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TNFRSF17 (tumor necrosis factor receptor superfamily, member 17)

Written2014-10Abigail Gillespie, Eric Sanchez, George Tang, Haiming Chen, James Berenson
Institute for Myeloma & Bone Cancer Research, 9201 W. Sunset Blvd., Ste. 300, West Hollywood, CA 90069, USA

Abstract B Cell Maturation Antigen (BCMA) is a transmembrane signaling protein preferentially expressed on plasma cells. Its ligands include B-Cell Activating Factor (BAFF) and A Proliferation Inducing Ligand (APRIL). BCMA is involved in JNK and NF-kB activation pathways that induce B-cell development and autoimmune responses. BCMA has been implicated in autoimmune disorders as well as B-lymphocyte malignancies.

Keywords BCMA, multiple myeloma, immunity, JNK, NF-kB

(Note : for Links provided by Atlas : click)

Identity

Alias_namesBCMA
tumor necrosis factor receptor superfamily
Alias_symbol (synonym)BCM
CD269
TNFRSF13A
Other alias
HGNC (Hugo) TNFRSF17
LocusID (NCBI) 608
Atlas_Id 42616
Location 16p13.13  [Link to chromosome band 16p13]
Location_base_pair Starts at 11965107 and ends at 11968068 bp from pter ( according to hg19-Feb_2009)  [Mapping TNFRSF17.png]
Fusion genes
(updated 2017)
Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)
IL2 (4q27) / TNFRSF17 (16p13.13)SNX29 (16p13.13) / TNFRSF17 (16p13.13)TNFRSF17 (16p13.13) / IL2 (4q27)

DNA/RNA

Description Spans 3.8 kb; 3 exons, 2 introns.
Transcription 961 nt mRNA.

Protein

Description 184 aa; a glycoprotein with a single transmembrane domain; N-terminally glycosylated at asparagine 42 regulates its function (Huang et al., 2013). BCMA is a signaling protein that activates the NF-kB. BCMA contains one cysteine rich domain and a DXL motif, comprised of (Phe/Tyr/Trp)-Asp-Xaa-Leu-(Val/Thr)-(Arg/Gly), to facilitate ligand binding with BAFF or APRIL (Hymowitz et al., 2005).
Expression Preferentially expressed in lymph node tissue, B lymphoblast, NK cells, and dendritic cells.
Localisation Plasma membrane.
Function BCMA mediates the development and survival of B cell lymphocytes that maintain humoral immunity.
Homology TNFRSF17 is conserved in P. Troglodytes, M. mulatta, C. lupus, B. taurus, M. musculus, and R. norvegicus.

Mutations

Note 22 single nucleotide polymorphisms (SNP) have been reported.

Implicated in

Note
  
Entity Multiple myeloma
Disease Multiple myeloma is a fatal malignancy that involves the abnormal proliferation and accumulation of plasma cells characterized by their resistance to apoptosis. Sanchez et al. not only showed increased expression of BCMA in patients' plasma cells, but that patients with multiple myeloma have a high concentration of BCMA protein circulating in their blood. Furthermore, the group found that higher levels of circulating BCMA are associated with a worse prognosis.
Prognosis Poor.
  
  
Entity Acute myelomonocytic leukemia (AMML) with eosinophilia
Disease AMML is a malignancy involving myeloid precursors of the bone marrow. Although this condition is rare, it is a common type of pediatric acute myeloid leukemia. In about 50% of the cases of AMML, increased numbers of abnormal eosinophils are observed in the bone marrow (eosinophilia). AMML patients with eosinophilia who carry a pericentric inversion at 16(p13q22) tend to have a better prognosis.
Prognosis 61% 5 year survival rate; AMML patients who carry the pericentric inversion have a higher rate of complete remission than those without the inversion (Chang et al., 2006).
Cytogenetics Pericentric inversion at 16(p13q22) in 3-5% of AMML cases.
  
  
Entity T cell lymphoma
Note (4;16)(q26;p13.1) chromosome translocation, which led to the discovery of BCMA, was noted by Laâbi et al. in a single case of T cell lymphoma. This translocation resulted in a IL-2/BCMA composite gene.
 
Partial R-Banded karyotype. The karyotype shows a (4;16) (q26;p13.1) chromosomal translocation that led to the identification of BCMA by Laâbi et al. (Laâbi et al., 1992).
  
  
Entity Acute monocytic leukemia
Note t(8;16)(p11;p13) translocation has been noted in cases of acute monocytic leukemia (Laâbi et al., 1992).
  
  
Entity Follicular lymphoma
Note Translocation (16;18)(p13;q21.3) has been reported in follicular lymphoma (Mahmoodi et al., 2004).
  

