CD40LG

gene
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Also known as CD40LTRAPgp39hCD40LCD154CD40-LHIGM1T-BAM

Summary

CD40LG (CD40 ligand, HGNC:11935) is a protein-coding gene on chromosome Xq26.3, encoding CD40 ligand (P29965). Cytokine that acts as a ligand to CD40/TNFRSF5. It is haploinsufficient (ClinGen: sufficient evidence).

The protein encoded by this gene is expressed on the surface of T cells. It regulates B cell function by engaging CD40 on the B cell surface. A defect in this gene results in an inability to undergo immunoglobulin class switch and is associated with hyper-IgM syndrome.

Source: NCBI Gene 959 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): hyper-IgM syndrome type 1 (Definitive, ClinGen)
  • GWAS associations: 4
  • Clinical variants (ClinVar): 347 total — 78 pathogenic, 31 likely-pathogenic
  • Phenotypes (HPO): 41
  • Druggable target: yes
  • Dosage sensitivity (ClinGen): haploinsufficiency sufficient evidence, triplosensitivity no evidence
  • MANE Select transcript: NM_000074

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:11935
Approved symbolCD40LG
NameCD40 ligand
LocationXq26.3
Locus typegene with protein product
StatusApproved
AliasesCD40L, TRAP, gp39, hCD40L, CD154, CD40-L, HIGM1, T-BAM
Ensembl geneENSG00000102245
Ensembl biotypeprotein_coding
OMIM300386
Entrez959

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 4 protein_coding, 3 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000370628, ENST00000370629, ENST00000695724, ENST00000695725, ENST00000695726, ENST00000695727, ENST00000695728, ENST00000695729

RefSeq mRNA: 1 — MANE Select: NM_000074 NM_000074

CCDS: CCDS14659

Canonical transcript exons

ENST00000370629 — 5 exons

ExonStartEnd
ENSE00000677016136650266136650397
ENSE00000677017136654373136654430
ENSE00000677018136656356136656418
ENSE00001125156136659039136660390
ENSE00001453187136648158136648404

Expression profiles

Bgee: expression breadth ubiquitous, 124 present calls, max score 87.82.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 5.0913 / max 815.4538, expressed in 150 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
1977214.1941142
1977220.897281

Top tissues by expression

278 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
granulocyteCL:000009487.82gold quality
lymph nodeUBERON:000002978.93gold quality
bloodUBERON:000017876.57gold quality
vermiform appendixUBERON:000115474.90gold quality
rectumUBERON:000105270.28gold quality
caecumUBERON:000115369.10gold quality
spleenUBERON:000210668.19gold quality
ileal mucosaUBERON:000033168.09silver quality
gall bladderUBERON:000211068.03gold quality
cervix squamous epitheliumUBERON:000692267.79gold quality
mucosa of transverse colonUBERON:000499167.52gold quality
small intestine Peyer’s patchUBERON:000345465.66gold quality
small intestineUBERON:000210863.88gold quality
leukocyteCL:000073862.72gold quality
bone marrowUBERON:000237162.53gold quality
colonic epitheliumUBERON:000039762.12silver quality
duodenumUBERON:000211461.46gold quality
endothelial cellCL:000011560.88gold quality
bone marrow cellCL:000209260.86silver quality
mononuclear cellCL:000084260.08gold quality
tonsilUBERON:000237259.92gold quality
monocyteCL:000057659.83gold quality
upper lobe of left lungUBERON:000895258.90gold quality
right coronary arteryUBERON:000162558.36gold quality
smooth muscle tissueUBERON:000113557.83gold quality
omental fat padUBERON:001041457.55gold quality
peritoneumUBERON:000235857.51gold quality
upper lobe of lungUBERON:000894857.48gold quality
adipose tissue of abdominal regionUBERON:000780856.69gold quality
right lungUBERON:000216756.59gold quality

Single-cell (SCXA)

Detected in 5 experiment(s), a significant marker in 5.

ExperimentMarker?Max mean expression
E-CURD-122yes58.04
E-CURD-46yes36.56
E-HCAD-1yes35.74
E-MTAB-8410yes15.88
E-ANND-3yes5.59

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

1 targets.

TargetRegulation
IGSF6Repression

Upstream regulators (CollecTRI, top): AKNA, AP1, EGR1, EGR3, FOS, GATA3, JUN, JUND, MITF, NFAM1, NFATC2, NFATC3, NFIL3, NFKB1, NFKB, NR3C1, REL, RELA, STAT1, TFE3, TFEB, USF1, USF2

miRNA regulators (miRDB)

73 targeting CD40LG, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-6867-5P100.0082.213464
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-5692B100.0071.322622
HSA-MIR-5692C100.0071.322622
HSA-MIR-5692A100.0074.406850
HSA-MIR-4795-3P100.0074.624024
HSA-MIR-12118100.0065.881270
HSA-MIR-607799.9968.042299
HSA-MIR-453499.9966.581907
HSA-MIR-6891-5P99.9866.531372
HSA-MIR-3173-3P99.9866.491217
HSA-MIR-551B-5P99.9671.283493
HSA-MIR-808299.9567.271170
HSA-MIR-452599.9464.38675
HSA-MIR-5010-5P99.9464.11705
HSA-MIR-515-5P99.9269.822343
HSA-MIR-519E-5P99.9269.622358
HSA-MIR-627-3P99.9071.423316
HSA-MIR-369-3P99.8570.522264
HSA-MIR-3121-3P99.8271.963630
HSA-MIR-442099.8270.081624
HSA-MIR-181B-2-3P99.8170.061646
HSA-MIR-181B-3P99.8170.061646
HSA-MIR-34B-5P99.7867.561175
HSA-MIR-449C-5P99.7867.631168
HSA-MIR-6794-5P99.7666.381048
HSA-MIR-674599.7465.331321
HSA-MIR-2682-5P99.7367.381055
HSA-MIR-430699.7270.503630
HSA-MIR-377-5P99.7065.28712

