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CD40 (CD40 molecule)

Identity

Alias (NCBI)Bp50
CDW40
TNFRSF5
p50
HGNC (Hugo) CD40
HGNC Alias symbp50
Bp50
HGNC Previous nameTNFRSF5
HGNC Previous nametumor necrosis factor receptor superfamily, member 5
 CD40 molecule, TNF receptor superfamily member 5
LocusID (NCBI) 958
Atlas_Id 42627
Location 20q13.12  [Link to chromosome band 20q13]
Location_base_pair Starts at 46118314 and ends at 46129855 bp from pter ( according to hg38-Dec_2013)
Fusion genes
(updated 2017)
Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)
APLP2 (11q24.3)::CD40 (20q13.12)APLP2 11q24.3::CD40 20q13.12

Note

Non-annotated gene. Preliminary data : if you are an author
who wish to write a full paper/card on this gene, go to  How to contribute

DNA/RNA

 



Other Leukemias implicated (Data extracted from papers in the Atlas) [ 2 ]
  Classical Hodgkin lymphoma
Hodgkin lymphoma


External links

 

Nomenclature
HGNC (Hugo)CD40   11919
LRG (Locus Reference Genomic)LRG_40
Cards
Entrez_Gene (NCBI)CD40    CD40 molecule
AliasesBp50; CDW40; TNFRSF5; p50
GeneCards (Weizmann)CD40
Ensembl hg19 (Hinxton)ENSG00000101017 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000101017 [Gene_View]  ENSG00000101017 [Sequence]  chr20:46118314-46129855 [Contig_View]  CD40 [Vega]
ICGC DataPortalENSG00000101017
TCGA cBioPortalCD40
AceView (NCBI)CD40
Genatlas (Paris)CD40
SOURCE (Princeton)CD40
Genetics Home Reference (NIH)CD40
Genomic and cartography
GoldenPath hg38 (UCSC)CD40  -     chr20:46118314-46129855 +  20q13.12   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)CD40  -     20q13.12   [Description]    (hg19-Feb_2009)
GoldenPathCD40 - 20q13.12 [CytoView hg19]  CD40 - 20q13.12 [CytoView hg38]
ImmunoBaseENSG00000101017
Genome Data Viewer NCBICD40 [Mapview hg19]  
OMIM109535   606843   
Gene and transcription
Genbank (Entrez)AB209660 AJ300189 AK222896 AY225405 BC012419
RefSeq transcript (Entrez)NM_001250 NM_001302753 NM_001322421 NM_001322422 NM_001362758 NM_152854
Consensus coding sequences : CCDS (NCBI)CD40
Gene ExpressionCD40 [ NCBI-GEO ]   CD40 [ EBI - ARRAY_EXPRESS ]   CD40 [ SEEK ]   CD40 [ MEM ]
Gene Expression Viewer (FireBrowse)CD40 [ Firebrowse - Broad ]
GenevisibleExpression of CD40 in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)958
GTEX Portal (Tissue expression)CD40
Human Protein AtlasENSG00000101017-CD40 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtP25942   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtP25942  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP25942
PhosPhoSitePlusP25942
Domaine pattern : Prosite (Expaxy)TNFR_NGFR_1 (PS00652)    TNFR_NGFR_2 (PS50050)   
Domains : Interpro (EBI)TNFR/NGFR_Cys_rich_reg    TNFR_5    TNFRSF5_N   
Domain families : Pfam (Sanger)TNFR_c6 (PF00020)   
Domain families : Pfam (NCBI)pfam00020   
Domain families : Smart (EMBL)TNFR (SM00208)  
Conserved Domain (NCBI)CD40
PDB (RSDB)1CDF    1CZZ    1D00    1FLL    1LB6    3QD6    5DMI    5DMJ    5IHL    6FAX    6PE8    6PE9   
PDB Europe1CDF    1CZZ    1D00    1FLL    1LB6    3QD6    5DMI    5DMJ    5IHL    6FAX    6PE8    6PE9   
PDB (PDBSum)1CDF    1CZZ    1D00    1FLL    1LB6    3QD6    5DMI    5DMJ    5IHL    6FAX    6PE8    6PE9   
PDB (IMB)1CDF    1CZZ    1D00    1FLL    1LB6    3QD6    5DMI    5DMJ    5IHL    6FAX    6PE8    6PE9   
Structural Biology KnowledgeBase1CDF    1CZZ    1D00    1FLL    1LB6    3QD6    5DMI    5DMJ    5IHL    6FAX    6PE8    6PE9   
SCOP (Structural Classification of Proteins)1CDF    1CZZ    1D00    1FLL    1LB6    3QD6    5DMI    5DMJ    5IHL    6FAX    6PE8    6PE9   
