • Clinical trials: 42

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

FieldValue
Canonical namecommon variable immunodeficiency
Mondo IDMONDO:0015517
MeSHD017074
OMIM607594
Orphanet1572
DOIDDOID:12177
ICD-10-CMD83
ICD-111908371517
NCITC26725
SNOMED CT23238000
UMLSC0009447
MedGen40407
GARD0006140
MedDRA10021449
NORD990
Is cancer (heuristic)no

Also known as: common variable hypogamma-globulinemia · Common Variable Immune Deficiency · common variable immune deficiency · hypogamma-globulinemia, acquired · Immunoglobulin deficiency, late-onset · primary antibody deficiency · primary hypogammaglobulinemia · secondary hypogammaglobulinemia

Data availability: 294 ClinVar variants · 52 GWAS associations (3 studies) · 15 GenCC gene-disease records · 23 cell lines.

Disease family

An umbrella term covering 16 Mondo subtypes.

Classification path: disease › human disease › disease by body system or component › syndromic diseasesyndromic agammaglobulinemiacommon variable immunodeficiency

Related subtypes (2): transient hypogammaglobulinemia, agammaglobulinemia-microcephaly-craniosynostosis-severe dermatitis syndrome

Subtypes (16): immune deficiency, familial variable, immunodeficiency, common variable, 2, immunodeficiency, common variable, 1, immunodeficiency, common variable, 3, immunodeficiency, common variable, 4, immunodeficiency, common variable, 5, immunodeficiency, common variable, 6, immunodeficiency, common variable, 7, combined immunodeficiency due to LRBA deficiency, immunodeficiency, common variable, 10, IL21-related infantile inflammatory bowel disease, immunodeficiency, common variable, 12, pancytopenia due to IKZF1 mutations, immunodeficiency, common variable, 14, immunodeficiency, common variable, due to APRIL deficiency, immunodeficiency, common variable, 15

Genetics & variants

GWAS landscape

52 GWAS associations across 3 studies. Top hits map to 38 distinct genes (as reported by GWAS).

Top associations by p-value

rsIDp-valueGeneRisk alleleOdds ratio
rs10492255e-16HLA-DQB1-AS1, HLA-DQB1A0.56
rs115800788e-11IL23R, C1orf141G
rs77250528e-11RNU1-150P - TTC33C
rs66796778e-11PHTF1 - RSBN1A
rs108220508e-11LINC02929 - ALDH7A1P4C
rs178857858e-11INS-IGF2, IGF2, IGF2-AST
rs727434778e-11SMAD3G
rs1173723898e-11NKD1T
rs20663638e-11ADGRL2C
rs76605208e-11TENM3 - DCTDA
rs71000258e-11LINC00993G
rs360014888e-11ATG16L1C
rs46258e-11BSN-DT, DAG1G
rs13320999e-11NKX2-3 - SLC25A28T
rs77316261e-10ANKRD55A
rs7553742e-10IL12B-AS1T
rs174666263e-10LRRK2G
rs117412552e-09IRF1, CARINHA
rs178060562e-09CLEC16AA0.66
rs16895104e-09SUOXC
rs125983574e-09SBK1 - NPIPB6G
rs7067786e-09IL2RAT
rs771500436e-09ADCY7T
rs42469051e-08TNFSF15T
rs12505631e-08ZMIZ1C
rs28072641e-08RNU6-320P - LINC00892C
rs623242123e-08IL21-AS1A
rs111457633e-08CARD9C
rs6026625e-08FUT2G
rs28368825e-08LINC02940 - RPL23AP12A

Top studies (by case count)

StudyLead authorYearCasesControlsTitle
GCST90301675Li J201577810,999Association of CLEC16A with human common variable immunodeficiency disorder and role in murine B cells.
GCST001039Orange JS20111791,917Genome-wide association identifies diverse causes of common variable immunodeficiency.
GCST003097Li YR20159710,718Meta-analysis of shared genetic architecture across ten pediatric autoimmune diseases.

Variant details and genetic-evidence tiers

Tier distribution (top 50 variants)

TierVariants
Tier 1: coding1
Tier 2: splice/UTR4
Tier 3: regulatory1
Tier 4: intronic/intergenic44

MAF distribution

BucketVariants
common (>=0.05)46
low_freq (0.01-0.05)4
rare (<0.01)0
unknown0

Functional consequences

ConsequenceCount
intron_variant29
intergenic_variant15
3_prime_UTR_variant3
missense_variant1
regulatory_region_variant1
splice_region_variant1

Top variants

rsIDChrPosAllelesMAFConsequenceGenep-valueTier
rs1049225632659970A>C,G,T0.263_prime_UTR_variantHLA-DQB1-AS1, HLA-DQB15e-16Tier 2: splice/UTR
rs11580078167203951C>A,G,T0.43intron_variantIL23R, C1orf1418e-11Tier 4: intronic/intergenic
rs7725052540487168C>T0.43intron_variantRNU1-150P - TTC338e-11Tier 4: intronic/intergenic
rs66796771113761186C>A,T0.09intergenic_variantPHTF1 - RSBN18e-11Tier 4: intronic/intergenic
rs108220501062679011T>C,G0.39intergenic_variantLINC02929 - ALDH7A1P48e-11Tier 4: intronic/intergenic
rs17885785112146620C>T0.2intron_variantINS-IGF2, IGF2, IGF2-AS8e-11Tier 4: intronic/intergenic
rs727434771567171953A>C,G,T0.21intron_variantSMAD38e-11Tier 4: intronic/intergenic
rs1173723891650634166G>T0.023_prime_UTR_variantNKD18e-11Tier 2: splice/UTR
rs2066363181771892C>A,T0.34intron_variantADGRL28e-11Tier 4: intronic/intergenic
rs76605204182824168G>A,C0.26intergenic_variantTENM3 - DCTD8e-11Tier 4: intronic/intergenic
rs71000251037303610G>A0.34intron_variantLINC009938e-11Tier 4: intronic/intergenic
rs360014882233276621C>G,T0.48intron_variantATG16L18e-11Tier 4: intronic/intergenic
rs4625349534707A>G0.313_prime_UTR_variantBSN-DT, DAG18e-11Tier 2: splice/UTR
rs13320991099538694T>A,C,G0.46intergenic_variantNKX2-3 - SLC25A289e-11Tier 4: intronic/intergenic
rs7731626556148856G>A,C0.39intron_variantANKRD551e-10Tier 4: intronic/intergenic
rs7553745159402286C>A,G,T0.32intergenic_variantIL12B-AS12e-10Tier 4: intronic/intergenic
rs174666261240366829A>G0.02intron_variantLRRK23e-10Tier 4: intronic/intergenic
rs117412555132475490G>A0.42intron_variantIRF1, CARINH2e-09Tier 4: intronic/intergenic
rs178060561611098642T>A0.23intron_variantCLEC16A2e-09Tier 4: intronic/intergenic
rs16895101256002984G>A,C0.31intron_variantSUOX4e-09Tier 4: intronic/intergenic
rs125983571628329624A>G,T0.39intergenic_variantSBK1 - NPIPB64e-09Tier 4: intronic/intergenic
rs706778106056986C>G,T0.41intron_variantIL2RA6e-09Tier 4: intronic/intergenic
rs771500431650270338C>T0.23intron_variantADCY76e-09Tier 4: intronic/intergenic
rs42469059114790969T>A,C0.28intron_variantTNFSF151e-08Tier 4: intronic/intergenic
rs12505631079287626G>C0.29intron_variantZMIZ11e-08Tier 4: intronic/intergenic
rs2807264X136583619C>A,G,T0.21intergenic_variantRNU6-320P - LINC008921e-08Tier 4: intronic/intergenic
rs623242124122639784C>A,G0.42intron_variantIL21-AS13e-08Tier 4: intronic/intergenic
rs111457639136369144A>C,G,T0.4intron_variantCARD93e-08Tier 4: intronic/intergenic
rs6026621948703728G>A0.49missense_variantFUT25e-08Tier 1: coding
rs28368822139094644G>A0.27regulatory_region_variantLINC02940 - RPL23AP125e-08Tier 3: regulatory

ClinVar germline variants

294 retrieved; paginated sample, class counts are floors:

153 uncertain significance, 105 likely benign, 10 benign, 10 pathogenic, 5 conflicting classifications of pathogenicity, 4 benign/likely benign, 3 pathogenic/likely pathogenic, 3 likely pathogenic, 1 conflicting classifications of pathogenicity; risk factor

