Human Gene TNFRSF13B (uc002gqs.1)
  Description: Homo sapiens tumor necrosis factor receptor superfamily, member 13B (TNFRSF13B), mRNA.
RefSeq Summary (NM_012452): The protein encoded by this gene is a lymphocyte-specific member of the tumor necrosis factor (TNF) receptor superfamily. It interacts with calcium-modulator and cyclophilin ligand (CAML). The protein induces activation of the transcription factors NFAT, AP1, and NF-kappa-B and plays a crucial role in humoral immunity by interacting with a TNF ligand. This gene is located within the Smith-Magenis syndrome region on chromosome 17. [provided by RefSeq, Jul 2008].
Transcript (Including UTRs)
   Position: hg19 chr17:16,842,398-16,875,402 Size: 33,005 Total Exon Count: 5 Strand: -
Coding Region
   Position: hg19 chr17:16,842,861-16,875,389 Size: 32,529 Coding Exon Count: 5 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsMalaCards
CTDGene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein Structure
Other SpeciesGO AnnotationsmRNA DescriptionsPathwaysOther NamesModel Information
Methods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr17:16,842,398-16,875,402)mRNA (may differ from genome)Protein (293 aa)
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WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: TR13B_HUMAN
DESCRIPTION: RecName: Full=Tumor necrosis factor receptor superfamily member 13B; AltName: Full=Transmembrane activator and CAML interactor; AltName: CD_antigen=CD267;
FUNCTION: Receptor for TNFSF13/APRIL and TNFSF13B/TALL1/BAFF/BLYS that binds both ligands with similar high affinity. Mediates calcineurin-dependent activation of NF-AT, as well as activation of NF-kappa-B and AP-1. Involved in the stimulation of B- and T- cell function and the regulation of humoral immunity.
SUBUNIT: Binds TRAF2, TRAF5 and TRAF6. Binds the NH2-terminal domain of CAMLG with its C-terminus.
INTERACTION: Q99836:MYD88; NbExp=12; IntAct=EBI-519160, EBI-447677; Q9Y275:TNFSF13B; NbExp=7; IntAct=EBI-519160, EBI-519169;
SUBCELLULAR LOCATION: Membrane; Single-pass type III membrane protein.
TISSUE SPECIFICITY: Highly expressed in spleen, thymus, small intestine and peripheral blood leukocytes. Expressed in resting B- cells and activated T-cells, but not in resting T-cells.
DISEASE: Defects in TNFRSF13B are the cause of immunodeficiency common variable type 2 (CVID2) [MIM:240500]. CVID2 is a primary immunodeficiency characterized by antibody deficiency, hypogammaglobulinemia, recurrent bacterial infections and an inability to mount an antibody response to antigen. The defect results from a failure of B-cell differentiation and impaired secretion of immunoglobulins; the numbers of circulating B-cells is usually in the normal range, but can be low.
DISEASE: Defects in TNFRSF13B are a cause of immunoglobulin A deficiency 2 (IGAD2) [MIM:609529]. Selective deficiency of immunoglobulin A (IGAD) is the most common form of primary immunodeficiency, with an incidence of approximately 1 in 600 individuals in the western world. Individuals with symptomatic IGAD often have deficiency of IgG subclasses or decreased antibody response to carbohydrate antigens such as pneumococcal polysaccharide vaccine. Individuals with IGAD also suffer from recurrent sinopulmonary and gastrointestinal infections and have an increased incidence of autoimmune disorders and of lymphoid and non-lymphoid malignancies. In vitro studies have suggested that some individuals with IGAD have impaired isotype class switching to IgA and others may have a post-switch defect. IGAD and CVID have been known to coexist in families. Some individuals initially present with IGAD1 and then develop CVID. These observations suggest that some cases of IGAD and CVID may have a common etiology.
SIMILARITY: Contains 2 TNFR-Cys repeats.
WEB RESOURCE: Name=TNFRSF13Bbase; Note=TNFRSF13B mutation db; URL="http://bioinf.uta.fi/TNFRSF13Bbase/";
WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/TNFRSF13B";

