Atlas of Genetics and Cytogenetics in Oncology and Haematology


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CD40 (CD40 molecule)

Identity

Alias_namesTNFRSF5
tumor necrosis factor receptor superfamily, member 5
CD40 molecule, TNF receptor superfamily member 5
Alias_symbol (synonym)p50
Bp50
HGNC (Hugo) CD40
LocusID (NCBI) 958
Atlas_Id 42627
Location 20q13.12  [Link to chromosome band 20q13]
Location_base_pair Starts at 44746893 and ends at 44758384 bp from pter ( according to hg19-Feb_2009)
Fusion genes
(updated 2016)
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  958  CD40 molecule
AliasesBp50; CDW40; TNFRSF5; p50
GeneCards (Weizmann)CD40
Ensembl hg19 (Hinxton)ENSG00000101017 [Gene_View]  chr20:44746893-44758384 [Contig_View]  CD40 [Vega]
Ensembl hg38 (Hinxton)ENSG00000101017 [Gene_View]  chr20:44746893-44758384 [Contig_View]  CD40 [Vega]
ICGC DataPortalENSG00000101017
TCGA cBioPortalCD40
AceView (NCBI)CD40
Genatlas (Paris)CD40
WikiGenes958
SOURCE (Princeton)CD40
Genetics Home Reference (NIH)CD40
Genomic and cartography
GoldenPath hg19 (UCSC)CD40  -     chr20:44746893-44758384 +  20q13.12   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)CD40  -     20q13.12   [Description]    (hg38-Dec_2013)
EnsemblCD40 - 20q13.12 [CytoView hg19]  CD40 - 20q13.12 [CytoView hg38]
Mapping of homologs : NCBICD40 [Mapview hg19]  CD40 [Mapview hg38]
OMIM109535   606843   
Gene and transcription
Genbank (Entrez)AB209660 AJ300189 AK222896 AY225405 BC012419
RefSeq transcript (Entrez)NM_001250 NM_001302753 NM_001322421 NM_001322422 NM_152854
RefSeq genomic (Entrez)NC_000020 NC_018931 NG_007279 NT_011362 NW_004929418
Consensus coding sequences : CCDS (NCBI)CD40
Cluster EST : UnigeneHs.472860 [ NCBI ]
CGAP (NCI)Hs.472860
Alternative Splicing GalleryENSG00000101017
Gene ExpressionCD40 [ NCBI-GEO ]   CD40 [ EBI - ARRAY_EXPRESS ]   CD40 [ SEEK ]   CD40 [ MEM ]
Gene Expression Viewer (FireBrowse)CD40 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)958
GTEX Portal (Tissue expression)CD40
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
Splice isoforms : SwissVarP25942
PhosPhoSitePlusP25942
Domaine pattern : Prosite (Expaxy)TNFR_NGFR_1 (PS00652)    TNFR_NGFR_2 (PS50050)   
Domains : Interpro (EBI)TNFR/NGFR_Cys_rich_reg    TNFR_5   
Domain families : Pfam (Sanger)TNFR_c6 (PF00020)   
Domain families : Pfam (NCBI)pfam00020   
Domain families : Smart (EMBL)TNFR (SM00208)  
Conserved Domain (NCBI)CD40
DMDM Disease mutations958
Blocks (Seattle)CD40
PDB (SRS)1CDF    1CZZ    1D00    1FLL    1LB6    3QD6   
PDB (PDBSum)1CDF    1CZZ    1D00    1FLL    1LB6    3QD6   
PDB (IMB)1CDF    1CZZ    1D00    1FLL    1LB6    3QD6   
PDB (RSDB)1CDF    1CZZ    1D00    1FLL    1LB6    3QD6   
Structural Biology KnowledgeBase1CDF    1CZZ    1D00    1FLL    1LB6    3QD6   
SCOP (Structural Classification of Proteins)1CDF    1CZZ    1D00    1FLL    1LB6    3QD6   
CATH (Classification of proteins structures)1CDF    1CZZ    1D00    1FLL    1LB6    3QD6   
SuperfamilyP25942
Human Protein AtlasENSG00000101017
Peptide AtlasP25942
HPRD00178
IPIIPI00018282   IPI00218464   IPI00556230   IPI00980079   
Protein Interaction databases
DIP (DOE-UCLA)P25942
IntAct (EBI)P25942
FunCoupENSG00000101017
BioGRIDCD40
STRING (EMBL)CD40
ZODIACCD40
Ontologies - Pathways
QuickGOP25942
Ontology : AmiGOpositive regulation of protein phosphorylation  immune response-regulating cell surface receptor signaling pathway  antigen binding  signal transducer activity  receptor activity  tumor necrosis factor-activated receptor activity  protein binding  extracellular space  cytoplasm  plasma membrane  plasma membrane  integral component of plasma membrane  protein complex assembly  cellular calcium ion homeostasis  inflammatory response  immune response  multicellular organism development  external side of plasma membrane  cell surface  enzyme binding  platelet activation  positive regulation of B cell proliferation  ubiquitin protein ligase binding  response to lipopolysaccharide  positive regulation of interleukin-12 production  tumor necrosis factor-mediated signaling pathway  CD40 receptor complex  B cell proliferation  regulation of cell proliferation  positive regulation of tyrosine phosphorylation of Stat1 protein  defense response to protozoan  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 GTPase activity  positive regulation of transcription from RNA polymerase II promoter  positive regulation of isotype switching to IgG isotypes  regulation of immune response  regulation of immunoglobulin secretion  positive regulation of NF-kappaB transcription factor activity  defense response to virus  extracellular exosome  cellular response to lipopolysaccharide  cellular response to mechanical stimulus  positive regulation of protein kinase C signaling  apoptotic signaling pathway  positive regulation of endothelial cell apoptotic process  