ClinVarVariant (HGVS)GeneClassificationReview
636694NM_003998.4(NFKB1):c.830dup (p.Lys278fs)NFKB1Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
827719NM_003998.4(NFKB1):c.260T>G (p.Ile87Ser)NFKB1Pathogeniccriteria provided, single submitter
827720NM_003998.4(NFKB1):c.293T>A (p.Val98Asp)NFKB1Pathogeniccriteria provided, single submitter
827721NM_003998.4(NFKB1):c.843C>G (p.Ile281Met)NFKB1Pathogeniccriteria provided, single submitter
827723NM_003998.4(NFKB1):c.1423del (p.Ala475fs)NFKB1Pathogeniccriteria provided, single submitter
827726NM_003998.4(NFKB1):c.850C>T (p.Arg284Ter)NFKB1Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
827830Single alleleNFKB1Pathogeniccriteria provided, single submitter
827831Single alleleNFKB1Pathogeniccriteria provided, single submitter
65385NM_001322934.2(NFKB2):c.2557C>T (p.Arg853Ter)NFKB2Pathogeniccriteria provided, multiple submitters, no conflicts
13138NM_000536.4(RAG2):c.1352G>C (p.Gly451Ala)RAG2Pathogenicreviewed by expert panel
827734NM_000536.4(RAG2):c.629T>C (p.Ile210Thr)RAG2Pathogeniccriteria provided, single submitter
203368NM_012452.3(TNFRSF13B):c.492C>G (p.Tyr164Ter)TNFRSF13BPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
942527NM_012452.3(TNFRSF13B):c.61+2T>ATNFRSF13BPathogeniccriteria provided, single submitter
2574621NM_000061.3(BTK):c.1787T>C (p.Met596Thr)BTKLikely pathogeniccriteria provided, single submitter
633147NM_000074.3(CD40LG):c.288+1G>ACD40LGLikely pathogeniccriteria provided, single submitter
2827689NM_003998.4(NFKB1):c.1753-1G>CNFKB1Likely pathogeniccriteria provided, multiple submitters, no conflicts
5302NM_012452.3(TNFRSF13B):c.310T>C (p.Cys104Arg)TNFRSF13BConflicting classifications of pathogenicity; risk factorcriteria provided, conflicting classifications
5303NM_012452.3(TNFRSF13B):c.542C>A (p.Ala181Glu)TNFRSF13BConflicting classifications of pathogenicitycriteria provided, conflicting classifications
618436NM_012452.3(TNFRSF13B):c.260T>A (p.Ile87Asn)TNFRSF13BConflicting classifications of pathogenicitycriteria provided, conflicting classifications
624092NM_003809.3(TNFSF12):c.674G>A (p.Arg225Gln)TNFSF12Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
827747NM_020458.4(TTC7A):c.1802+3G>CTTC7AConflicting classifications of pathogenicitycriteria provided, conflicting classifications
827752NM_020458.4(TTC7A):c.793C>T (p.Arg265Trp)TTC7AConflicting classifications of pathogenicitycriteria provided, conflicting classifications
2424768NC_000017.10:g.(?7123304)(7606804_?)delACADVLUncertain significancecriteria provided, single submitter
827696NM_000074.3(CD40LG):c.98T>A (p.Ile33Asn)CD40LGUncertain significancecriteria provided, multiple submitters, no conflicts
1414300NM_003809.3(TNFSF12):c.68C>T (p.Pro23Leu)LOC130060153Uncertain significancecriteria provided, single submitter
1435998NM_003809.3(TNFSF12):c.88C>G (p.Leu30Val)LOC130060153Uncertain significancecriteria provided, single submitter
1436026NM_003809.3(TNFSF12):c.46C>A (p.Pro16Thr)LOC130060153Uncertain significancecriteria provided, single submitter
1443273NM_003809.3(TNFSF12):c.26G>A (p.Arg9Gln)LOC130060153Uncertain significancecriteria provided, single submitter
1495617NM_003809.3(TNFSF12):c.35G>C (p.Arg12Pro)LOC130060153Uncertain significancecriteria provided, single submitter
1524145NM_003809.3(TNFSF12):c.55G>A (p.Ala19Thr)LOC130060153Uncertain significancecriteria provided, single submitter

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 52 · Orphanet: 80 · OMIM-shared: 0 · Dual-evidence (GWAS+Mendelian): 3

Dual-evidence genes (GWAS + Mendelian — highest-confidence targets)

GeneHGNCEvidence routes
CD40LGCD40LGGWAS, Orphanet
IKZF3IKZF3GWAS, Orphanet
IL2RAIL2RAGWAS, Orphanet

GenCC gene–disease validity (cohort genes)

the Disease column is the GenCC-asserted condition — a cohort gene’s strongest validity may be for a related predisposition syndrome.

GeneClassificationInheritanceDiseaseRecords
CD19DefinitiveAutosomal recessiveimmunodeficiency, common variable, 33
CR2DefinitiveAutosomal recessiveimmunodeficiency, common variable, 75
ICOSStrongAutosomal recessiveimmunodeficiency, common variable, 15
NFKB1StrongAutosomal dominantimmunodeficiency, common variable, 123
NFKB2StrongAutosomal dominantimmunodeficiency, common variable, 105
TNFRSF13BStrongAutosomal recessiveimmunodeficiency, common variable, 26
BLKModerateAutosomal dominantcommon variable immunodeficiency5
MS4A1ModerateAutosomal recessiveimmunodeficiency, common variable, 53
TNFRSF13CModerateAutosomal recessiveimmunodeficiency, common variable, 44
CD81SupportiveAutosomal dominantcommon variable immunodeficiency2
PRKCDSupportiveAutosomal dominantcommon variable immunodeficiency5
TNFSF12SupportiveAutosomal dominantcommon variable immunodeficiency3
TNFSF13LimitedAutosomal recessivecommon variable immunodeficiency2
VAV1LimitedAutosomal dominantcommon variable immunodeficiency

Orphanet rare-disease linkage (cohort genes)

GeneOrphanet IDRare disease
TNFSF12Orphanet:696931Common variable immunodeficiency phenotype due to TWEAK deficiency
CD40LGOrphanet:101088X-linked hyper-IgM syndrome
TNFRSF13BOrphanet:696907Common variable immunodeficiency phenotype due to homozygous TACI deficiency
NFKB1Orphanet:696874NFKB1-related immune dysregulation
NFKB2Orphanet:293978Deficiency in anterior pituitary function-variable immunodeficiency syndrome
BLKOrphanet:536Systemic lupus erythematosus
BLKOrphanet:552MODY
CD19Orphanet:696881Common variable immunodeficiency phenotype due to CD19/CD81 deficiency
CD81Orphanet:696881Common variable immunodeficiency phenotype due to CD19/CD81 deficiency
TNFRSF13COrphanet:696925Adult-onset common variable immunodeficiency due to BAFF-receptor deficiency
CR2Orphanet:536Systemic lupus erythematosus
CR2Orphanet:696894Common variable immunodeficiency phenotype due to CD21 deficiency
ICOSOrphanet:695183Late-onset combined immunodeficiency due to ICOS deficiency
PRKCDOrphanet:664711EBV-induced lymphoproliferative disease due to PRKCD deficiency
BTKOrphanet:47X-linked agammaglobulinemia
BTKOrphanet:632Short stature due to isolated growth hormone deficiency with X-linked hypogammaglobulinemia
SUOXOrphanet:99731Isolated sulfite oxidase deficiency
TNFSF15Orphanet:186Primary biliary cholangitis
TYK2Orphanet:300865Primary cutaneous anaplastic large cell lymphoma
TYK2Orphanet:331226Susceptibility to infection due to TYK2 deficiency
TYK2Orphanet:98842Lymphomatoid papulosis
IKZF3Orphanet:67038B-cell chronic lymphocytic leukemia
IKZF3Orphanet:699590Immune dysregulation with immunodeficiency due to AIOLOS haploinsufficiency
IKZF3Orphanet:699593Combined immunodeficiency-lymphopenia-cancer predisposing syndrome due to AIOLOS deficiency
CARD9Orphanet:457088Predisposition to invasive fungal disease due to CARD9 deficiency
ZMIZ1Orphanet:528084Non-specific syndromic intellectual disability
ZNF365Orphanet:2073Narcolepsy type 1
ZNF365Orphanet:83465Narcolepsy type 2
LRRK2Orphanet:2828Young-onset Parkinson disease
LRRK2Orphanet:411602Hereditary late-onset Parkinson disease
IL23ROrphanet:117Behçet disease
TTC7AOrphanet:436252Combined immunodeficiency-multiple intestinal atresia
CRB1Orphanet:251295Pigmented paravenous retinochoroidal atrophy
CRB1Orphanet:35612Nanophthalmos
CRB1Orphanet:65Leber congenital amaurosis
CRB1Orphanet:791Retinitis pigmentosa
ANKRD55Orphanet:85408Rheumatoid factor-negative polyarticular juvenile idiopathic arthritis
ANKRD55Orphanet:85410Oligoarticular juvenile idiopathic arthritis
DAG1Orphanet:206599Isolated asymptomatic elevation of creatine phosphokinase
DAG1Orphanet:280333Alpha-dystroglycan-related limb-girdle muscular dystrophy R16
DAG1Orphanet:370997Muscle-eye-brain disease with bilateral multicystic leucodystrophy
DAG1Orphanet:899Walker-Warburg syndrome
GPR35Orphanet:171Primary sclerosing cholangitis
NOD2Orphanet:90340Blau syndrome
IKBKGOrphanet:464Incontinentia pigmenti
IKBKGOrphanet:69088Hypohidrotic ectodermal dysplasia-immunodeficiency-osteopetrosis-lymphedema syndrome
IKBKGOrphanet:699605NEMO deleted exon 5 autoinflammatory syndrome
IKBKGOrphanet:98813Hypohidrotic ectodermal dysplasia with immunodeficiency
IL10Orphanet:117Behçet disease
IL10Orphanet:238569Immune dysregulation-inflammatory bowel disease-arthritis-recurrent infections syndrome

Cohort genes → proteins

65 cohort genes, 63 distinct canonical proteins.