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): TNFRSF13B
CDC HuGE Published Literature: TNFRSF13B
Positive Disease Associations: aneurysm, intracranial , Blood Proteins , Iron
Related Studies:
  1. aneurysm, intracranial
    Inoue, K. et al. 2006, Search on Chromosome 17 Centromere Reveals TNFRSF13B as a Susceptibility Gene for Intracranial Aneurysm. A Preliminary Study, Circulation 2006. [PubMed 16618819]
    We propose that TNFRSF13B is one of the susceptibility genes for IA.
  2. Blood Proteins
    Yoichiro Kamatani et al. Nature genetics 2010, Genome-wide association study of hematological and biochemical traits in a Japanese population., Nature genetics. [PubMed 20139978]
  3. Blood Proteins
    Wael Osman et al. PloS one 2012, Association of common variants in TNFRSF13B, TNFSF13, and ANXA3 with serum levels of non-albumin protein and immunoglobulin isotypes in Japanese., PloS one. [PubMed 22558069]
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: TNFRSF13B
Diseases sorted by gene-association score: immunodeficiency, common variable, 2* (1255), immunoglobulin a deficiency 2* (1253), tnfrsf13b-related common variable immune deficiency* (525), common variable immunodeficiency* (274), immunoglobulin alpha deficiency (14), primary agammaglobulinemia (14), smith-magenis syndrome (13), cryptococcal meningitis (8), primary immunodeficiency disease (7), macroglobulinemia (6), b cell deficiency (6), chronic lymphocytic leukemia (2), lymphoma, non-hodgkin (1)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 66.42 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 86.13 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
3' UTR -111.76463-0.241 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR015384 - TACI_Cys-rich-dom
IPR022317 - TNFR_13B

Pfam Domains:
PF09305 - TACI, cysteine-rich domain

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1XU1 - X-ray MuPIT 1XUT - NMR MuPIT


ModBase Predicted Comparative 3D Structure on O14836
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-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
      
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0038023 signaling receptor activity

Biological Process:
GO:0001782 B cell homeostasis
GO:0002244 hematopoietic progenitor cell differentiation
GO:0002250 adaptive immune response
GO:0002376 immune system process
GO:0007166 cell surface receptor signaling pathway
GO:0030889 negative regulation of B cell proliferation
GO:0033209 tumor necrosis factor-mediated signaling pathway

Cellular Component:
GO:0005886 plasma membrane
GO:0005887 integral component of plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane


-  Descriptions from all associated GenBank mRNAs
  AK303298 - Homo sapiens cDNA FLJ52819 complete cds, highly similar to Tumor necrosis factor receptor superfamilymember 13B.
AX772740 - Sequence 1 from Patent WO03045421.
AF023614 - Homo sapiens transmembrane activator and CAML interactor (TACI) mRNA, complete cds.
AX766384 - Sequence 1 from Patent WO03041730.
AK097261 - Homo sapiens cDNA FLJ39942 fis, clone SPLEN2023024, highly similar to Macaca mulatta transmembrane activator (NF-AT) mRNA.
JD254208 - Sequence 235232 from Patent EP1572962.
AK223453 - Homo sapiens mRNA for tumor necrosis factor receptor 13B variant, clone: FCC114F06.
JD437986 - Sequence 419010 from Patent EP1572962.
JD064277 - Sequence 45301 from Patent EP1572962.
JD441090 - Sequence 422114 from Patent EP1572962.
JD186242 - Sequence 167266 from Patent EP1572962.
JD178949 - Sequence 159973 from Patent EP1572962.
JD442170 - Sequence 423194 from Patent EP1572962.
JD204928 - Sequence 185952 from Patent EP1572962.
JD178952 - Sequence 159976 from Patent EP1572962.
JD064249 - Sequence 45273 from Patent EP1572962.
JD445451 - Sequence 426475 from Patent EP1572962.
JD064276 - Sequence 45300 from Patent EP1572962.
JD103757 - Sequence 84781 from Patent EP1572962.
JD066037 - Sequence 47061 from Patent EP1572962.
JD064250 - Sequence 45274 from Patent EP1572962.
JD437368 - Sequence 418392 from Patent EP1572962.
JD103604 - Sequence 84628 from Patent EP1572962.
JD186222 - Sequence 167246 from Patent EP1572962.
JD064020 - Sequence 45044 from Patent EP1572962.
JD330766 - Sequence 311790 from Patent EP1572962.
JD043493 - Sequence 24517 from Patent EP1572962.
JD202846 - Sequence 183870 from Patent EP1572962.
JD214242 - Sequence 195266 from Patent EP1572962.
JD064248 - Sequence 45272 from Patent EP1572962.
JD436276 - Sequence 417300 from Patent EP1572962.
JD483635 - Sequence 464659 from Patent EP1572962.
JD317006 - Sequence 298030 from Patent EP1572962.
JD442070 - Sequence 423094 from Patent EP1572962.
JD331248 - Sequence 312272 from Patent EP1572962.
JD442009 - Sequence 423033 from Patent EP1572962.
JD064268 - Sequence 45292 from Patent EP1572962.
JD178951 - Sequence 159975 from Patent EP1572962.
JD063852 - Sequence 44876 from Patent EP1572962.
BC109392 - Homo sapiens tumor necrosis factor receptor superfamily, member 13B, mRNA (cDNA clone MGC:133214 IMAGE:40030781), complete cds.
JD331227 - Sequence 312251 from Patent EP1572962.
JD077119 - Sequence 58143 from Patent EP1572962.
JD178496 - Sequence 159520 from Patent EP1572962.
JD332985 - Sequence 314009 from Patent EP1572962.
JD471484 - Sequence 452508 from Patent EP1572962.
JD342729 - Sequence 323753 from Patent EP1572962.
JD445340 - Sequence 426364 from Patent EP1572962.
JD108476 - Sequence 89500 from Patent EP1572962.
JD492695 - Sequence 473719 from Patent EP1572962.
AY302137 - Homo sapiens transmembrane activator and CAML interactor (TNFRSF13B) mRNA, complete cds; alternatively spliced.
AK313302 - Homo sapiens cDNA, FLJ93815, highly similar to Homo sapiens tumor necrosis factor receptor superfamily, member 13B (TNFRSF13B), mRNA.
KJ902345 - Synthetic construct Homo sapiens clone ccsbBroadEn_11739 TNFRSF13B gene, encodes complete protein.
KR711554 - Synthetic construct Homo sapiens clone CCSBHm_00025940 TNFRSF13B (TNFRSF13B) mRNA, encodes complete protein.
KR711555 - Synthetic construct Homo sapiens clone CCSBHm_00025943 TNFRSF13B (TNFRSF13B) mRNA, encodes complete protein.
KR711556 - Synthetic construct Homo sapiens clone CCSBHm_00025946 TNFRSF13B (TNFRSF13B) mRNA, encodes complete protein.
KR711557 - Synthetic construct Homo sapiens clone CCSBHm_00025951 TNFRSF13B (TNFRSF13B) mRNA, encodes complete protein.
KR712223 - Synthetic construct Homo sapiens clone CCSBHm_00900178 TNFRSF13B (TNFRSF13B) mRNA, encodes complete protein.
KR712231 - Synthetic construct Homo sapiens clone CCSBHm_00900189 TNFRSF13B (TNFRSF13B) mRNA, encodes complete protein.
KR712232 - Synthetic construct Homo sapiens clone CCSBHm_00900190 TNFRSF13B (TNFRSF13B) mRNA, encodes complete protein.
AK301032 - Homo sapiens cDNA FLJ52770 complete cds, highly similar to Tumor necrosis factor receptor superfamily member 13B.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04060 - Cytokine-cytokine receptor interaction
hsa04672 - Intestinal immune network for IgA production
hsa05340 - Primary immunodeficiency

Reactome (by CSHL, EBI, and GO)

Protein O14836 (Reactome details) participates in the following event(s):

R-HSA-5676607 sBAFF,sAPRIL binds TACI,BCMA
R-HSA-5669034 TNFs bind their physiological receptors
R-HSA-5668541 TNFR2 non-canonical NF-kB pathway
R-HSA-1280215 Cytokine Signaling in Immune system
R-HSA-168256 Immune System

-  Other Names for This Gene
  Alternate Gene Symbols: B2R8B0, NM_012452, NP_036584, O14836, Q32LX4, Q7Z6F5, TACI, TR13B_HUMAN
UCSC ID: uc002gqs.1
RefSeq Accession: NM_012452
Protein: O14836 (aka TR13B_HUMAN or T13X_HUMAN)
CCDS: CCDS11181.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_012452.2
exon count: 5CDS single in 3' UTR: no RNA size: 1377
ORF size: 882CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1910.00frame shift in genome: no % Coverage: 98.62
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 572# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.