Functional genomics

ClinGen dosage: haploinsufficiency 3 (sufficient evidence), triplosensitivity 0 (no evidence). ClinGen Gene Dosage Map

Literature-anchored findings (GeneRIF, showing 40)

  • Review. In some cases of CLL the malignant cells express both CD40 and CD154. Implications for autoimmunity and therapy are discussed. (PMID:11042507)
  • The capacity of natural killer cells to induce B cell activation is regulated by the interaction of CD40 with its ligand CD154. (PMID:11714772)
  • the CD40L gene 3’-flanking region acts as a T cell-specific classical transcriptional enhancer by a NF-kappaB p50-dependent mechanism. (PMID:11751888)
  • CD40/CD40L interactions are important for the activation of macrophages as effector cells that mediate inflammation and tissue damage in T cell-mediated inflammatory processes. (PMID:11792121)
  • CD40 ligand contacts between fibroblasts and cells secreting IL-4 may promote the profibrotic effects of IL-4 by affecting signal transduction and reducing the anti-fibrotic effects of IFN-gamma. (PMID:11801648)
  • CD40L-deficient T cells in carriers of X-linked hyper-IgM syndrome are minimally impaired in comparison with CD40L-expressing T cells in several parameters of T cell priming. (PMID:11801691)
  • sCD40L levels in blood, quantities released from platelets ex vivo, and quantities released from SFFLRN stimulated platelets ex vivo were compared for preeclamptic and normal pregnancies. (PMID:11816717)
  • CD40:CD40L interactions in X-linked and non-X-linked hyper-IgM syndromes. (PMID:11817328)
  • CD40 and CD40L are important in autoimmunity and other immune processes. At least 5 signal transduction pathways are involved. (PMID:11826760)
  • review of the role of CD154 and the type-1 cytokine response (PMID:11865444)
  • CD40L appears to be an alphaIIbbeta3 integrin ligand, a platelet agonist, and necessary for stability of arterial thrombi. (PMID:11875495)
  • Latent sensitivity to Fas-mediated apoptosis after CD40 ligation may explain activity of CD154 gene therapy in chronic lymphocytic leukemia (PMID:11891278)
  • Role of surface IgM and IgD on survival/apoptosis of B-cell chronic lymphocytic leukemia cells. (PMID:11902141)
  • Association of CD40 ligand expression on HTLV-I-infected T cells and maturation of dendritic cells. (PMID:11902332)
  • dinucleotide microsatellite in multiple sclerosis (PMID:11918631)
  • Elevated soluble CD40 ligand is related to the endothelial adhesion molecules in patients with acute coronary syndrome. (PMID:11922919)
  • Burkitt lymphoma cell population depletion activates autonomous CD154-dependent survival. (PMID:11964311)
  • role in inducing tissue factor expression in endothelial cells (PMID:11978801)
  • Levels of soluble CD40 ligand (CD154) in serum are increased in human immunodeficiency virus type 1-infected patients and correlate with CD4(+) T-cell counts (PMID:11986259)
  • Clustering of CD40 ligand is required to form a functional contact with CD40 (PMID:12011072)
  • cd154 (cd40 ligand)is expressed during treatment with calcineurin inhibitors after organ transplantation. (PMID:12042657)
  • Leishmania priming of human dendritic cells for CD40 ligand-induced interleukin-12p70 secretion is strain and species dependent (PMID:12117904)
  • CD40 ligand (CD154) does not contribute to lymphocyte-mediated inhibition of virulent Mycobacterium tuberculosis within human monocytes (PMID:12117990)
  • association of a common variant in CD40L with a malaria resistance phenotype (PMID:12140747)
  • effect of platelet-derived CD40L on the tissue factor activity of human CD40-positive melanoma cells and monocytes (PMID:12192302)
  • In human lung myofibroblasts,CD40 ligand is induced by lipopolysaccharide, thrombin and TNF-alpha. (PMID:12207328)
  • CD154 expression in renal cell carcinoma (PMID:12209602)
  • Treatment of human gingival fibroblasts with human leukocyte elastase down-regulated CD40 binding to CD40 ligand. HLE treatment of HGF decreases IL-8 and macrophage chemoattractant protein-1 production by HGF when stimulated by CD40L. (PMID:12223522)
  • Impact of both donor and recipient strains on cardiac allograft survival after blockade of the cd40 costimulatory pathway (PMID:12352896)
  • upregulation of CD40L on platelets triggers CD40L-dependent matrix degradation by vascular endothelial cells (PMID:12379582)
  • CD40L induces proliferation, self-renewal, rescue from apoptosis, and production of cytokines by CD40-expressing AML blasts. (PMID:12423681)
  • CD40L has a role in activating antigen-presenting cells (APCs) and thereby initiating the human immune response in HIV infection (PMID:12427285)
  • findings suggests that there are two groups of immune thrombocytopenic purpura (ITP) patients, one with elevated and one with normal of sCD40L; pathogenesis of ITP may in some patients include alterations of the CD40/CD40L pathway (PMID:12460235)
  • CD154 function is determined by binding to PTB and PTB-T and is involved in autoimmune disease (PMID:12509450)
  • CD40L expression on CD4+ T-cells is significantly higher in patients with Kawasaki disease (KD) than in the febrile control group, which implies that CD40L over-expression might play a role in the immunopathogenesis of KD. (PMID:12563087)
  • CD40L can induce maturation of monocyte-derived dendritic cells and elicit sustained antiviral cytotoxic T lymphocyte responses, either alone or cooperatively with TNF-alpha or RANKL. (PMID:12574344)
  • Proapoptotic genes BAX and CD40L are predictors of survival in transitional cell carcinoma of the bladder. (PMID:12592374)
  • Serum levels of sCD40L significantly higher in MCTD than in healthy individuals. May play role in pathogenesis of MCTD. (PMID:12605316)
  • A key mechanism in the pathogenesis of MS is the increased expression of CD86 and CD40L and the increased production of IL12 during disease progression. (PMID:12672403)
  • high shear stress induces CD40L translocation to the platelet surface, which is mediated by the von Willebrand factor (VWF)-GP Ibalpha interaction and enhanced in the presence of a low concentration of epinephrine (PMID:12676191)