Evidence partition

SubsetGenes
gwas_only43
gwas_and_clinvar1
multi_evidence21

Cohort genes (full)

SymbolHGNCEnsemblUniProtNameEvidence
TNFSF12HGNC:11927ENSG00000239697O43508Tumor necrosis factor ligand superfamily member 12gencc,clinvar
CD40LGHGNC:11935ENSG00000102245P29965CD40 ligandgwas,clinvar
TNFRSF13BHGNC:18153ENSG00000240505O14836Tumor necrosis factor receptor superfamily member 13Bgencc,clinvar
NFKB1HGNC:7794ENSG00000109320P19838Nuclear factor NF-kappa-B p105 subunitgencc,clinvar
NFKB2HGNC:7795ENSG00000077150Q00653Nuclear factor NF-kappa-B p100 subunitgencc,clinvar
BLKHGNC:1057ENSG00000136573P51451Tyrosine-protein kinase Blkgencc
TNFSF13HGNC:11928ENSG00000161955O75888Tumor necrosis factor ligand superfamily member 13gencc
VAV1HGNC:12657ENSG00000141968P15498Proto-oncogene vavgencc
CD19HGNC:1633ENSG00000177455P15391B-lymphocyte antigen CD19gencc
CD81HGNC:1701ENSG00000110651P60033CD81 antigengencc
TNFRSF13CHGNC:17755ENSG00000159958Q96RJ3Tumor necrosis factor receptor superfamily member 13Cgencc
CR2HGNC:2336ENSG00000117322P20023Complement receptor type 2gencc
ICOSHGNC:5351ENSG00000163600Q9Y6W8Inducible T-cell costimulatorgencc
MS4A1HGNC:7315ENSG00000156738P11836B-lymphocyte antigen CD20gencc
PRKCDHGNC:9399ENSG00000163932Q05655Protein kinase C delta typegencc
BTKHGNC:1133ENSG00000010671Q06187Tyrosine-protein kinase BTKclinvar
SUOXHGNC:11460ENSG00000139531P51687Sulfite oxidase, mitochondrialgwas
TNFRSF6BHGNC:11921ENSG00000243509O95407Tumor necrosis factor receptor superfamily member 6Bgwas
TNFSF15HGNC:11931ENSG00000181634O95150Tumor necrosis factor ligand superfamily member 15gwas
TNFSF18HGNC:11932ENSG00000120337Q9UNG2Tumor necrosis factor ligand superfamily member 18gwas
TRG-GCC2-6HGNC:12273tRNA-Gly (anticodon GCC) 2-6clinvar
EIPR1HGNC:12383ENSG00000032389Q53HC9EARP and GARP complex-interacting protein 1gwas
TYK2HGNC:12440ENSG00000105397P29597Non-receptor tyrosine-protein kinase TYK2gwas
IKZF3HGNC:13178ENSG00000161405Q9UKT9Zinc finger protein Aiolosgwas
CARD9HGNC:16391ENSG00000187796Q9H257Caspase recruitment domain-containing protein 9gwas
ZMIZ1HGNC:16493ENSG00000108175Q9ULJ6Zinc finger MIZ domain-containing protein 1gwas
FNBP1HGNC:17069ENSG00000187239Q96RU3Formin-binding protein 1gwas
ANKRD30AHGNC:17234ENSG00000148513Q9BXX3Ankyrin repeat domain-containing protein 30Agwas
SBK1HGNC:17699ENSG00000188322Q52WX2Serine/threonine-protein kinase SBK1gwas
ZNF365HGNC:18194ENSG00000138311Q70YC4Talaningwas
ADGRL2HGNC:18582ENSG00000117114O95490Adhesion G protein-coupled receptor L2gwas
LRRK2HGNC:18618ENSG00000188906Q5S007Leucine-rich repeat serine/threonine-protein kinase 2gwas
IL23RHGNC:19100ENSG00000162594Q5VWK5Interleukin-23 receptorgwas
TTC7AHGNC:19750ENSG00000068724Q9ULT0Tetratricopeptide repeat protein 7Aclinvar
ATG16L1HGNC:21498ENSG00000085978Q676U5Autophagy-related protein 16-1gwas
CRB1HGNC:2343ENSG00000134376P82279Protein crumbs homolog 1gwas
ADCY7HGNC:238ENSG00000121281P51828Adenylate cyclase type 7gwas
CYTL1HGNC:24435ENSG00000170891Q9NRR1Cytokine-like protein 1gwas
ANKRD55HGNC:25681ENSG00000164512Q3KP44Ankyrin repeat domain-containing protein 55gwas
DAG1HGNC:2666ENSG00000173402Q14118Dystroglycan 1gwas
ERAP2HGNC:29499ENSG00000164308Q6P179Endoplasmic reticulum aminopeptidase 2gwas
PSMG1HGNC:3043ENSG00000183527O95456Proteasome assembly chaperone 1gwas
ATXN2LHGNC:31326ENSG00000168488Q8WWM7Ataxin-2-like proteingwas
LURAP1LHGNC:31452ENSG00000153714Q8IV03Leucine rich adaptor protein 1-likegwas
EFNB2HGNC:3227ENSG00000125266P52799Ephrin-B2gwas
TNFSF12-TNFSF13HGNC:33537ENSG00000248871TNFSF12-TNFSF13 readthroughclinvar
FUT2HGNC:4013ENSG00000176920Q10981Galactoside alpha-(1,2)-fucosyltransferase 2gwas
GPR35HGNC:4492ENSG00000178623Q9HC97G-protein coupled receptor 35gwas
NOD2HGNC:5331ENSG00000167207Q9HC29Nucleotide-binding oligomerization domain-containing protein 2gwas
IKBKGHGNC:5961ENSG00000269335Q9Y6K9NF-kappa-B essential modulatorclinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

