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Aliases for TNFRSF13B Gene

Aliases for TNFRSF13B Gene

  • TNF Receptor Superfamily Member 13B 2 3 5
  • Transmembrane Activator And CAML Interactor 3 4
  • TACI 3 4
  • Tumor Necrosis Factor Receptor Superfamily, Member 13B 2
  • Tumor Necrosis Factor Receptor Superfamily Member 13B 3
  • Tumor Necrosis Factor Receptor 13B 3
  • CD267 Antigen 4
  • TNFRSF14B 3
  • CD267 3
  • CVID2 3
  • IGAD2 3
  • CVID 3
  • RYZN 3

External Ids for TNFRSF13B Gene

Previous GeneCards Identifiers for TNFRSF13B Gene

  • GC17M017204
  • GC17M017953
  • GC17M016785
  • GC17M017042
  • GC17M016783
  • GC17M016595
  • GC17M016832

Summaries for TNFRSF13B Gene

Entrez Gene Summary for TNFRSF13B Gene

  • 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]

GeneCards Summary for TNFRSF13B Gene

TNFRSF13B (TNF Receptor Superfamily Member 13B) is a Protein Coding gene. Diseases associated with TNFRSF13B include Immunodeficiency, Common Variable, 2 and Immunoglobulin A Deficiency 2. Among its related pathways are Akt Signaling and TNFs bind their physiological receptors.

UniProtKB/Swiss-Prot for TNFRSF13B Gene

  • 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.

Gene Wiki entry for TNFRSF13B Gene

Additional gene information for TNFRSF13B Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for TNFRSF13B Gene

Genomics for TNFRSF13B Gene

GeneHancer (GH) Regulatory Elements for TNFRSF13B Gene

Promoters and enhancers for TNFRSF13B Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH17J016969 Promoter/Enhancer 1.8 EPDnew FANTOM5 ENCODE dbSUPER 657.7 -3.4 -3438 12.9 HDGF PKNOX1 SMAD1 RB1 BATF KLF5 IRF4 ZNF335 ZNF207 ETV6 TNFRSF13B NCOR1 PIGL MPRIP PLD6 LOC644422 LOC284191
GH17J016397 Enhancer 1.1 Ensembl ENCODE 5.4 +573.5 573513 1.8 ATF1 FOXA2 ARNT NCOA2 YY1 TCF12 FOS ATF7 RXRA NCOA1 CENPV LRRC75A-AS1 LRRC75A TRPV2 TNFRSF13B GC17P016393
GH17J016968 Enhancer 0.5 dbSUPER 0.7 +3.7 3741 0.6 IKZF1 EBF1 MLLT1 IKZF2 MPRIP TNFRSF13B GC17M016946
GH17J016962 Enhancer 0.8 dbSUPER 0.4 +6.8 6809 4.8 HDGF PKNOX1 STAT5A BATF KLF5 IRF4 ZNF207 ZNF143 ATF7 FOS MPRIP PLD6 TBC1D27P KRT17P4 TNFRSF13B GC17M016946
GH17J016960 Enhancer 0.5 dbSUPER 0.4 +10.7 10694 2.1 ZNF316 KLF5 RUNX3 MAFK PLD6 TBC1D27P TNFRSF13B GC17M016946
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around TNFRSF13B on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the TNFRSF13B gene promoter:
  • AP-1
  • c-Jun
  • ATF-2
  • POU2F1a
  • POU2F1
  • FOXD1

Genomic Locations for TNFRSF13B Gene

Genomic Locations for TNFRSF13B Gene
chr17:16,929,816-16,972,118
(GRCh38/hg38)
Size:
42,303 bases
Orientation:
Minus strand
chr17:16,832,849-16,875,432
(GRCh37/hg19)
Size:
42,584 bases
Orientation:
Minus strand

Genomic View for TNFRSF13B Gene

Genes around TNFRSF13B on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
TNFRSF13B Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for TNFRSF13B Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for TNFRSF13B Gene

Proteins for TNFRSF13B Gene

  • Protein details for TNFRSF13B Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O14836-TR13B_HUMAN
    Recommended name:
    Tumor necrosis factor receptor superfamily member 13B
    Protein Accession:
    O14836
    Secondary Accessions:
    • B2R8B0
    • B7Z6V8
    • Q32LX4
    • Q7Z6F5

    Protein attributes for TNFRSF13B Gene

    Size:
    293 amino acids
    Molecular mass:
    31816 Da
    Quaternary structure:
    • Binds TRAF2, TRAF5 and TRAF6. Binds the NH2-terminal domain of CAMLG with its C-terminus.