Bibliography

Acute myelomonocytic leukemia with abnormal eosinophils: a case report with multi-modality diagnostic work-up.
Chang ST, Hsieh YC, Lee LP, Tzeng CC, Chuang SS.
Chang Gung Med J. 2006 Sep-Oct;29(5):532-7.
PMID 17214400
 
B-cell maturation antigen is modified by a single N-glycan chain that modulates ligand binding and surface retention.
Huang HW, Chen CH, Lin CH, Wong CH, Lin KI.
Proc Natl Acad Sci U S A. 2013 Jul 2;110(27):10928-33. doi: 10.1073/pnas.1309417110. Epub 2013 Jun 17.
PMID 23776238
 
Structures of APRIL-receptor complexes: like BCMA, TACI employs only a single cysteine-rich domain for high affinity ligand binding.
Hymowitz SG, Patel DR, Wallweber HJ, Runyon S, Yan M, Yin J, Shriver SK, Gordon NC, Pan B, Skelton NJ, Kelley RF, Starovasnik MA.
J Biol Chem. 2005 Feb 25;280(8):7218-27. Epub 2004 Nov 12.
PMID 15542592
 
A new gene, BCM, on chromosome 16 is fused to the interleukin 2 gene by a t(4;16)(q26;p13) translocation in a malignant T cell lymphoma.
Laabi Y, Gras MP, Carbonnel F, Brouet JC, Berger R, Larsen CJ, Tsapis A.
EMBO J. 1992 Nov;11(11):3897-904.
PMID 1396583
 
Translocation (16;18)(p13;q21.3) in follicular lymphoma.
Mahmoodi M, Tanev SS, Punnett HH, Crilley P, Hou JS.
Cancer Genet Cytogenet. 2004 Oct 15;154(2):160-2.
PMID 15474153
 

Citation

This paper should be referenced as such :
Abigail Gillespie, Eric Sanchez, George Tang, Haiming Chen, James Berenson
TNFRSF17 (tumor necrosis factor receptor superfamily, member 17)
Atlas Genet Cytogenet Oncol Haematol. 2015;19(10):603-604.
Free journal version : [ pdf ]   [ DOI ]
On line version : http://AtlasGeneticsOncology.org/Genes/TNFRSF17ID42616ch16p13.html


Other Leukemias implicated (Data extracted from papers in the Atlas) [ 1 ]
  t(4;16)(q26;p13) IL2/TNFRSF17