SymbolProtein nameFunction (lead sentence)
TNFSF12Tumor necrosis factor ligand superfamily member 12Binds to FN14 and possibly also to TNRFSF12/APO3.
CD40LGCD40 ligandCytokine that acts as a ligand to CD40/TNFRSF5.
TNFRSF13BTumor necrosis factor receptor superfamily member 13BReceptor for TNFSF13/APRIL and TNFSF13B/TALL1/BAFF/BLYS that binds both ligands with similar high affinity.
NFKB1Nuclear factor NF-kappa-B p105 subunitNF-kappa-B is a pleiotropic transcription factor present in almost all cell types and is the endpoint of a series of signal transduction events that are initiated by a vast array of stimuli related to many biological processes such as infl…
NFKB2Nuclear factor NF-kappa-B p100 subunitNF-kappa-B is a pleiotropic transcription factor present in almost all cell types and is the endpoint of a series of signal transduction events that are initiated by a vast array of stimuli related to many biological processes such as infl…
BLKTyrosine-protein kinase BlkNon-receptor tyrosine kinase involved in B-lymphocyte development, differentiation and signaling.
TNFSF13Tumor necrosis factor ligand superfamily member 13Cytokine that binds to TNFRSF13B/TACI and to TNFRSF17/BCMA.
VAV1Proto-oncogene vavCouples tyrosine kinase signals with the activation of the Rho/Rac GTPases, thus leading to cell differentiation and/or proliferation.
CD19B-lymphocyte antigen CD19Functions as a coreceptor for the B-cell antigen receptor complex (BCR) on B-lymphocytes.
CD81CD81 antigenStructural component of specialized membrane microdomains known as tetraspanin-enriched microdomains (TERMs), which act as platforms for receptor clustering and signaling.
TNFRSF13CTumor necrosis factor receptor superfamily member 13CB-cell receptor specific for TNFSF13B/TALL1/BAFF/BLyS.
CR2Complement receptor type 2Serves as a receptor for various ligands including complement component CD3d, HNRNPU OR IFNA1.
ICOSInducible T-cell costimulatorStimulatory receptor expressed in activated or antigen-experienced T-cells that plays an important role in the immune response.
MS4A1B-lymphocyte antigen CD20B-lymphocyte-specific membrane protein that plays a role in the regulation of cellular calcium influx necessary for the development, differentiation, and activation of B-lymphocytes.
PRKCDProtein kinase C delta typeCalcium-independent, phospholipid- and diacylglycerol (DAG)-dependent serine/threonine-protein kinase that plays contrasting roles in cell death and cell survival by functioning as a pro-apoptotic protein during DNA damage-induced apoptosi…
BTKTyrosine-protein kinase BTKNon-receptor tyrosine kinase indispensable for B lymphocyte development, differentiation and signaling.
SUOXSulfite oxidase, mitochondrialCatalyzes the oxidation of sulfite to sulfate, the terminal reaction in the oxidative degradation of sulfur-containing amino acids.
TNFRSF6BTumor necrosis factor receptor superfamily member 6BDecoy receptor that can neutralize the cytotoxic ligands TNFS14/LIGHT, TNFSF15 and TNFSF6/FASL.
TNFSF15Tumor necrosis factor ligand superfamily member 15Receptor for TNFRSF25 and TNFRSF6B.
TNFSF18Tumor necrosis factor ligand superfamily member 18Cytokine that binds to TNFRSF18/AITR/GITR.
EIPR1EARP and GARP complex-interacting protein 1Acts as a component of endosomal retrieval machinery that is involved in protein transport from early endosomes to either recycling endosomes or the trans-Golgi network.
TYK2Non-receptor tyrosine-protein kinase TYK2Tyrosine kinase of the non-receptor type involved in numerous cytokines and interferons signaling, which regulates cell growth, development, cell migration, innate and adaptive immunity.
IKZF3Zinc finger protein AiolosTranscription factor that plays an important role in the regulation of lymphocyte differentiation.
CARD9Caspase recruitment domain-containing protein 9Adapter protein that plays a key role in innate immune response against fungi by forming signaling complexes downstream of C-type lectin receptors.
ZMIZ1Zinc finger MIZ domain-containing protein 1Acts as a transcriptional coactivator.
FNBP1Formin-binding protein 1May act as a link between RND2 signaling and regulation of the actin cytoskeleton.
SBK1Serine/threonine-protein kinase SBK1May be involved in signal-transduction pathways related to the control of brain development.
ZNF365TalaninMay play a role in uric acid excretion.
ADGRL2Adhesion G protein-coupled receptor L2Orphan adhesion G-protein coupled receptor (aGPCR), which mediates synapse specificity.
LRRK2Leucine-rich repeat serine/threonine-protein kinase 2Serine/threonine-protein kinase which phosphorylates a broad range of proteins involved in multiple processes such as neuronal plasticity, innate immunity, autophagy, and vesicle trafficking.
IL23RInterleukin-23 receptorAssociates with IL12RB1 to form the interleukin-23 receptor.
TTC7ATetratricopeptide repeat protein 7AComponent of a complex required to localize phosphatidylinositol 4-kinase (PI4K) to the plasma membrane.
ATG16L1Autophagy-related protein 16-1Plays an essential role in both canonical and non-canonical autophagy: interacts with ATG12-ATG5 to mediate the lipidation to ATG8 family proteins (MAP1LC3A, MAP1LC3B, MAP1LC3C, GABARAPL1, GABARAPL2 and GABARAP).
CRB1Protein crumbs homolog 1Plays a role in photoreceptor morphogenesis in the retina.
ADCY7Adenylate cyclase type 7Adenylate cyclase that mediates formation of both cyclic AMP (cAMP) and cyclic di-AMP (c-di-AMP).
DAG1Dystroglycan 1The dystroglycan complex is involved in a number of signaling events and processes including laminin deposition and extracellular matrix assembly, acetylcholine receptor clustering, sarcolemmal stability, cell survival, peripheral nerve my…
ERAP2Endoplasmic reticulum aminopeptidase 2Aminopeptidase that plays a central role in peptide trimming, a step required for the generation of most HLA class I-binding peptides.
PSMG1Proteasome assembly chaperone 1Chaperone protein which promotes assembly of the 20S proteasome as part of a heterodimer with PSMG2.
ATXN2LAtaxin-2-like proteinInvolved in the regulation of stress granule and P-body formation.
EFNB2Ephrin-B2Cell surface transmembrane ligand for Eph receptors, a family of receptor tyrosine kinases which are crucial for migration, repulsion and adhesion during neuronal, vascular and epithelial development.
FUT2Galactoside alpha-(1,2)-fucosyltransferase 2Catalyzes the transfer of L-fucose, from a guanosine diphosphate-beta-L-fucose, to the terminal galactose on both O- and N-linked glycans chains of cell surface glycoproteins and glycolipids and the resulting epitope regulates several proc…
GPR35G-protein coupled receptor 35G-protein coupled receptor that binds to several ligands including the tryptophan metabolite kynurenic acid (KYNA), lysophosphatidic acid (LPA) or 5-hydroxyindoleacetic acid (5-HIAA) with high affinity, leading to rapid and transient activ…
NOD2Nucleotide-binding oligomerization domain-containing protein 2Pattern recognition receptor (PRR) that detects bacterial peptidoglycan fragments and other danger signals and plays an important role in gastrointestinal immunity.
IKBKGNF-kappa-B essential modulatorRegulatory subunit of the IKK core complex which phosphorylates inhibitors of NF-kappa-B thus leading to the dissociation of the inhibitor/NF-kappa-B complex and ultimately the degradation of the inhibitor.
IL10Interleukin-10Major immune regulatory cytokine that acts on many cells of the immune system where it has profound anti-inflammatory functions, limiting excessive tissue disruption caused by inflammation.
IL12BInterleukin-12 subunit betaCytokine that can act as a growth factor for activated T and NK cells, enhance the lytic activity of NK/lymphokine-activated killer cells, and stimulate the production of IFN-gamma by resting PBMC.
IL18R1Interleukin-18 receptor 1Within the IL18 receptor complex, responsible for the binding of the pro-inflammatory cytokine IL18, but not IL1A nor IL1B.
IL21Interleukin-21Cytokine with immunoregulatory activity.
IL2RAInterleukin-2 receptor subunit alphaReceptor for interleukin-2.
IL5Interleukin-5Homodimeric cytokine expressed predominantly by T-lymphocytes and NK cells that plays an important role in the survival, differentiation, and chemotaxis of eosinophils.

Protein-family classification

Druggable: 24 · Difficult: 13 · Unknown: 28 · Druggable fraction: 0.37

Family distribution

Cohort families vs a genome-wide background (hypergeometric, BH-FDR; fold = observed/expected). Counts kept; sorted by enrichment, so the catch-all Other/Unknown bucket no longer leads.

FamilyGenesFoldFDR
Complement28.2×0.082
Kinase73.0×0.082
Antibody/Immunoglobulin62.7×0.082
Scaffold/PPI61.6×0.432
Phosphatase11.3×0.903
GPCR31.1×0.903
Transcription factor70.9×0.928
Enzyme (other)40.7×0.928
Protease10.6×0.928
Other/Unknown280.8×0.986