Cross-species orthologs

2 orthologs

OrganismSymbolGene ID
mus_musculusCd40lgENSMUSG00000031132
rattus_norvegicusCd40lgENSRNOG00000000871

Paralogs (8): FASLG (ENSG00000117560), TNFSF11 (ENSG00000120659), TNFSF10 (ENSG00000121858), TNFSF14 (ENSG00000125735), TNFSF15 (ENSG00000181634), LTA (ENSG00000226979), LTB (ENSG00000227507), TNF (ENSG00000232810)

Protein

Protein identifiers

CD40 ligandP29965 (reviewed: P29965)

Alternative names: T-cell antigen Gp39, TNF-related activation protein, Tumor necrosis factor ligand superfamily member 5

All UniProt accessions (4): P29965, A0A8Q3WKP2, A0A8Q3WL88, Q3L8U2

UniProt curated annotations — full annotation on UniProt →

Function. Cytokine that acts as a ligand to CD40/TNFRSF5. Costimulates T-cell proliferation and cytokine production. Its cross-linking on T-cells generates a costimulatory signal which enhances the production of IL4 and IL10 in conjunction with the TCR/CD3 ligation and CD28 costimulation. Induces the activation of NF-kappa-B. Induces the activation of kinases MAPK8 and PAK2 in T-cells. Induces tyrosine phosphorylation of isoform 3 of CD28. Mediates B-cell proliferation in the absence of co-stimulus as well as IgE production in the presence of IL4. Involved in immunoglobulin class switching. Acts as a ligand for integrins, specifically ITGA5:ITGB1 and ITGAV:ITGB3; both integrins and the CD40 receptor are required for activation of CD40-CD40LG signaling, which have cell-type dependent effects, such as B-cell activation, NF-kappa-B signaling and anti-apoptotic signaling.

Subunit / interactions. Homotrimer. Interacts with isoform 3 of CD28. CD40 ligand, soluble form: Exists as either a monomer or a homotrimer. Forms a ternary complex between CD40 and integrins for CD40-CD40LG signaling.

Subcellular location. Cell membrane. Cell surface Secreted.

Tissue specificity. Specifically expressed on activated CD4+ T-lymphocytes.

Post-translational modifications. The soluble form derives from the membrane form by proteolytic processing. N-linked glycan is a mixture of high mannose and complex type. Glycan structure does not influence binding affinity to CD40. Not O-glycosylated.

Disease relevance. Immunodeficiency with hyper-IgM, type 1 (HIGM1) [MIM:308230] Immunoglobulin isotype switch defect characterized by elevated concentrations of serum IgM and decreased amounts of all other isotypes. Affected males present at an early age (usually within the first year of life) recurrent bacterial and opportunistic infections, including Pneumocystis carinii pneumonia and intractable diarrhea due to cryptosporidium infection. Despite substitution treatment with intravenous immunoglobulin, the overall prognosis is rather poor, with a death rate of about 10% before adolescence. The disease is caused by variants affecting the gene represented in this entry.

Similarity. Belongs to the tumor necrosis factor family.

RefSeq proteins (1): NP_000065* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR003263CD40LFamily
IPR006052TNF_domDomain
IPR008983Tumour_necrosis_fac-like_domHomologous_superfamily
IPR021184TNF_CSConserved_site

Pfam: PF00229

UniProt features (64 total): sequence variant 35, strand 12, mutagenesis site 4, chain 2, topological domain 2, turn 2, glycosylation site 2, transmembrane region 1, domain 1, site 1, helix 1, disulfide bond 1

Structure

Experimental structures (PDB)

8 structures.