Ontology : EGO-EBIpositive regulation of protein phosphorylation  immune response-regulating cell surface receptor signaling pathway  antigen binding  signal transducer activity  receptor activity  tumor necrosis factor-activated receptor activity  protein binding  extracellular space  cytoplasm  plasma membrane  plasma membrane  integral component of plasma membrane  protein complex assembly  cellular calcium ion homeostasis  inflammatory response  immune response  multicellular organism development  external side of plasma membrane  cell surface  enzyme binding  platelet activation  positive regulation of B cell proliferation  ubiquitin protein ligase binding  response to lipopolysaccharide  positive regulation of interleukin-12 production  tumor necrosis factor-mediated signaling pathway  CD40 receptor complex  B cell proliferation  regulation of cell proliferation  positive regulation of tyrosine phosphorylation of Stat1 protein  defense response to protozoan  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 GTPase activity  positive regulation of transcription from RNA polymerase II promoter  positive regulation of isotype switching to IgG isotypes  regulation of immune response  regulation of immunoglobulin secretion  positive regulation of NF-kappaB transcription factor activity  defense response to virus  extracellular exosome  cellular response to lipopolysaccharide  cellular response to mechanical stimulus  positive regulation of protein kinase C signaling  apoptotic signaling pathway  positive regulation of endothelial cell apoptotic process  
Pathways : BIOCARTAAntigen Dependent B Cell Activation [Genes]    Th1/Th2 Differentiation [Genes]    Dendritic cells in regulating TH1 and TH2 Development [Genes]    Bystander B Cell Activation [Genes]    CD40L Signaling Pathway [Genes]    B Lymphocyte Cell Surface Molecules [Genes]   
Pathways : KEGGCytokine-cytokine receptor interaction    NF-kappa B signaling pathway    Cell adhesion molecules (CAMs)    Toll-like receptor signaling pathway    Intestinal immune network for IgA production    Malaria    Toxoplasmosis    HTLV-I infection    Epstein-Barr virus infection    Transcriptional misregulation in cancer    Asthma    Autoimmune thyroid disease    Systemic lupus erythematosus    Allograft rejection    Primary immunodeficiency    Viral myocarditis   
NDEx NetworkCD40
Atlas of Cancer Signalling NetworkCD40
Wikipedia pathwaysCD40
Orthology - Evolution
OrthoDB958
GeneTree (enSembl)ENSG00000101017
Phylogenetic Trees/Animal Genes : TreeFamCD40
HOVERGENP25942
HOGENOMP25942
Homologs : HomoloGeneCD40
Homology/Alignments : Family Browser (UCSC)CD40
Gene fusions - Rearrangements
Fusion : MitelmanAPLP2/CD40 [11q24.3/20q13.12]  [t(11;20)(q24;q13)]  
Fusion: TCGAAPLP2 11q24.3 CD40 20q13.12 THCA
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerCD40 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)CD40
dbVarCD40
ClinVarCD40
1000_GenomesCD40 
Exome Variant ServerCD40
ExAC (Exome Aggregation Consortium)CD40 (select the gene name)
Genetic variants : HAPMAP958
Genomic Variants (DGV)CD40 [DGVbeta]
DECIPHER (Syndromes)20:44746893-44758384  ENSG00000101017
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]  
Mutations and Diseases : HGMDCD40
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
LOVD (Leiden Open Variation Database)**PUBLIC** CCHMC Molecular Genetics Laboratory Mutation Database
BioMutasearch CD40
DgiDB (Drug Gene Interaction Database)CD40
DoCM (Curated mutations)CD40 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)CD40 (select a term)
intoGenCD40
Cancer3DCD40(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM109535    606843   
Orphanet14801   
MedgenCD40
Genetic Testing Registry CD40
NextProtP25942 [Medical]
TSGene958
GENETestsCD40
Huge Navigator CD40 [HugePedia]
snp3D : Map Gene to Disease958
BioCentury BCIQCD40
ClinGenCD40
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD958
Chemical/Pharm GKB GenePA36612
Clinical trialCD40
Miscellaneous
canSAR (ICR)CD40 (select the gene name)
Probes
Litterature
PubMed499 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineCD40
EVEXCD40
GoPubMedCD40
iHOPCD40
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 : Fri Nov 18 19:33:22 CET 2016

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