Per-gene assignment

SymbolFamilyDruggable?ECInterPro (top 3)
TNFSF12Other/UnknownnoTNF_dom, Tumour_necrosis_fac-like_dom, TNF_Ligand_Superfamily
CD40LGOther/UnknownnoCD40L, TNF_dom, Tumour_necrosis_fac-like_dom
TNFRSF13BOther/UnknownnoTACI_Cys-rich-dom, TNFR_13B
NFKB1Transcription factornoNFkB/Dor, Death_dom, Ankyrin_rpt
NFKB2Transcription factornoNFkB/Dor, Death_dom, Ankyrin_rpt
BLKKinaseyes2.7.10.2Prot_kinase_dom, SH2, Ser-Thr/Tyr_kinase_cat_dom
TNFSF13Other/UnknownnoTNF_dom, Tumour_necrosis_fac-like_dom, TNF_CS
VAV1Scaffold/PPInoDH_dom, SH2, GDS_CDC24_CS
CD19Antibody/ImmunoglobulinyesIg_sub, Ig-like_dom, Ig-like_fold
CD81Other/UnknownnoTetraspanin_animals, Tetraspanin_EC2_sf, Tetraspanin/Peripherin
TNFRSF13COther/UnknownnoTNFR_13C_TALL-1-bd, TNFR_13C, TNFR_13C/17
CR2ComplementyesSushi_SCR_CCP_dom, Sushi/SCR/CCP_sf, SEZ6_CSMD_C4BPB_Regulators
ICOSAntibody/ImmunoglobulinyesIg_V-set, Ig-like_fold, ICOS
MS4A1Other/UnknownnoCD20-like_TM, MS4A
PRKCDKinaseyes2.7.11.13C2_dom, Prot_kinase_dom, AGC-kinase_C
BTKKinaseyes2.7.10.2Prot_kinase_dom, SH2, Ser-Thr/Tyr_kinase_cat_dom
SUOXEnzyme (other)yes1.8.3.1OxRdtase_Mopterin-bd_dom, Cyt_B5-like_heme/steroid-bd, MoCF_OxRdtse_dimer
TNFRSF6BOther/UnknownnoTNFR/NGFR_Cys_rich_reg, TNFRSF6B_N, TNFRSF_decoy_receptor
TNFSF15Other/UnknownnoTNF_dom, TNF, Tumour_necrosis_fac-like_dom
TNFSF18Other/UnknownnoTNF_dom, Tumour_necrosis_fac-like_dom, TNFSF18
TRG-GCC2-6Other/Unknownno
EIPR1Scaffold/PPInoWD40_rpt, WD40/YVTN_repeat-like_dom_sf, WD40_repeat_CS
TYK2Kinaseyes2.7.10.2FERM_domain, Prot_kinase_dom, SH2
IKZF3Transcription factornoZnf_C2H2_type, Znf_C2H2_sf, Ikaros_C2H2-ZF
CARD9Other/UnknownnoCARD, DEATH-like_dom_sf, CARD_CARD9
ZMIZ1Transcription factornoZnf_MIZ, Znf_RING/FYVE/PHD, ZMIZ1_N
FNBP1Scaffold/PPInoFCH_dom, SH3_domain, HR1_rho-bd
ANKRD30AScaffold/PPInoAnkyrin_rpt, Ankyrin_rpt-contain_sf, CC144C-like_CC_dom
SBK1KinaseyesProt_kinase_dom, Ser/Thr_kinase_AS, Kinase-like_dom_sf
ZNF365Transcription factornoGenomicStab_NeuMorph_Reg, FBX41/ZN365_Znf-C2H2
ADGRL2GPCRyesGPS, GPCR_2_secretin-like, Lectin_gal-bd_dom
LRRK2KinaseyesProt_kinase_dom, Leu-rich_rpt, Leu-rich_rpt_typical-subtyp
IL23RAntibody/ImmunoglobulinyesFN3_dom, Ig-like_fold, FN3_sf
TTC7AOther/UnknownnoTPR-like_helical_dom_sf, TPR_rpt, TTC7_N
ATG16L1Scaffold/PPInoWD40_rpt, Autophagy-rel_prot_16_dom, WD40/YVTN_repeat-like_dom_sf
CRB1Other/UnknownnoEGF-type_Asp/Asn_hydroxyl_site, EGF, Laminin_G
ADCY7Enzyme (other)yes4.6.1.1A/G_cyclase, Adcy_conserved_dom, A/G_cyclase_CS
CYTL1Other/UnknownnoCYTL1
ANKRD55Scaffold/PPInoAnkyrin_rpt, Ankyrin_rpt-contain_sf
DAG1Antibody/ImmunoglobulinyesCadg, DAG1_C, Ig-like_fold
ERAP2Proteaseyes3.4.11.1Peptidase_M1, Peptidase_M1_dom, ERAP1-like_C_dom
PSMG1Other/UnknownnoProteasome_assmbl_chp_1
ATXN2LOther/UnknownnoLsmAD_domain, PAM2_motif, SM_dom_ATX
LURAP1LOther/UnknownnoLURAP1, LURA1/LRA25
EFNB2Other/UnknownnoEphrin_RBD, Cupredoxin, Ephrin_CS
TNFSF12-TNFSF13Other/Unknownno
FUT2Enzyme (other)yes2.4.1.344Glyco_trans_11
GPR35GPCRyesGPCR_Rhodpsn, GPCR_Rhodpsn_7TM, GPR35_7tmA
NOD2Other/UnknownnoCARD, Leu-rich_rpt, NACHT_NTPase
IKBKGOther/UnknownnoNEMO_N, CC2-LZ_dom, NEMO_ZF

Expression context

Cohort genes with no expression data: 1.

57 cohort genes are a single-cell marker in ≥1 SCXA experiment.

Breadth distribution (Bgee present_calls)

BucketGenes
narrow (1-5 tissues)0
moderate (6-20)0
broad (>20)64
unknown1

Top tissues across cohort

TissueCohort genes
granulocyte10
spleen10
monocyte10
lymph node9
leukocyte7
male germ line stem cell (sensu Vertebrata) in testis5
vermiform appendix5
mononuclear cell5
cartilage tissue4
ganglionic eminence4
left testis4
right testis4
blood3
olfactory bulb3
type B pancreatic cell3
calcaneal tendon3
olfactory segment of nasal mucosa3
right hemisphere of cerebellum3
right lung3
ventricular zone3

Per-gene tissue summary (top 30)

SymbolBgee breadthFANTOM5 breadthSCXATop tissues
TNFSF12134tissue_specificmarkerright coronary artery, thoracic aorta, ascending aorta
CD40LG124tissue_specificmarkergranulocyte, lymph node, blood
TNFRSF13B158tissue_specificmarkertype B pancreatic cell, olfactory bulb, spleen
NFKB1252ubiquitousmarkerendometrium epithelium, cartilage tissue, calcaneal tendon
NFKB2221ubiquitousmarkergranulocyte, muscle layer of sigmoid colon, spleen
BLK145tissue_specificmarkerspleen, male germ line stem cell (sensu Vertebrata) in testis, lymph node
TNFSF13134ubiquitousmarkermonocyte, leukocyte, granulocyte
VAV1188broadmarkergranulocyte, monocyte, leukocyte
CD19164tissue_specificmarkerspleen, lymph node, vermiform appendix
CD81302ubiquitousmarkerstromal cell of endometrium, seminal vesicle, body of uterus
TNFRSF13C151broadmarkerspleen, lymph node, vermiform appendix
CR2150broadmarkersecondary oocyte, oocyte, spleen
ICOS110tissue_specificmarkerlymph node, vermiform appendix, thymus
MS4A1197broadmarkerepithelium of nasopharynx, spleen, lymph node
PRKCD229ubiquitousmarkermonocyte, mononuclear cell, leukocyte
BTK206broadmarkermonocyte, mononuclear cell, leukocyte
SUOX267ubiquitousmarkerright lobe of liver, right adrenal gland, right adrenal gland cortex
TNFRSF6B127broadyesolfactory segment of nasal mucosa, spleen, subcutaneous adipose tissue
TNFSF15149broadmarkercartilage tissue, jejunal mucosa, duodenum
TNFSF1898broadyesmale germ line stem cell (sensu Vertebrata) in testis, gall bladder, stromal cell of endometrium
TRG-GCC2-6
EIPR1249ubiquitousmarkerprefrontal cortex, adenohypophysis, nucleus accumbens
TYK2288ubiquitousmarkergranulocyte, right hemisphere of cerebellum, adenohypophysis
IKZF3155broadmarkergranulocyte, lymph node, epithelium of nasopharynx
CARD9172broadmarkermonocyte, mononuclear cell, leukocyte
ZMIZ1295ubiquitousmarkerdorsal motor nucleus of vagus nerve, tibia, seminal vesicle
FNBP1292ubiquitousmarkercorpus callosum, mucosa of stomach, lower esophagus muscularis layer
ANKRD30A69tissue_specificmarkerepithelium of mammary gland, mammary duct, male germ line stem cell (sensu Vertebrata) in testis
SBK1195broadyescortical plate, ganglionic eminence, cerebellar vermis
ZNF365206broadyesmiddle temporal gyrus, lateral nuclear group of thalamus, Brodmann (1909) area 23

Protein interactions among cohort

Intra-cohort edges: 57.