    Three dimensional structures from OCA and Proteopedia for TNFRSF13B Gene

    Alternative splice isoforms for TNFRSF13B Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for TNFRSF13B Gene

Post-translational modifications for TNFRSF13B Gene

  • Glycosylation at posLast=128128
  • Modification sites at PhosphoSitePlus

Other Protein References for TNFRSF13B Gene

Antibody Products

  • R&D Systems Antibodies for TNFRSF13B (TACI/TNFRSF13B)
  • Abcam antibodies for TNFRSF13B

Assay Products

  • Abcam assays for TNFRSF13B

No data available for DME Specific Peptides for TNFRSF13B Gene

Domains & Families for TNFRSF13B Gene

Gene Families for TNFRSF13B Gene

HGNC:
IUPHAR :
Human Protein Atlas (HPA):
  • CD markers
  • Disease related genes
  • Predicted intracellular proteins
  • Predicted membrane proteins

Protein Domains for TNFRSF13B Gene

Suggested Antigen Peptide Sequences for TNFRSF13B Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with TNFRSF13B: view

No data available for UniProtKB/Swiss-Prot for TNFRSF13B Gene

Function for TNFRSF13B Gene

Molecular function for TNFRSF13B Gene

UniProtKB/Swiss-Prot 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.

Phenotypes From GWAS Catalog for TNFRSF13B Gene

Gene Ontology (GO) - Molecular Function for TNFRSF13B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 10801128
GO:0038023 signaling receptor activity TAS 9311921
genes like me logo Genes that share ontologies with TNFRSF13B: view
genes like me logo Genes that share phenotypes with TNFRSF13B: view

Human Phenotype Ontology for TNFRSF13B Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for TNFRSF13B Gene

MGI Knock Outs for TNFRSF13B:

Animal Model Products

Clone Products

  • R&D Systems cDNA Clones for TNFRSF13B (TACI/TNFRSF13B)

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for TNFRSF13B Gene

Localization for TNFRSF13B Gene

Subcellular locations from UniProtKB/Swiss-Prot for TNFRSF13B Gene

Membrane; Single-pass type III membrane protein.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for TNFRSF13B gene
Compartment Confidence
plasma membrane 5
extracellular 1
mitochondrion 1
nucleus 1
endoplasmic reticulum 1
cytosol 1
lysosome 1
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for TNFRSF13B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane TAS,IBA --
GO:0005887 integral component of plasma membrane TAS,IEA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with TNFRSF13B: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for TNFRSF13B Gene

Pathways & Interactions for TNFRSF13B Gene

genes like me logo Genes that share pathways with TNFRSF13B: view

SIGNOR curated interactions for TNFRSF13B Gene

Is activated by:

Gene Ontology (GO) - Biological Process for TNFRSF13B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001782 B cell homeostasis IBA --
GO:0002244 hematopoietic progenitor cell differentiation IBA --
GO:0002250 adaptive immune response IEA --
GO:0002376 immune system process IEA --
GO:0007166 cell surface receptor signaling pathway TAS 9311921
genes like me logo Genes that share ontologies with TNFRSF13B: view

Drugs & Compounds for TNFRSF13B Gene

(3) Drugs for TNFRSF13B Gene - From: DGIdb, IUPHAR, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
BAFF Pharma 0
LYMPHORAD Pharma 0

(2) Additional Compounds for TNFRSF13B Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with TNFRSF13B: view

Transcripts for TNFRSF13B Gene

mRNA/cDNA for TNFRSF13B Gene

(1) REFSEQ mRNAs :
(7) Additional mRNA sequences :
(12) Selected AceView cDNA sequences:
(7) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for TNFRSF13B Gene

Tumor necrosis factor receptor superfamily, member 13B:
Representative Sequences:

Clone Products

  • R&D Systems cDNA Clones for TNFRSF13B (TACI/TNFRSF13B)

Alternative Splicing Database (ASD) splice patterns (SP) for TNFRSF13B Gene

No ASD Table

Relevant External Links for TNFRSF13B Gene

GeneLoc Exon Structure for
TNFRSF13B
ECgene alternative splicing isoforms for
TNFRSF13B

Expression for TNFRSF13B Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for TNFRSF13B Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for TNFRSF13B Gene

This gene is overexpressed in Spleen (x6.3).

