Gene Gene information from NCBI Gene database.
Entrez ID 958
Gene name CD40 molecule
Gene symbol CD40
Synonyms (NCBI Gene)
Bp50CDW40TNFRSF5p50
Chromosome 20
Chromosome location 20q13.12
Summary This gene is a member of the TNF-receptor superfamily. The encoded protein is a receptor on antigen-presenting cells of the immune system and is essential for mediating a broad variety of immune and inflammatory responses including T cell-dependent immuno
SNPs SNP information provided by dbSNP.
4
SNP ID Visualize variation Clinical significance Consequence
rs28931586 T>C Pathogenic Missense variant, coding sequence variant, non coding transcript variant
rs774195387 T>C Pathogenic Splice donor variant
rs1568905451 TAA>- Pathogenic Non coding transcript variant, inframe deletion, coding sequence variant
rs1568906348 A>T Pathogenic Splice acceptor variant
miRNA miRNA information provided by mirtarbase database.
64
miRTarBase ID miRNA Experiments Reference
MIRT003393 hsa-miR-224-5p MicroarrayqRT-PCR 19475450
MIRT004620 hsa-miR-486-5p MicroarrayqRT-PCR 19475450
MIRT006789 hsa-miR-503-5p Luciferase reporter assay 22429276
MIRT736408 hsa-miR-491-3p qRT-PCRFlow cytometry 33679688
MIRT875349 hsa-miR-103a CLIP-seq
Transcription factors Transcription factors information provided by TRRUST V2 database.
16
Transcription factor Regulation Reference
IRF1 Activation 18694960
NFKB1 Activation 19164127;9733827
NFKB1 Unknown 11027342;11313274;17031478
NFKBIA Repression 9733827
NR3C2 Activation 16179010
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
79
GO ID Ontology Definition Evidence Reference
GO:0002376 Process Immune system process IEA
GO:0002637 Process Regulation of immunoglobulin production IEA
GO:0002768 Process Immune response-regulating cell surface receptor signaling pathway IBA
GO:0002768 Process Immune response-regulating cell surface receptor signaling pathway IEA
GO:0003823 Function Antigen binding IEA
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
109535 11919 ENSG00000101017
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
P25942
Protein name Tumor necrosis factor receptor superfamily member 5 (B-cell surface antigen CD40) (Bp50) (CD40L receptor) (CDw40) (CD antigen CD40)
Protein function Receptor for TNFSF5/CD40LG (PubMed:31331973). Transduces TRAF6- and MAP3K8-mediated signals that activate ERK in macrophages and B cells, leading to induction of immunoglobulin secretion (By similarity). {ECO:0000250|UniProtKB:P27512, ECO:000026
PDB 1CZZ , 1D00 , 1FLL , 1LB6 , 3QD6 , 5DMI , 5DMJ , 5IHL , 6FAX , 6PE8 , 6PE9 , 7P3I , 8YX1 , 8YX9
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF00020 TNFR_c6 62 103 TNFR/NGFR cysteine-rich region Domain
Tissue specificity TISSUE SPECIFICITY: B-cells and in primary carcinomas.
Sequence
MVRLPLQCVLWGCLLTAVHPEPPTACREKQYLINSQCCSLCQPGQKLVSDCTEFTETECL
PCGESEFLDTWNRETHCHQHKYCDPNLGLRVQQKGTSETDTICTCEEGWHCTSEACESCV
LHRSCSPGFGVKQIATGVSDTICEPCPVGFFSNVSSAFEKCHPWTSCETKDLVVQQAGTN
KTDVVCGPQDRLRALVVIPIIFGILFAILLVLVFIKKVAKKPTNKAPHPKQEPQEINFPD
DLPGSNTAAPVQETLHGCQPVTQEDGKESRISVQERQ
Sequence length 277
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
  KEGG  Reactome
  Cytokine-cytokine receptor interaction
NF-kappa B signaling pathway
Cell adhesion molecules
Toll-like receptor signaling pathway
Intestinal immune network for IgA production
Malaria
Toxoplasmosis
Human T-cell leukemia virus 1 infection
Epstein-Barr virus infection
Transcriptional misregulation in cancer
Asthma
Autoimmune thyroid disease
Systemic lupus erythematosus
Allograft rejection
Primary immunodeficiency
Viral myocarditis
Lipid and atherosclerosis
  Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell
TNFR2 non-canonical NF-kB pathway
TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
41
Evidence Score: ★☆☆☆☆  Gene-disease association found in Text Mining only ★★☆☆☆  Found in Text Mining and Unknown/Other Associations ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession Evidence Score
Hyper-IgM syndrome type 3 Pathogenic rs2145595063, rs28931586, rs1568906348, rs1568905451 RCV000019324
RCV000019325
RCV000019326
RCV000022450
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Phenotype Name Clinical Significance Source Evidence Score
ANKYLOSING SPONDYLITIS GWAS catalog
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
ARTHRITIS Disgenet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
ARTHRITIS, RHEUMATOID CTD
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
ASTHMA Disgenet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Associations from Text Mining Disease associations identified through text mining
Disease Name Disease (Merged) Source PMID Relationship Type Evidence Score
Acquired Hypogammaglobulinemia Common Variable Immunodeficiency BEFREE 26279205, 7515919
★☆☆☆☆
Found in Text Mining only
Acute Coronary Syndrome Coronary Syndrome BEFREE 16627810, 19679244, 20127135, 20137882, 20552594, 21091218, 30924686, 31183392
★☆☆☆☆
Found in Text Mining only
Acute lymphocytic leukemia Lymphocytic Leukemia BEFREE 1702326, 17101562, 17285277, 18552209
★☆☆☆☆
Found in Text Mining only
Acute monocytic leukemia Monocytic Leukemia BEFREE 12423681
★☆☆☆☆
Found in Text Mining only
Adenocarcinoma Adenocarcinoma BEFREE 19475450, 29523597
★☆☆☆☆
Found in Text Mining only
Adenocarcinoma Of Esophagus Esophageal Cancer BEFREE 21750116
★☆☆☆☆
Found in Text Mining only
Adenocarcinoma of large intestine Colorectal Cancer BEFREE 29436396
★☆☆☆☆
Found in Text Mining only
Adenocarcinoma of pancreas Pancreatic adenocarcinoma BEFREE 18437082
★☆☆☆☆
Found in Text Mining only
Adult Acute Lymphocytic Leukemia Lymphocytic Leukemia BEFREE 17285277
★☆☆☆☆
Found in Text Mining only
Adult Diffuse Large B-Cell Lymphoma B-cell Lymphoma BEFREE 20155735, 21411738, 22335531, 28281555
★☆☆☆☆
Found in Text Mining only