Hub genes (top 10 by interactor count)

SymbolInteractor count
INS11,670
NFKB110,484
LRRK27,628
SMAD36,440
JAK26,197
IL106,185
IKBKG4,981
BTK4,467
RBMX4,460
NFKB24,041

Intra-cohort edges

ABSources
ADGRL2ATG16L1intact
ADGRL2LURAP1Lstring_interaction
ANKRD55PTPN22string_interaction
ATG16L1NKX2-3string_interaction
ATG16L1NOD2biogrid_interaction, string_interaction
ATG16L1TNFSF15string_interaction
BTKCD19intact
BTKVAV1string_interaction
CARD9NKX2-3string_interaction
CARD9NOD2string_interaction
CD19CD81biogrid_interaction
CD19CR2biogrid_interaction, string_interaction
CD19IL21string_interaction
CD19TNFRSF13Cstring_interaction
CD19VAV1biogrid_interaction
CD40LGICOSstring_interaction
CD40LGIL21string_interaction
CD40LGTNFRSF13Bstring_interaction
CD40LGTNFRSF13Cstring_interaction
CD81CR2biogrid_interaction
CD81GPR35biogrid_interaction, intact
CR2TNFRSF13Bstring_interaction
EFNB2TYK2biogrid_interaction
ICOSIL21string_interaction
ICOSTNFRSF13Bstring_interaction
IKBKGNFKB1string_interaction
IKBKGNFKB2string_interaction
IL10IL12Bstring_interaction
IL10IL23Rstring_interaction
IL10IL2RAstring_interaction
IL10IL5string_interaction
IL10NFKB2biogrid_interaction
IL10TNFSF13string_interaction
IL12BIL23Rstring_interaction
IL12BTYK2string_interaction
IL18R1NKX2-3string_interaction
IL23RJAK2string_interaction
IL23RNKX2-3string_interaction
IL23RNOD2string_interaction
IL23RTYK2string_interaction
JAK2TYK2string_interaction
LURAP1LNOD2intact
NFKB1NFKB2intact, string_interaction
NFKB2TNFRSF13Cstring_interaction
NKX2-3NOD2string_interaction
NKX2-3TNFSF15string_interaction
NOD2TNFSF15string_interaction
PRKCDPTPN22intact
PSMG1TNFRSF6Bstring_interaction
PTPN22VAV1intact

Structural data

PDB: 49 · AlphaFold-only: 14 · No structure: 2

Cohort genes with PDB structures (top 30)

SymbolUniProtPDB entries
INSP01308382
JAK2O60674164
BTKQ06187156
TYK2P2959752
LRRK2Q5S00744
IL12BP2946020
IKBKGQ9Y6K917
CD81P6003316
ATG16L1Q676U516
NFKB1P1983815
ERAP2Q6P17914
PTPN22Q9Y2R214
PSMG1O9545613
SMAD3P8402212
NFKB2Q0065311
VAV1P1549810
MS4A1P1183610
EFNB2P5279910
IL2RAP0158910
PTGER4P3540810
CR2P200239
IL10P223019
CD40LGP299658
TNFRSF13CQ96RJ38
TNFRSF6BO954078
CARD9Q9H2578
DAG1Q141188
TNFSF15O951507
TNFSF18Q9UNG27
IL5P051135

AlphaFold-only cohort genes (top 30 by pLDDT)

SymbolUniProtpLDDT
FUT2Q1098190.65
EIPR1Q53HC989.26
CYTL1Q9NRR185.86
NOD2Q9HC2984.76
TTC7AQ9ULT084.59
BLKP5145181.89
SBK1Q52WX277.87
ADCY7P5182877.32
LURAP1LQ8IV0366.08
ANKRD55Q3KP4463.43
NKX2-3Q8TAU060.75
ATXN2LQ8WWM749.52
IKZF3Q9UKT948.06
ZNF365Q70YC430.21

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 401. Enrichment computed across 65 evidence-associated genes (50 with Reactome annotation).

Pathways by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 50 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

PathwayCohort genesFoldFDRSample cohort genes
Interleukin-23 signaling4101.5×2e-05TYK2, IL23R, IL12B, JAK2
TNFs bind their physiological receptors539.4×3e-05TNFRSF13B, TNFRSF6B, TNFSF13, TNFSF15, TNFSF18
IkBA variant leads to EDA-ID397.9×4e-04NFKB1, NFKB2, IKBKG
Antigen activates B Cell Receptor (BCR) leading to generation of second messengers428.6×1e-03BLK, BTK, VAV1, CD19
Signaling by the B Cell Receptor (BCR)427.7×1e-03BLK, BTK, CD19, IKBKG
TAK1-dependent IKK and NF-kappa-B activation424.0×0.001NFKB1, NFKB2, NOD2, IKBKG
RIP-mediated NFkB activation via ZBP1340.3×0.003NFKB1, NFKB2, IKBKG
TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway340.3×0.003TNFSF12, CD40LG, TNFRSF13C
Interleukin-4 and Interleukin-13 signaling510.3×0.005TYK2, IL23R, IL10, IL12B, JAK2
TRAF6 mediated NF-kB activation327.4×0.007NFKB1, NFKB2, IKBKG
Interleukin-12 signaling324.5×0.008TYK2, IL12B, JAK2
Interleukin receptor SHC signaling324.5×0.008IL2RA, IL5, JAK2
DEx/H-box helicases activate type I IFN and inflammatory cytokines production265.3×0.012NFKB1, NFKB2
CLEC7A (Dectin-1) signaling411.4×0.012NFKB1, CARD9, IKBKG, PRKCD
NOD1/2 Signaling Pathway319.0×0.013CARD9, NOD2, IKBKG
Interleukin-3, Interleukin-5 and GM-CSF signaling319.0×0.013VAV1, IL5, JAK2
Interleukin-1 processing250.8×0.015NFKB1, NFKB2
HuR (ELAVL1) binds and stabilizes mRNA250.8×0.015TNFSF13, PRKCD
MAPK1 (ERK2) activation245.7×0.017TYK2, JAK2
MAPK3 (ERK1) activation241.5×0.018TYK2, JAK2
Interleukin-27 signaling241.5×0.018TYK2, JAK2
Interleukin-6 signaling238.1×0.018TYK2, JAK2
SUMOylation of immune response proteins238.1×0.018NFKB2, IKBKG
Interleukin-35 Signalling238.1×0.018TYK2, JAK2
C-type lectin receptors (CLRs)314.3×0.018CARD9, IKBKG, PRKCD
Interleukin-10 signaling314.0×0.018TYK2, IL10, IL12B
Regulation of Complement cascade314.0×0.018CD19, CD81, CR2
Potential therapeutics for SARS49.1×0.018BTK, TYK2, VAV1, JAK2
Diseases of Immune System235.1×0.019BTK, IKBKG
Diseases associated with the TLR signaling cascade235.1×0.019BTK, IKBKG

GO biological processes by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 60 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

GO termCohort genesFoldFDRSample cohort genes
positive regulation of interleukin-17 production770.2×5e-09TYK2, CARD9, IL23R, NOD2, IL12B, IL21, JAK2
B cell proliferation756.2×9e-09CD40LG, VAV1, CD19, CR2, IL10, MS4A1, PRKCD
immune response1411.0×9e-09TNFSF12, TNFSF13, TNFSF15, TYK2, CR2, ICOS, IKBKG, IL10 (+6 more)
positive regulation of T-helper 17 type immune response5117.0×8e-08TYK2, CARD9, IL23R, IL12B, JAK2
positive regulation of T cell proliferation730.2×5e-07CD40LG, TYK2, TNFRSF13C, IL23R, IL12B, IL21, JAK2
positive regulation of type II interferon production726.2×1e-06TYK2, IL23R, IL12B, IL18R1, IL21, JAK2, PTPN22
obsolete positive regulation of NF-kappaB transcription factor activity724.0×2e-06CD40LG, BTK, TNFSF18, CARD9, NOD2, IKBKG, IL18R1
positive regulation of B cell proliferation634.4×2e-06BTK, TNFSF13, CD81, TNFRSF13C, IL21, IL5
positive regulation of natural killer cell proliferation493.6×7e-06TYK2, IL23R, IL12B, JAK2
B cell differentiation621.9×3e-05CD40LG, IKZF3, CR2, IL10, MS4A1, RAG2
B cell receptor signaling pathway533.4×3e-05NFKB1, BLK, BTK, CD19, MS4A1
T cell costimulation531.2×3e-05CD40LG, VAV1, TNFRSF13C, EFNB2, ICOS
adaptive immune response811.2×3e-05TNFRSF13B, BTK, TNFSF18, TNFRSF13C, ERAP2, NOD2, IL18R1, JAK2
interleukin-23-mediated signaling pathway3140.4×5e-05TYK2, IL23R, JAK2
positive regulation of NK T cell proliferation3140.4×5e-05TYK2, IL12B, JAK2
positive regulation of canonical NF-kappaB signal transduction89.7×8e-05CD40LG, BTK, TNFSF15, CARD9, LURAP1L, NOD2, IKBKG, INS
positive regulation of cytokine production522.6×1e-04CARD9, IL10, IL21, INS, PTGER4
JNK cascade522.6×1e-04NFKB1, CARD9, LRRK2, SMAD3, PTGER4
positive regulation of tumor necrosis factor production615.3×1e-04BTK, CARD9, LRRK2, NOD2, IL12B, JAK2
interleukin-12-mediated signaling pathway393.6×1e-04TYK2, IL12B, JAK2
negative regulation of inflammatory response613.7×2e-04NFKB1, IL10, IL2RA, SMAD3, PRKCD, PTGER4
positive regulation of immunoglobulin production432.1×3e-04BTK, IL10, IL21, IL5
positive regulation of receptor signaling pathway via JAK-STAT428.8×4e-04TYK2, IL10, IL5, JAK2
cellular response to virus516.7×4e-04NFKB1, TYK2, IL21, JAK2, SMAD3
positive regulation of interleukin-10 production426.8×5e-04CD40LG, NOD2, IL12B, IL21
canonical NF-kappaB signal transduction424.4×7e-04NFKB1, NFKB2, NOD2, IKBKG
positive regulation of granulocyte macrophage colony-stimulating factor production349.6×9e-04CARD9, IL23R, IL12B
tumor necrosis factor-mediated signaling pathway422.0×1e-03NFKB1, TNFSF18, TNFRSF13C, JAK2
negative regulation of B cell proliferation346.8×1e-03TNFRSF13B, BTK, IL10
cell surface receptor signaling pathway via JAK-STAT419.4×0.001TYK2, IL23R, IL12B, JAK2