PDBMethodResolution (Å)
6W9GX-RAY DIFFRACTION1.82
1ALYX-RAY DIFFRACTION2
7SGMX-RAY DIFFRACTION2
3LKJX-RAY DIFFRACTION2.5
6BRBX-RAY DIFFRACTION2.82
1I9RX-RAY DIFFRACTION3.1
9I5NELECTRON MICROSCOPY3.4
3QD6X-RAY DIFFRACTION3.5

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P29965-F182.340.55

Antibody-complex structures (SAbDab): 11I9R

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Catalytic / active sites (1): 112–113 (cleavage)

Disulfide bonds (1): 178–218

Glycosylation sites (2): 240, 240

Mutagenesis-validated functional residues (4):

PositionPhenotype
170decreases itga5:itgb1 binding, b-cell activation, activation of nf-kappa-b signaling, and anti-apoptotic signaling; in s
224decreases itga5:itgb1 binding, b-cell activation, activation of nf-kappa-b signaling, and anti-apoptotic signaling; when
226decreases itga5:itgb1 binding, b-cell activation, activation of nf-kappa-b signaling, and anti-apoptotic signaling; when
252decreases itga5:itgb1 binding, b-cell activation, activation of nf-kappa-b signaling, and anti-apoptotic signaling; in s

Function

Pathways and Gene Ontology

Reactome pathways

6 pathways

IDPathway
R-HSA-198933Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell
R-HSA-5668541TNFR2 non-canonical NF-kB pathway
R-HSA-5676594TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway
R-HSA-1280215Cytokine Signaling in Immune system
R-HSA-1280218Adaptive Immune System
R-HSA-168256Immune System

MSigDB gene sets: 413 (showing top): GOBP_REGULATION_OF_CELL_ACTIVATION, GOBP_REGULATION_OF_LEUKOCYTE_PROLIFERATION, REACTOME_ADAPTIVE_IMMUNE_SYSTEM, REACTOME_CYTOKINE_SIGNALING_IN_IMMUNE_SYSTEM, GOBP_INFLAMMATORY_RESPONSE, GOBP_B_CELL_ACTIVATION, GCANCTGNY_MYOD_Q6, GOBP_PLATELET_ACTIVATION, GOBP_CANONICAL_NF_KAPPAB_SIGNAL_TRANSDUCTION, GOBP_LYMPHOCYTE_COSTIMULATION, GOCC_CELL_SURFACE, GOBP_B_CELL_PROLIFERATION, GOBP_EXTRINSIC_APOPTOTIC_SIGNALING_PATHWAY, GOBP_POSITIVE_REGULATION_OF_CYTOKINE_PRODUCTION, GOBP_LEUKOCYTE_MEDIATED_IMMUNITY

GO Biological Process (26): regulation of immunoglobulin production (GO:0002637), inflammatory response (GO:0006954), leukocyte cell-cell adhesion (GO:0007159), cell surface receptor signaling pathway (GO:0007166), integrin-mediated signaling pathway (GO:0007229), CD40 signaling pathway (GO:0023035), platelet activation (GO:0030168), B cell differentiation (GO:0030183), T cell costimulation (GO:0031295), positive regulation of interleukin-10 production (GO:0032733), positive regulation of interleukin-12 production (GO:0032735), positive regulation of interleukin-4 production (GO:0032753), B cell proliferation (GO:0042100), positive regulation of T cell proliferation (GO:0042102), negative regulation of apoptotic process (GO:0043066), positive regulation of canonical NF-kappaB signal transduction (GO:0043123), isotype switching (GO:0045190), obsolete positive regulation of NF-kappaB transcription factor activity (GO:0051092), positive regulation of endothelial cell apoptotic process (GO:2000353), positive regulation of extrinsic apoptotic signaling pathway (GO:2001238), regulation of immune system process (GO:0002682), immune response (GO:0006955), cell communication (GO:0007154), signal transduction (GO:0007165), regulation of gene expression (GO:0010468), signaling (GO:0023052)

GO Molecular Function (7): cytokine activity (GO:0005125), tumor necrosis factor receptor binding (GO:0005164), CD40 receptor binding (GO:0005174), integrin binding (GO:0005178), protein serine/threonine kinase activator activity (GO:0043539), signaling receptor binding (GO:0005102), protein binding (GO:0005515)

GO Cellular Component (7): obsolete extracellular space (GO:0005615), Golgi apparatus (GO:0005794), plasma membrane (GO:0005886), external side of plasma membrane (GO:0009897), cell surface (GO:0009986), membrane (GO:0016020), extracellular region (GO:0005576)

Reactome top-level categories

Rollup of top-4 pathways:

CategoryPathways
Immune System2
Adaptive Immune System1
Cytokine Signaling in Immune system1
TNFR2 non-canonical NF-kB pathway1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
positive regulation of cytokine production3
cellular anatomical structure3
cell surface receptor signaling pathway2
B cell activation2
positive regulation of T cell activation2
tumor necrosis factor receptor superfamily binding2
immunoglobulin production1
regulation of production of molecular mediator of immune response1
defense response1
cell-cell adhesion1
signal transduction1
cell activation1
blood coagulation1
lymphocyte differentiation1
lymphocyte costimulation1
interleukin-10 production1
regulation of interleukin-10 production1
interleukin-12 production1
regulation of interleukin-12 production1
interleukin-4 production1
regulation of interleukin-4 production1
lymphocyte proliferation1
T cell proliferation1
regulation of T cell proliferation1
positive regulation of lymphocyte proliferation1
apoptotic process1
regulation of apoptotic process1
negative regulation of programmed cell death1
canonical NF-kappaB signal transduction1
regulation of canonical NF-kappaB signal transduction1
positive regulation of intracellular signal transduction1
somatic recombination of immunoglobulin genes involved in immune response1
B cell activation involved in immune response1
positive regulation of apoptotic process1
endothelial cell apoptotic process1
regulation of endothelial cell apoptotic process1
extrinsic apoptotic signaling pathway1
positive regulation of apoptotic signaling pathway1
regulation of extrinsic apoptotic signaling pathway1
receptor ligand activity1