External links

Nomenclature
HGNC (Hugo)TNFRSF17   11913
Cards
AtlasTNFRSF17ID42616ch16p13
Entrez_Gene (NCBI)TNFRSF17  608  TNF receptor superfamily member 17
AliasesBCM; BCMA; CD269; TNFRSF13A
GeneCards (Weizmann)TNFRSF17
Ensembl hg19 (Hinxton)ENSG00000048462 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000048462 [Gene_View]  chr16:11965107-11968068 [Contig_View]  TNFRSF17 [Vega]
ICGC DataPortalENSG00000048462
TCGA cBioPortalTNFRSF17
AceView (NCBI)TNFRSF17
Genatlas (Paris)TNFRSF17
WikiGenes608
SOURCE (Princeton)TNFRSF17
Genetics Home Reference (NIH)TNFRSF17
Genomic and cartography
GoldenPath hg38 (UCSC)TNFRSF17  -     chr16:11965107-11968068 +  16p13.13   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)TNFRSF17  -     16p13.13   [Description]    (hg19-Feb_2009)
EnsemblTNFRSF17 - 16p13.13 [CytoView hg19]  TNFRSF17 - 16p13.13 [CytoView hg38]
Mapping of homologs : NCBITNFRSF17 [Mapview hg19]  TNFRSF17 [Mapview hg38]
OMIM109545   
Gene and transcription
Genbank (Entrez)AY684975 BC058291 EF152353 EF152354 EF152355
RefSeq transcript (Entrez)NM_001192
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)TNFRSF17
Cluster EST : UnigeneHs.2556 [ NCBI ]
CGAP (NCI)Hs.2556
Alternative Splicing GalleryENSG00000048462
Gene ExpressionTNFRSF17 [ NCBI-GEO ]   TNFRSF17 [ EBI - ARRAY_EXPRESS ]   TNFRSF17 [ SEEK ]   TNFRSF17 [ MEM ]
Gene Expression Viewer (FireBrowse)TNFRSF17 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)608
GTEX Portal (Tissue expression)TNFRSF17
Human Protein AtlasENSG00000048462-TNFRSF17 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ02223   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ02223  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ02223
Splice isoforms : SwissVarQ02223
PhosPhoSitePlusQ02223
Domains : Interpro (EBI)BCMA_Tall-1-bd    TNFR_17   
Domain families : Pfam (Sanger)BCMA-Tall_bind (PF09257)   
Domain families : Pfam (NCBI)pfam09257   
Conserved Domain (NCBI)TNFRSF17
DMDM Disease mutations608
Blocks (Seattle)TNFRSF17
PDB (SRS)1OQD    1XU2    2KN1    4ZFO   
PDB (PDBSum)1OQD    1XU2    2KN1    4ZFO   
PDB (IMB)1OQD    1XU2    2KN1    4ZFO   
PDB (RSDB)1OQD    1XU2    2KN1    4ZFO   
Structural Biology KnowledgeBase1OQD    1XU2    2KN1    4ZFO   
SCOP (Structural Classification of Proteins)1OQD    1XU2    2KN1    4ZFO   
CATH (Classification of proteins structures)1OQD    1XU2    2KN1    4ZFO   
SuperfamilyQ02223
Human Protein Atlas [tissue]ENSG00000048462-TNFRSF17 [tissue]
Peptide AtlasQ02223
HPRD00144
IPIIPI00293877   IPI00855949   IPI00941387   IPI00026452   IPI00718919   
Protein Interaction databases
DIP (DOE-UCLA)Q02223
IntAct (EBI)Q02223
FunCoupENSG00000048462
BioGRIDTNFRSF17
STRING (EMBL)TNFRSF17
ZODIACTNFRSF17
Ontologies - Pathways
QuickGOQ02223
Ontology : AmiGOadaptive immune response  lymphocyte homeostasis  receptor activity  plasma membrane  signal transduction  multicellular organism development  cell proliferation  endomembrane system  integral component of membrane  tumor necrosis factor-mediated signaling pathway  
Ontology : EGO-EBIadaptive immune response  lymphocyte homeostasis  receptor activity  plasma membrane  signal transduction  multicellular organism development  cell proliferation  endomembrane system  integral component of membrane  tumor necrosis factor-mediated signaling pathway  
Pathways : BIOCARTATACI and BCMA stimulation of B cell immune responses. [Genes]   
Pathways : KEGGCytokine-cytokine receptor interaction    Intestinal immune network for IgA production   
REACTOMEQ02223 [protein]
REACTOME PathwaysR-HSA-5669034 [pathway]   
NDEx NetworkTNFRSF17
Atlas of Cancer Signalling NetworkTNFRSF17
Wikipedia pathwaysTNFRSF17
Orthology - Evolution
OrthoDB608
GeneTree (enSembl)ENSG00000048462
Phylogenetic Trees/Animal Genes : TreeFamTNFRSF17
HOVERGENQ02223
HOGENOMQ02223
Homologs : HomoloGeneTNFRSF17
Homology/Alignments : Family Browser (UCSC)TNFRSF17
Gene fusions - Rearrangements
Fusion : MitelmanIL2/TNFRSF17 [4q27/16p13.13]  [t(4;16)(q27;p13)]  
Fusion : MitelmanSNX29/TNFRSF17 [16p13.13/16p13.13]  [t(16;16)(p13;p13)]  
Fusion: TCGASNX29 16p13.13 TNFRSF17 16p13.13 LUAD
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerTNFRSF17 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)TNFRSF17
dbVarTNFRSF17
ClinVarTNFRSF17
1000_GenomesTNFRSF17 
Exome Variant ServerTNFRSF17
ExAC (Exome Aggregation Consortium)ENSG00000048462
GNOMAD BrowserENSG00000048462
Genetic variants : HAPMAP608
Genomic Variants (DGV)TNFRSF17 [DGVbeta]
DECIPHERTNFRSF17 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisTNFRSF17 
Mutations
ICGC Data PortalTNFRSF17 
TCGA Data PortalTNFRSF17 
Broad Tumor PortalTNFRSF17
OASIS PortalTNFRSF17 [ Somatic mutations - Copy number]
Cancer Gene: CensusTNFRSF17 
Somatic Mutations in Cancer : COSMICTNFRSF17  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDTNFRSF17
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
BioMutasearch TNFRSF17
DgiDB (Drug Gene Interaction Database)TNFRSF17
DoCM (Curated mutations)TNFRSF17 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)TNFRSF17 (select a term)
intoGenTNFRSF17
NCG5 (London)TNFRSF17
Cancer3DTNFRSF17(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM109545   
Orphanet
MedgenTNFRSF17
Genetic Testing Registry TNFRSF17
NextProtQ02223 [Medical]
TSGene608
GENETestsTNFRSF17
Target ValidationTNFRSF17
Huge Navigator TNFRSF17 [HugePedia]
snp3D : Map Gene to Disease608
BioCentury BCIQTNFRSF17
ClinGenTNFRSF17
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD608
Chemical/Pharm GKB GenePA36606
Clinical trialTNFRSF17
Miscellaneous
canSAR (ICR)TNFRSF17 (select the gene name)
Probes
Litterature
PubMed48 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineTNFRSF17
EVEXTNFRSF17
GoPubMedTNFRSF17
iHOPTNFRSF17
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Thu Oct 12 16:35:40 CEST 2017

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