Therapeutics

Drugs indicated for this disease

0 approved, 1 in late-stage (phase 3) trials. Disease-direct ChEMBL indications, not inferred from the associated-gene cohort below.

DrugDevelopment status
Human Immunoglobulin GPhase 3 (in late-stage trials)

Drug target analysis

Approved (phase 4): 15 · Phase ≥3: 15 · Phased (≥1): 17 · Undrugged: 48

Druggability breadth: 42 of 65 evidence-associated genes (65%) have a ChEMBL target (buckets above are over the deeply-mined display cohort).

Genes with an approved drug

The molecule shown is one approved compound that hits the gene — not necessarily a drug of choice or one indicated for this disease.

SymbolExample approved molecule
NFKB1INDOPROFEN
NFKB2INDOPROFEN
BLKAFATINIB
PRKCDINGENOL MEBUTATE
BTKPONATINIB
TYK2FEDRATINIB
IKZF3POMALIDOMIDE
SBK1AFATINIB
LRRK2PONATINIB
GPR35AMLEXANOX
NOD2PACLITAXEL
IL5BUDESONIDE
JAK2FEDRATINIB
SMAD3FLUORESCEIN
PTGER4DINOPROSTONE

Top cohort targets by molecule count

SymbolMoleculesMax phase
NFKB11524
JAK21004
BTK844
TYK2724
BLK624
PRKCD494
LRRK2424
GPR35304
NFKB2154
SBK1144

Drugs targeting cohort genes (top 30)

MoleculeMax phaseTargets in cohort
INDOPROFEN4NFKB1, NFKB2
VAMOROLONE4NFKB1, NFKB2
BORTEZOMIB4NFKB1, NFKB2
DEXAMETHASONE4NFKB1, NFKB2
SULFASALAZINE4NFKB1, NFKB2
LEVOSALBUTAMOL4NFKB1
CLOTRIMAZOLE4NFKB1
GLIPIZIDE4NFKB1
SALMETEROL XINAFOATE4NFKB1
PHENELZINE4NFKB1
SULFAPHENAZOLE4NFKB1
AMOXAPINE4NFKB1
PROPANTHELINE4NFKB1
DECAMETHONIUM4NFKB1
NICARDIPINE HYDROCHLORIDE4NFKB1
PHENTOLAMINE MESYLATE4NFKB1
PHENYLEPHRINE4NFKB1
CARISOPRODOL4NFKB1
AZELAIC ACID4NFKB1
CARBETAPENTANE CITRATE4NFKB1
NIALAMIDE4NFKB1
EPINEPHRINE BITARTRATE4NFKB1
NILUTAMIDE4NFKB1
BUDESONIDE4IL5, NFKB1
ESTRONE4NFKB1
METHAPYRILENE4NFKB1
PIMOZIDE4NFKB1
TRIAMCINOLONE4NFKB1
BISOPROLOL FUMARATE4NFKB1
AZACITIDINE4NFKB1

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 11.

Cohort genes with ChEMBL bioactivity (full, sorted by assay count)

SymbolAssaysType breakdown
JAK22,018Binding:1911, Functional:51, ADMET:48, Unclassified:4, Toxicity:4
BTK1,836Binding:1810, Functional:23, ADMET:3
TYK21,083Binding:1043, Functional:39, ADMET:1
LRRK2809Binding:799, ADMET:7, Functional:3
PRKCD804Binding:790, Functional:14
BLK483Binding:477, ADMET:4, Functional:2
PTGER4288Binding:207, Functional:80, ADMET:1
NFKB1256Binding:249, Functional:7
NFKB2230Binding:226, Functional:4
GPR35162Binding:84, Functional:78
PTPN22137Binding:122, Functional:10, ADMET:5
NOD2126Binding:121, Functional:5
IKZF3101Binding:100, Functional:1
SBK197Binding:97
ERAP246Binding:40, ADMET:4, Functional:2
IKBKG38Binding:30, Functional:8
SMAD324Binding:18, Functional:6
ADCY716Binding:14, Functional:2
IL23R13Binding:13
CD40LG8Binding:8
INS8Binding:7, ADMET:1
CD817Binding:7
ICOS7Binding:7
RBMX6Binding:6
PSMG15Binding:5
DAG14Binding:4
IL54Binding:4
FUT22Binding:2
IL2RA2Binding:2
ACADVL2Binding:2
VAV11Binding:1
ATXN2L1Binding:1

Cohort enzymes (BRENDA EC)

SymbolEC numbersNames
BLK2.7.10.2non-specific protein-tyrosine kinase
PRKCD2.7.11.13protein kinase C
BTK2.7.10.2non-specific protein-tyrosine kinase
SUOX1.8.3.1sulfite oxidase
TYK22.7.10.2non-specific protein-tyrosine kinase
ADCY74.6.1.1adenylate cyclase
ERAP23.4.11.1, 3.4.11.6leucyl aminopeptidase, aminopeptidase B
FUT22.4.1.344, 2.4.1.69type 2 galactoside alpha-(1,2)-fucosyltransferase, type 1 galactoside alpha-(1,2)-fucosyltransferase
JAK22.7.10.2non-specific protein-tyrosine kinase
ACADVL1.3.8.8, 1.3.8.9long-chain acyl-CoA dehydrogenase, very-long-chain acyl-CoA dehydrogenase
PTPN223.1.3.48protein-tyrosine-phosphatase

Cohort genes with high screening signal

≥100 ChEMBL assays — a studied-ness signal; see Therapeutics for approved-drug status.

SymbolChEMBL assays
NFKB1256
NFKB2230
BLK483
PRKCD804
BTK1,836
TYK21,083
IKZF3101
LRRK2809
GPR35162
NOD2126
JAK22,018
PTGER4288
PTPN22137

Pharmacogenomics

Cohort genes with a PharmGKB record: 64; with CPIC/DPWG dosing guidelines: 0.

No cohort gene has a CPIC/DPWG genotype-guided dosing guideline (PharmGKB).

Chemical tractability of cohort targets

30 approved/phased compounds have measured bioactivity against a cohort gene (and aren’t yet in disease-level trials). This is a research / tractability signal, NOT a therapeutic recommendation — a bioactivity row often reflects off-target or screening binding (e.g. promiscuous kinase inhibitors against a cohort kinase), implying no disease mechanism.

CompoundMax phaseCohort target (bioactivity)
INDOPROFEN4NFKB1, NFKB2
VAMOROLONE4NFKB1, NFKB2
BORTEZOMIB4NFKB1, NFKB2
DEXAMETHASONE4NFKB1, NFKB2
SULFASALAZINE4NFKB1, NFKB2
LEVOSALBUTAMOL4NFKB1
CLOTRIMAZOLE4NFKB1
GLIPIZIDE4NFKB1
SALMETEROL XINAFOATE4NFKB1
PHENELZINE4NFKB1
SULFAPHENAZOLE4NFKB1
AMOXAPINE4NFKB1
PROPANTHELINE4NFKB1
DECAMETHONIUM4NFKB1
NICARDIPINE HYDROCHLORIDE4NFKB1
PHENTOLAMINE MESYLATE4NFKB1
PHENYLEPHRINE4NFKB1
CARISOPRODOL4NFKB1
AZELAIC ACID4NFKB1
CARBETAPENTANE CITRATE4NFKB1
NIALAMIDE4NFKB1
EPINEPHRINE BITARTRATE4NFKB1
NILUTAMIDE4NFKB1
BUDESONIDE4IL5, NFKB1
ESTRONE4NFKB1
METHAPYRILENE4NFKB1
PIMOZIDE4NFKB1
TRIAMCINOLONE4NFKB1
BISOPROLOL FUMARATE4NFKB1
AZACITIDINE4NFKB1

Druggability pyramid

Cohort genes binned by druggability tier (high → low):

TierDefinitionGenesSymbols
AApproved (phase 4 drug)15NFKB1, NFKB2, BLK, PRKCD, BTK, TYK2, IKZF3, SBK1, LRRK2, GPR35 (+5 more)
BPhased (≥1) drug, not yet approved2ERAP2, ACADVL
CDruggable family + PDB, no drug11CD19, CR2, ICOS, SUOX, ADGRL2, IL23R, DAG1, IL12B, IL18R1, IL2RA (+1 more)
DDruggable family + AlphaFold only, no drug2ADCY7, FUT2
EDifficult family or no structure, no drug35TNFSF12, CD40LG, TNFRSF13B, TNFSF13, VAV1, CD81, TNFRSF13C, MS4A1, TNFRSF6B, TNFSF15 (+25 more)

Undrugged target profiles

48 cohort genes are undrugged. Ranked by ‘starting-point quality’ (assay depth + drugged-partner adjacency).