Protein interactions and networks

STRING

3058 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
CD40LGCD40P25942999
CD40LGCD80P33681998
CD40LGCD86P42081998
CD40LGCD28P10747997
CD40LGICOSQ9Y6W8990
CD40LGICOSLGO75144989
CD40LGA0A087X1L8A0A087X1L8988
CD40LGSELPLGQ14242982
CD40LGCD4P01730976
CD40LGCD70P32970964
CD40LGTNFSF4P23510958
CD40LGSELPP16109944
CD40LGTNFRSF13BO14836937
CD40LGTNFRSF4P43489936
CD40LGCD276Q5ZPR3935

IntAct

2 interactions, top by confidence:

ABTypeScore
CD40LGCD40psi-mi:“MI:0407”(direct interaction)0.440

BioGRID (12): CD40LG (Affinity Capture-RNA), HPR (Affinity Capture-Western), APOA1 (Affinity Capture-Western), RNF128 (Affinity Capture-Western), CD40LG (Biochemical Activity), PHB (Reconstituted Complex), CD40LG (Affinity Capture-MS), CD40 (Affinity Capture-Western), TRAF2 (Affinity Capture-Western), BIRC2 (Affinity Capture-Western), BIRC3 (Affinity Capture-Western), TRAF1 (Affinity Capture-Western)

ESM2 similar proteins: D5K8A9, O02757, O02765, O35734, O97605, O97626, P04924, P06804, P16599, P23563, P27548, P29965, P31042, P35330, P36939, P36940, P41047, P43303, P43488, P48023, P51749, P59694, P63304, P63305, P63306, P63307, P63308, Q28071, Q539C2, Q5NKV2, Q5U462, Q75N23, Q7TS55, Q861W5, Q8BHK6, Q8IYV9, Q95MQ5, Q9BDM3, Q9BDM7, Q9BDN1

Diamond homologs: O97605, O97626, P27548, P29965, P51749, P63304, P63305, Q95MQ5, Q9BDM3, Q9BDM7, Q9BDN3, Q9I8D8, Q9Z2V2, P59694, Q75N23, O35734, O77510, O77764, P01374, P01375, P04924, P06804, P09225, P10154, P13296, P16599, P19101, P23383, P23563, P26445, P29553, P33620, P36939, P36940, P41047, P48094, P51435, P51742, P51743, P59684

SIGNOR signaling

4 interactions.

AEffectBMechanism
CD40LGdown-regulatesPTPN7
CD40LG“up-regulates activity”CD40binding
CD40LG“down-regulates quantity by repression”IGSF6“transcriptional regulation”

Disease & clinical

Clinical variants and AI predictions

ClinVar

347 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic78
Likely pathogenic31
Uncertain significance79
Likely benign84
Benign30

Top pathogenic / likely-pathogenic (30)

Variant IDHGVSClassification
1070422NM_000074.3(CD40LG):c.470del (p.Asn157fs)Pathogenic
1071618NM_000074.3(CD40LG):c.15C>A (p.Tyr5Ter)Pathogenic
1074317NM_000074.3(CD40LG):c.346+1G>APathogenic
11157NM_000074.3(CD40LG):c.703G>C (p.Ala235Pro)Pathogenic
11159NM_000074.3(CD40LG):c.680G>T (p.Gly227Val)Pathogenic
11160NM_000074.3(CD40LG):c.464T>C (p.Leu155Pro)Pathogenic
11161CD40LG, THR211ASPPathogenic
11163NM_000074.3(CD40LG):c.419G>A (p.Trp140Ter)Pathogenic
11166NM_000074.3(CD40LG):c.412_419delPathogenic
11167CD40LG, 10-BP DELPathogenic
11168NM_000074.3(CD40LG):c.368C>A (p.Ala123Glu)Pathogenic
11169NM_000074.3(CD40LG):c.189dup (p.Val64fs)Pathogenic
11170NG_007280.1:g.5145_5146insAluAluYb8invPathogenic
1195319NM_000074.3(CD40LG):c.289-2A>CPathogenic
1327990NM_000074.3(CD40LG):c.166G>T (p.Glu56Ter)Pathogenic
1381599NM_000074.3(CD40LG):c.156+2T>CPathogenic
1402799NM_000074.3(CD40LG):c.409+1G>CPathogenic
1405864NM_000074.3(CD40LG):c.385G>T (p.Glu129Ter)Pathogenic
1413373NM_000074.3(CD40LG):c.598A>T (p.Arg200Ter)Pathogenic
1423116NM_000074.3(CD40LG):c.289-1G>APathogenic
1444168NM_000074.3(CD40LG):c.478C>T (p.Gln160Ter)Pathogenic
1454482NC_000023.10:g.(?135730388)(135737600_?)delPathogenic
1706555NM_000074.3(CD40LG):c.161_162insG (p.Asp55fs)Pathogenic
1803793NM_000074.3(CD40LG):c.229del (p.Arg77fs)Pathogenic
1996844NM_000074.3(CD40LG):c.43del (p.Thr15fs)Pathogenic
1997026NM_000074.3(CD40LG):c.268C>T (p.Gln90Ter)Pathogenic
2013065NM_000074.3(CD40LG):c.431del (p.Gly144fs)Pathogenic
2039120NM_000074.3(CD40LG):c.299T>A (p.Leu100Ter)Pathogenic
2054209NM_000074.3(CD40LG):c.756del (p.Phe253fs)Pathogenic
2092047NM_000074.3(CD40LG):c.340del (p.Gln114fs)Pathogenic