CATH (Classification of proteins structures)1CDF    1CZZ    1D00    1FLL    1LB6    3QD6    5DMI    5DMJ    5IHL    6FAX    6PE8    6PE9   
SuperfamilyP25942
AlphaFold pdb e-kbP25942   
Human Protein Atlas [tissue]ENSG00000101017-CD40 [tissue]
HPRD00178
Protein Interaction databases
DIP (DOE-UCLA)P25942
IntAct (EBI)P25942
BioGRIDCD40
STRING (EMBL)CD40
ZODIACCD40
Ontologies - Pathways
QuickGOP25942
Ontology : AmiGOpositive regulation of protein phosphorylation  immune response-regulating cell surface receptor signaling pathway  antigen binding  protein binding  plasma membrane  plasma membrane  integral component of plasma membrane  cellular calcium ion homeostasis  inflammatory response  external side of plasma membrane  cell surface  B cell mediated immunity  enzyme binding  CD40 signaling pathway  CD40 signaling pathway  platelet activation  positive regulation of B cell proliferation  ubiquitin protein ligase binding  positive regulation of interleukin-12 production  response to interferon-gamma  CD40 receptor complex  CD40 receptor complex  TRIF-dependent toll-like receptor signaling pathway  signaling receptor activity  B cell proliferation  B cell activation  positive regulation of tyrosine phosphorylation of STAT protein  positive regulation of tyrosine phosphorylation of STAT protein  defense response to protozoan  positive regulation of I-kappaB kinase/NF-kappaB signaling  positive regulation of I-kappaB kinase/NF-kappaB signaling  intracellular membrane-bounded organelle  positive regulation of MAP kinase activity  protein kinase B signaling  positive regulation of blood vessel endothelial cell migration  positive regulation of blood vessel endothelial cell migration  positive regulation of GTPase activity  positive regulation of angiogenesis  positive regulation of angiogenesis  positive regulation of transcription by RNA polymerase II  positive regulation of transcription by RNA polymerase II  positive regulation of isotype switching to IgG isotypes  positive regulation of NF-kappaB transcription factor activity  positive regulation of NF-kappaB transcription factor activity  defense response to virus  protein-containing complex assembly  extracellular exosome  cellular response to mechanical stimulus  cellular response to interleukin-1  cellular response to tumor necrosis factor  positive regulation of protein kinase C signaling  positive regulation of endothelial cell apoptotic process  positive regulation of endothelial cell apoptotic process  
Ontology : EGO-EBIpositive regulation of protein phosphorylation  immune response-regulating cell surface receptor signaling pathway  antigen binding  protein binding  plasma membrane  plasma membrane  integral component of plasma membrane  cellular calcium ion homeostasis  inflammatory response  external side of plasma membrane  cell surface  B cell mediated immunity  enzyme binding  CD40 signaling pathway  CD40 signaling pathway  platelet activation  positive regulation of B cell proliferation  ubiquitin protein ligase binding  positive regulation of interleukin-12 production  response to interferon-gamma  CD40 receptor complex  CD40 receptor complex  TRIF-dependent toll-like receptor signaling pathway  signaling receptor activity  B cell proliferation  B cell activation  positive regulation of tyrosine phosphorylation of STAT protein  positive regulation of tyrosine phosphorylation of STAT protein  defense response to protozoan  positive regulation of I-kappaB kinase/NF-kappaB signaling  positive regulation of I-kappaB kinase/NF-kappaB signaling  intracellular membrane-bounded organelle  positive