SymbolChEMBL assaysDrugged partners (top 3)
CARD90NOD2
IL23R13JAK2
ATG16L10NOD2
NKX2-30NOD2
PTPN22137
TNFSF120
CD40LG8
TNFRSF13B0
TNFSF130
VAV11
CD190
CD817
TNFRSF13C0
CR20
ICOS7
MS4A10
SUOX0
TNFRSF6B0
TNFSF150
TNFSF180
TRG-GCC2-60
EIPR10
ZMIZ10
FNBP10
ANKRD30A0
ZNF3650
ADGRL20
TTC7A0
CRB10
ADCY716

Clinical trials & evidence

Clinical trials

Clinical trials: 42.

Phase distribution (across all retrieved trials)

PhaseTrials
Not specified18
PHASE29
PHASE38
PHASE44
PHASE1/PHASE22
PHASE11

Top trials by phase / activity

NCTPhaseStatusTitle
NCT05193552PHASE4RECRUITINGUsage of Spirometry in Managing IgG Therapy in CVID With Airway Disease
NCT00520494PHASE4COMPLETEDEfficacy and Safety of Vivaglobin® in Previously Untreated Patients With Primary Immunodeficiency
NCT01289847PHASE4COMPLETEDA Study to Find Out How Safe and Effective Gammaplex® is in Young People With Primary Immunodeficiency
NCT01946906PHASE4COMPLETEDThe Rifaximin Study in CVID
NCT00168012PHASE3COMPLETEDEfficacy and Safety of Intravenous Immunoglobulin IVIG-F10 in Patients With Primary Immunodeficiencies (PID)
NCT00168025PHASE3COMPLETEDEfficacy and Safety of Intravenous Immunoglobulin IgPro10 in Patients With Primary Immunodeficiencies (PID)
NCT00220766PHASE3COMPLETEDRapid Infusion of Immune Globulin Intravenous (Human) In Primary Immunodeficiency Patients
NCT00322556PHASE3COMPLETEDSafety and Efficacy of Intravenous Immunoglobulin IgPro10 in Patients With Primary Immunodeficiencies (PID)
NCT00542997PHASE3COMPLETEDStudy of Subcutaneous Immune Globulin in Patients Requiring IgG Replacement Therapy
NCT01884311PHASE3COMPLETEDPharmacokinetics (PK) and Safety of Subgam-VF in Primary Immunodeficiency Diseases
NCT01963143PHASE3COMPLETEDBioequivalence Study to Evaluate the Pharmacokinetics, Safety, and Tolerability of Gammaplex® 10 and Gammaplex® 5% in Primary Immunodeficiency Diseases
NCT02247141PHASE3COMPLETEDA Multi-centre Open Study to Assess the Safety and Efficacy of Subgam®
NCT01821781PHASE2ACTIVE_NOT_RECRUITINGImmune Disorder HSCT Protocol
NCT01852370PHASE1/PHASE2ENROLLING_BY_INVITATIONSequential Cadaveric Lung and Bone Marrow Transplant for Immune Deficiency Diseases
NCT02579967PHASE2RECRUITINGPilot Trial of Allogeneic Blood or Marrow Transplantation for Primary Immunodeficiencies
NCT03663933PHASE2ACTIVE_NOT_RECRUITINGAllogeneic Hematopoietic Cell Transplantation for Disorders of T-cell Proliferation and/or Dysregulation
NCT04339777PHASE2RECRUITINGAllogeneic Hematopoietic Stem Cell Transplant for Patients With Inborn Errors of Immunity
NCT04925375PHASE2RECRUITINGAbatacept for the Treatment of Common Variable Immunodeficiency With Interstitial Lung Disease
NCT05593588PHASE2ENROLLING_BY_INVITATIONSenolytics Treatment of Interstitial Lung Disease in Common Variable Immunodeficiency
NCT06897358PHASE2ACTIVE_NOT_RECRUITINGLeniolisib for Immune Dysregulation in CVID
NCT07284641PHASE2RECRUITINGHematopoietic Stem Cell Transplantation (HSCT) for Common Variable Immunodeficiency (CVID) and Other Autoimmune Manifestations of Primary Immune Regulatory Disorders (PIRD)
NCT01489618PHASE2TERMINATEDPrime Boost Vaccination Strategy Combining Conjugated Anti- Pneumococcal Vaccine (s0) and Polysaccharide Anti- Pneumococcal Vaccine (s4) Compared to Polysaccharide Anti- Pneumococcal Vaccine Alone (s4) In Patients With Common Variable Immunodeficiency
NCT03513328PHASE1/PHASE2COMPLETEDConditioning Regimen for Allogeneic Hematopoietic Stem-Cell Transplantation
NCT00263237PHASE1COMPLETEDSTA-5326 Meslylate to Treat Gut Inflammation Associated With Common Variable Immunodeficiency
NCT00943514Not specifiedRECRUITINGNatural History of Bronchiectasis
NCT01652092Not specifiedACTIVE_NOT_RECRUITINGAllogeneic Hematopoietic Stem Cell Transplant for Patients With Primary Immune Deficiencies
NCT05321407Not specifiedACTIVE_NOT_RECRUITINGCOVID-19 Vaccine Responses in PIDD Subjects
NCT07255157Not specifiedNOT_YET_RECRUITINGPeripheral Helper T-cells in Common Variable ImmunoDeficiency
NCT00004695Not specifiedCOMPLETEDRandomized Study of Polyethylene-Glycol-Conjugated Interleukin 2 in Patients With Common Variable Immunodeficiency
NCT00006054Not specifiedTERMINATEDAllogeneic Bone Marrow Transplantation in Patients With Primary Immunodeficiencies
NCT00015431Not specifiedCOMPLETEDImmune System and Gut Abnormalities in Patients With Common Variable Immunodeficiency With and Without Gastrointestinal Symptoms
NCT00661401Not specifiedCOMPLETEDSpecific IgG Antibody in Patients With Primary Antibody Deficiencies Treated With Subcutaneous Immunoglobulin
NCT01196702Not specifiedCOMPLETEDLymphocyte Immunophenotyping in Common Variable Immunodeficiency
NCT01981785Not specifiedUNKNOWNInvestigation of Immune Disorders and Deficiencies
NCT02960399Not specifiedTERMINATEDAssessment of Immunogenicity of Zostavax® in Patients With Antibody Deficiency 60 Years of Age and Older
NCT03188419Not specifiedCOMPLETEDBreadth of Donor Options for People With Inherited Diseases Requiring Allogeneic Hematopoietic Stem Cell Transplant in the Era of Alternative Donor Transplants Using Post-Transplantation Cyclophosphamide
NCT03211689Not specifiedCOMPLETEDThe Impact of Exercise on Stress, Fatigue, and Quality of Life in Individuals With Primary Immunodeficiency Disease
NCT03534479Not specifiedCOMPLETEDHuman IgGs and Endothelial Function in Vivo in Humans
NCT05310604Not specifiedCOMPLETEDEarly Detection of Primary Antibody Deficiencies in Primary Care Facilities by an Algorithm Driven Selection of Serologic Testing in Individuals at Risk.
NCT05481554Not specifiedUNKNOWNComposition and Function of Gut Microbiota in Porto-sinusoidal Vascular Disease Associated With Variable Common Immunodeficiency

Drugs tested across these trials (top 30)

MoleculeMax phaseTrials referencing
HUMAN IMMUNOGLOBULIN G43
DEXTROSE41
LENIOLISIB41
PENTOSTATIN41
RIFAXIMIN41
APILIMOD21
FISETIN21
CHEMBL42370701
CHEMBL364340901