SpliceAI

389 predictions. Top by Δscore:

VariantEffectΔscore
X:136650259:A:AGacceptor_gain1.0000
X:136650260:A:Gacceptor_gain1.0000
X:136650264:A:AGacceptor_gain1.0000
X:136650264:A:Gacceptor_loss1.0000
X:136650265:G:GGacceptor_gain1.0000
X:136650265:GATA:Gacceptor_gain1.0000
X:136650398:G:GCdonor_loss1.0000
X:136656350:TTTCA:Tacceptor_loss1.0000
X:136656351:TTCA:Tacceptor_loss1.0000
X:136656353:CA:Cacceptor_loss1.0000
X:136656355:G:GCacceptor_loss1.0000
X:136648400:ACAAG:Adonor_loss0.9900
X:136648402:AAGGT:Adonor_loss0.9900
X:136648403:AGG:Adonor_loss0.9900
X:136648405:GTA:Gdonor_loss0.9900
X:136648406:T:Gdonor_loss0.9900
X:136656354:A:AGacceptor_gain0.9900
X:136656355:G:GGacceptor_gain0.9900
X:136659037:A:AGacceptor_gain0.9900
X:136659038:G:GAacceptor_gain0.9900
X:136659038:GT:Gacceptor_gain0.9900
X:136650398:G:GGdonor_gain0.9800
X:136656354:AGGT:Aacceptor_gain0.9800
X:136656355:GGT:Gacceptor_gain0.9800
X:136656355:GGTG:Gacceptor_gain0.9800
X:136656417:TGGTA:Tdonor_loss0.9800
X:136656419:G:GGdonor_gain0.9800
X:136656419:G:Tdonor_loss0.9800
X:136656420:TAA:Tdonor_loss0.9800
X:136656421:AA:Adonor_loss0.9800

AlphaMissense

1733 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
X:136659047:T:AW140R0.996
X:136659047:T:CW140R0.996
X:136659049:G:CW140C0.996
X:136659049:G:TW140C0.996
X:136659345:T:AV239D0.989
X:136659399:G:AG257D0.987
X:136659158:T:CF177L0.985
X:136659160:C:AF177L0.985
X:136659160:C:GF177L0.985
X:136656391:A:CS128R0.983
X:136656393:T:AS128R0.983
X:136656393:T:GS128R0.983
X:136650323:T:AC72S0.982
X:136650324:G:CC72S0.982
X:136659048:G:CW140S0.981
X:136659321:T:CL231S0.981
X:136659314:T:CF229L0.979
X:136659316:T:AF229L0.979
X:136659316:T:GF229L0.979
X:136659111:T:CL161P0.978
X:136659134:T:GY169D0.977
X:136659398:G:CG257R0.976
X:136659153:T:AV175D0.975
X:136659246:T:CL206P0.975
X:136659117:T:AV163D0.973
X:136659405:T:CL259P0.972
X:136650323:T:CC72R0.971
X:136659390:C:AT254K0.971
X:136659392:T:CS255P0.971
X:136648385:T:CL46P0.970

dbSNP variants (sampled 300 via entrez): RS1000546748 (X:136650966 G>A), RS1000550722 (X:136660169 G>A), RS1000866634 (X:136656066 G>A), RS1001276404 (X:136655647 T>C), RS1001615881 (X:136650801 C>T), RS1001714115 (X:136657498 G>A), RS1001915392 (X:136659381 C>A), RS1002714772 (X:136652963 C>A,T), RS1003195609 (X:136655350 T>C), RS1003733851 (X:136652836 G>A), RS1003957406 (X:136657094 C>T), RS1004051141 (X:136654374 A>G), RS1004520254 (X:136647193 A>G), RS1004611925 (X:136646678 G>T), RS1004627667 (X:136656964 C>A,G,T)

Disease associations

OMIM: gene MIM:300386 | disease phenotypes: MIM:308230, MIM:607594

GenCC curated gene-disease

DiseaseClassificationInheritance
hyper-IgM syndrome type 1DefinitiveX-linked

ClinGen Gene-Disease Validity (1)

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

DiseaseClassificationInheritance
hyper-IgM syndrome type 1DefinitiveXL

Mondo (3): hyper-IgM syndrome type 1 (MONDO:0010626), common variable immunodeficiency (MONDO:0015517), hyper-IgM syndrome (MONDO:0003947)

Orphanet (2): X-linked hyper-IgM syndrome (Orphanet:101088), OBSOLETE: Common variable immunodeficiency (Orphanet:1572)

HPO phenotypes

41 total (30 of 41 shown, HPO-id order):