regulation of MAP kinase activity  protein kinase B signaling  positive regulation of blood vessel endothelial cell migration  positive regulation of blood vessel endothelial cell migration  positive regulation of GTPase activity  positive regulation of angiogenesis  positive regulation of angiogenesis  positive regulation of transcription by RNA polymerase II  positive regulation of transcription by RNA polymerase II  positive regulation of isotype switching to IgG isotypes  positive regulation of NF-kappaB transcription factor activity  positive regulation of NF-kappaB transcription factor activity  defense response to virus  protein-containing complex assembly  extracellular exosome  cellular response to mechanical stimulus  cellular response to interleukin-1  cellular response to tumor necrosis factor  positive regulation of protein kinase C signaling  positive regulation of endothelial cell apoptotic process  positive regulation of endothelial cell apoptotic process  
Pathways : BIOCARTABIOCARTA_BLYMPHOCYTEPATHWAY    BIOCARTA_BBCELLPATHWAY    BIOCARTA_ASBCELLPATHWAY    BIOCARTA_CD40PATHWAY    BIOCARTA_DCPATHWAY    BIOCARTA_TH1TH2PATHWAY   
Pathways : KEGGKEGG_SYSTEMIC_LUPUS_ERYTHEMATOSUS    KEGG_PRIMARY_IMMUNODEFICIENCY    KEGG_CYTOKINE_CYTOKINE_RECEPTOR_INTERACTION    KEGG_CELL_ADHESION_MOLECULES_CAMS    KEGG_TOLL_LIKE_RECEPTOR_SIGNALING    KEGG_INTESTINAL_IMMUNE_NETWORK_FOR_IGA_PRODUCTION    KEGG_ASTHMA    KEGG_AUTOIMMUNE_THYROID_DISEASE    KEGG_ALLOGRAFT_REJECTION    KEGG_VIRAL_MYOCARDITIS   
NDEx NetworkCD40
Atlas of Cancer Signalling NetworkCD40
Wikipedia pathwaysCD40
Orthology - Evolution
OrthoDB958
GeneTree (enSembl)ENSG00000101017
Phylogenetic Trees/Animal Genes : TreeFamCD40
Homologs : HomoloGeneCD40
Homology/Alignments : Family Browser (UCSC)CD40
Gene fusions - Rearrangements
Fusion : MitelmanAPLP2::CD40 [11q24.3/20q13.12]  
Fusion : QuiverCD40
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerCD40 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)CD40
dbVarCD40
ClinVarCD40
MonarchCD40
1000_GenomesCD40 
Exome Variant ServerCD40
GNOMAD BrowserENSG00000101017
Varsome BrowserCD40
ACMGCD40 variants
VarityP25942
Genomic Variants (DGV)CD40 [DGVbeta]
DECIPHERCD40 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisCD40 
Mutations
ICGC Data PortalCD40 
TCGA Data PortalCD40 
Broad Tumor PortalCD40
OASIS PortalCD40 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICCD40  [overview]  [genome browser]  [tissue]  [distribution]  
Somatic Mutations in Cancer : COSMIC3DCD40
Mutations and Diseases : HGMDCD40
LOVD (Leiden Open Variation Database)[gene] [transcripts] [variants]
BioMutaCD40
DgiDB (Drug Gene Interaction Database)CD40
DoCM (Curated mutations)CD40
CIViC (Clinical Interpretations of Variants in Cancer)CD40
Cancer3DCD40
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM109535    606843   
Orphanet14801   
DisGeNETCD40
MedgenCD40
Genetic Testing Registry CD40
NextProtP25942 [Medical]
GENETestsCD40
Target ValidationCD40
Huge Navigator CD40 [HugePedia]
ClinGenCD40
Clinical trials, drugs, therapy
MyCancerGenomeCD40
Protein Interactions : CTDCD40
Pharm GKB GenePA36612
PharosP25942
Clinical trialCD40
Miscellaneous
canSAR (ICR)CD40
HarmonizomeCD40
ARCHS4CD40
DataMed IndexCD40
Probes
Litterature
PubMed499 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
EVEXCD40
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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© Atlas of Genetics and Cytogenetics in Oncology and Haematology
indexed on : Thu Jan 20 12:26:30 CET 2022

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