HPOTerm
HP:0000155Oral ulcer
HP:0000230Gingivitis
HP:0001263Global developmental delay
HP:0001287Meningitis
HP:0001347Hyperreflexia
HP:0001394Cirrhosis
HP:0001419X-linked recessive inheritance
HP:0001508Failure to thrive
HP:0001744Splenomegaly
HP:0001873Thrombocytopenia
HP:0001875Decreased total neutrophil count
HP:0001878Hemolytic anemia
HP:0002014Diarrhea
HP:0002240Hepatomegaly
HP:0002376Developmental regression
HP:0002718Recurrent bacterial infections
HP:0002720Decreased circulating IgA concentration
HP:0002721Immunodeficiency
HP:0002783Recurrent lower respiratory tract infections
HP:0002847Impaired memory B cell generation
HP:0002849Absence of lymph node germinal center
HP:0002959Impaired Ig class switch recombination
HP:0002961Dysgammaglobulinemia
HP:0003261Increased circulating IgA concentration
HP:0003496Increased circulating IgM level
HP:0003593Infantile onset
HP:0004315Decreased circulating IgG concentration
HP:0005419Decreased T cell activation
HP:0005479Decreased circulating IgE concentration
HP:0009098Chronic oral candidiasis

GWAS associations

4 associations (top):

StudyTraitp-value
GCST003097_45Pediatric autoimmune diseases1.000000e-08
GCST009565_1CD40 ligand levels1.000000e-25
GCST90002388_278Lymphocyte count1.000000e-11
GCST90002400_6Plateletcrit5.000000e-10

EFO canonical traits (3, from GWAS)

EFO IDTrait name
EFO:0004790CD40 ligand measurement
EFO:0004587lymphocyte count
EFO:0007985platelet crit

MeSH disease descriptors (2)

DescriptorNameTree numbers
D017074Common Variable ImmunodeficiencyC20.673.330
D053306Hyper-IgM Immunodeficiency SyndromeC15.378.147.333.249; C16.320.413; C16.320.798.625; C20.673.430.250; C20.673.795.625

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (3): CHEMBL3580491 (SINGLE PROTEIN), CHEMBL4106121 (PROTEIN-PROTEIN INTERACTION), CHEMBL4106122 (PROTEIN-PROTEIN INTERACTION)

PharmGKB: 1 entry (VIP=true, CPIC=false)

PharmGKB variants

1 variants.

VariantGenesLevelScore#Clin annotsDrugs
rs1126535CD40LG0.000

ChEMBL bioactivities

8 potent at pChembl≥5 of 13 total, top 8 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChemblTypeValueUnitMolecule
6.77IC50170nMCHEMBL4080373
6.51IC50310nMCHEMBL4060985
6.44IC50360nMCHEMBL4090673
6.00IC50990nMCHEMBL4098397
5.65IC502260nMCHEMBL4082979
5.63IC502330nMCHEMBL4072368
5.35IC504500nMCHEMBL4080373
5.03IC509400nMCHEMBL4090673

PubChem BioAssay actives

8 with measured affinity, of 46 total; 6 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

CompoundAssayTypeValueUnit
8-[[4-[4-[(4-methoxycarbonylbenzoyl)amino]phenyl]benzoyl]amino]naphthalene-1-sulfonic acid1465876: Inhibition of human Fc-conjugated CD40/FLAG-tagged biotinylated CD40L costimulatory protein-protein interaction incubated for 1 hr by ELISA-type assayic500.1700uM
8-[[4-[4-[(4-nitrobenzoyl)amino]phenyl]benzoyl]amino]naphthalene-1-sulfonic acid1465876: Inhibition of human Fc-conjugated CD40/FLAG-tagged biotinylated CD40L costimulatory protein-protein interaction incubated for 1 hr by ELISA-type assayic500.3100uM
4-[[4-[4-[(4-nitrobenzoyl)amino]phenyl]benzoyl]amino]naphthalene-1-carboxylic acid1465876: Inhibition of human Fc-conjugated CD40/FLAG-tagged biotinylated CD40L costimulatory protein-protein interaction incubated for 1 hr by ELISA-type assayic500.3600uM
8-[[4-[4-(1H-benzotriazole-5-carbonylamino)phenyl]benzoyl]amino]naphthalene-1-sulfonic acid1465876: Inhibition of human Fc-conjugated CD40/FLAG-tagged biotinylated CD40L costimulatory protein-protein interaction incubated for 1 hr by ELISA-type assayic500.9900uM
4-hydroxy-7-[[5-hydroxy-7-sulfo-6-[[2-sulfo-4-[(4-sulfophenyl)diazenyl]phenyl]diazenyl]naphthalen-2-yl]carbamoylamino]-3-[[2-sulfo-4-[(4-sulfophenyl)diazenyl]phenyl]diazenyl]naphthalene-2-sulfonic acid1465876: Inhibition of human Fc-conjugated CD40/FLAG-tagged biotinylated CD40L costimulatory protein-protein interaction incubated for 1 hr by ELISA-type assayic502.2600uM
4-[[4-[4-[(4-nitrobenzoyl)amino]phenyl]benzoyl]amino]naphthalene-1-sulfonic acid1465876: Inhibition of human Fc-conjugated CD40/FLAG-tagged biotinylated CD40L costimulatory protein-protein interaction incubated for 1 hr by ELISA-type assayic502.3300uM

CTD chemical–gene interactions

68 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
(+)-JQ1 compoundaffects cotreatment, increases expression, decreases expression3
Tetrachlorodibenzodioxinaffects cotreatment, decreases reaction, increases expression, affects activity, increases reaction (+1 more)3
Atorvastatindecreases expression2
Air Pollutantsaffects expression2
Aspirindecreases expression2
Doxorubicindecreases response to substance, affects cotreatment, increases expression, decreases reaction, increases cleavage (+1 more)2
Erythrosineaffects binding, decreases reaction2
Paclitaxeldecreases reaction, increases cleavage, increases reaction, decreases response to substance, affects cotreatment (+1 more)2
Reactive Oxygen Speciesaffects cotreatment, decreases reaction, increases abundance, affects binding, increases reaction (+4 more)2
Particulate Matteraffects expression, decreases methylation, increases expression2
bisphenol Fdecreases expression1
aminomethylphosphonic acid (AMPA)increases expression1
diphenyleneiodoniumaffects binding, affects cotreatment, decreases reaction, increases abundance1
emulphogene BC 720increases expression1
galleindecreases reaction, affects binding1
3,3’-diindolylmethaneincreases expression1
sodium arsenitedecreases expression1
indirubinaffects cotreatment, decreases reaction, increases expression1
diphenyliodoniumaffects cotreatment, decreases reaction, increases abundance, increases reaction, increases expression (+1 more)1
candesartandecreases expression, increases reaction1
lipopolysaccharide, E. coli O26-B6decreases expression1
2-methyl-2H-pyrazole-3-carboxylic acid (2-methyl-4-o-tolylazophenyl)amideincreases expression, increases reaction, affects cotreatment, decreases reaction1
bisphenol Sincreases expression1
Aspirin, Dipyridamole Drug Combinationdecreases expression1
Fingolimod Hydrochloridedecreases expression1
Clopidogreldecreases reaction, increases expression1
Zoledronic Aciddecreases expression1
Arsenic Trioxideaffects cotreatment, increases expression1
Vemurafenibincreases expression, affects cotreatment1
Eptifibatidedecreases expression1

ChEMBL screening assays

8 unique, capped per target: 8 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL4688318BindingInhibition of CD40L (unknown origin)Biologic-like In Vivo Efficacy with Small Molecule Inhibitors of TNFα Identified Using Scaffold Hopping and Structure-Based Drug Design Approaches. — J Med Chem

Cellosaurus cell lines

14 cell lines: 10 transformed cell line, 2 cancer cell line, 1 telomerase immortalized cell line, 1 spontaneously immortalized cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_2Z02ID00002Transformed cell lineMale
CVCL_2Z27ID00063Transformed cell lineMale
CVCL_2Z28ID00064Transformed cell lineMale
CVCL_4V25293-CD40LTransformed cell lineFemale
CVCL_4V26293-CD40L-sCD40LTransformed cell lineFemale
CVCL_A2XKYK6-CD40Lg-IL21Telomerase immortalized cell lineMale
CVCL_B8D3Abcam HCT 116 CD40LG KOCancer cell lineMale
CVCL_B9FAAbcam A-549 CD40LG KOCancer cell lineMale
CVCL_E3RFHS5-CD40LTransformed cell lineMale
CVCL_E3RIHS5-CD40L-IL4Transformed cell lineMale

Clinical trials (associated diseases)

45 trials via MONDO — disease-level, not drug-specific.

TrialPhaseStatusTitle
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
NCT05193552PHASE4RECRUITINGUsage of Spirometry in Managing IgG Therapy in CVID With Airway Disease
NCT01884311PHASE3COMPLETEDPharmacokinetics (PK) and Safety of Subgam-VF in Primary Immunodeficiency Diseases
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
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®
NCT00278954PHASE3COMPLETEDEfficacy, Safety and Pharmacokinetics of Gammaplex in Primary Immunodeficiency Diseases.
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
NCT01821781PHASE2ACTIVE_NOT_RECRUITINGImmune Disorder HSCT Protocol
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)
NCT00263237PHASE1COMPLETEDSTA-5326 Meslylate to Treat Gut Inflammation Associated With Common Variable Immunodeficiency
NCT00004341Not specifiedUNKNOWNStudy of Genetic and Molecular Defects in Primary Immunodeficiency Disorders
NCT00006054Not specifiedTERMINATEDAllogeneic Bone Marrow Transplantation in Patients With Primary Immunodeficiencies
NCT01652092Not specifiedACTIVE_NOT_RECRUITINGAllogeneic Hematopoietic Stem Cell Transplant for Patients With Primary Immune Deficiencies
NCT01852370PHASE1/PHASE2ENROLLING_BY_INVITATIONSequential Cadaveric Lung and Bone Marrow Transplant for Immune Deficiency Diseases
NCT03513328PHASE1/PHASE2COMPLETEDConditioning Regimen for Allogeneic Hematopoietic Stem-Cell Transplantation
NCT00004695Not specifiedCOMPLETEDRandomized Study of Polyethylene-Glycol-Conjugated Interleukin 2 in Patients With Common Variable Immunodeficiency
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
NCT00943514Not specifiedRECRUITINGNatural History of Bronchiectasis
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.
NCT05321407Not specifiedACTIVE_NOT_RECRUITINGCOVID-19 Vaccine Responses in PIDD Subjects