Protein differential expression in normal tissues from HIPED for TNFRSF13B Gene

This gene is overexpressed in Peripheral blood mononuclear cells (47.6) and Heart (21.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for TNFRSF13B Gene



Protein tissue co-expression partners for TNFRSF13B Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of TNFRSF13B Gene:

TNFRSF13B

SOURCE GeneReport for Unigene cluster for TNFRSF13B Gene:

Hs.158341

mRNA Expression by UniProt/SwissProt for TNFRSF13B Gene:

O14836-TR13B_HUMAN
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.

Evidence on tissue expression from TISSUES for TNFRSF13B Gene

  • Spleen(4.6)
  • Blood(2.6)
  • Lymph node(2.3)
  • Bone marrow(2.1)

Phenotype-based relationships between genes and organs from Gene ORGANizer for TNFRSF13B Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • endocrine
  • immune
  • integumentary
  • lymphatic
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
Regions:
Head and neck:
  • brain
  • ear
  • eye
  • head
  • hypothalamus
  • meninges
  • middle ear
  • neck
  • pituitary gland
  • sinus
  • skull
  • thyroid
Thorax:
  • bronchus
  • heart
  • lung
Abdomen:
  • adrenal gland
  • intestine
  • large intestine
  • liver
  • small intestine
  • spleen
  • stomach
Pelvis:
  • anus
  • rectum
  • uterus
Limb:
  • ankle
  • digit
  • elbow
  • finger
  • foot
  • hand
  • hip
  • knee
  • lower limb
  • shoulder
  • toe
  • upper limb
  • wrist
General:
  • blood
  • blood vessel
  • bone marrow
  • coagulation system
  • lymph node
  • peripheral nerve
  • peripheral nervous system
  • red blood cell
  • skin
  • white blood cell
genes like me logo Genes that share expression patterns with TNFRSF13B: view

Orthologs for TNFRSF13B Gene

This gene was present in the common ancestor of chordates.

Orthologs for TNFRSF13B Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia TNFRSF13B 34 33
  • 99.54 (n)
OneToOne
dog
(Canis familiaris)
Mammalia TNFRSF13B 34 33
  • 77.25 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Tnfrsf13b 16 34 33
  • 68.64 (n)
cow
(Bos Taurus)
Mammalia TNFRSF13B 34
  • 56 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia TNFRSF13B 34
  • 46 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia TNFRSF13B 34
  • 42 (a)
OneToOne
chicken
(Gallus gallus)
Aves TNFRSF13B 34 33
  • 56.09 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia TNFRSF13B 34
  • 38 (a)
OneToOne
Species where no ortholog for TNFRSF13B was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)
  • zebrafish (Danio rerio)

Evolution for TNFRSF13B Gene

ENSEMBL:
Gene Tree for TNFRSF13B (if available)
TreeFam:
Gene Tree for TNFRSF13B (if available)
Aminode:
Evolutionary constrained regions (ECRs) for TNFRSF13B: view image

Paralogs for TNFRSF13B Gene

(1) SIMAP similar genes for TNFRSF13B Gene using alignment to 3 proteins:

  • TR13B_HUMAN
  • E7ER05_HUMAN
  • J3QR67_HUMAN
genes like me logo Genes that share paralogs with TNFRSF13B: view

No data available for Paralogs for TNFRSF13B Gene

Variants for TNFRSF13B Gene

Sequence variations from dbSNP and Humsavar for TNFRSF13B Gene

SNP ID Clin Chr 17 pos Variation AA Info Type
rs1006646448 uncertain-significance, Common Variable Immune Deficiency, Dominant 16,939,572(-) G/A/T coding_sequence_variant, missense_variant
rs1010499665 uncertain-significance, Common Variable Immune Deficiency, Dominant 16,939,176(-) G/A 3_prime_UTR_variant
rs104894649 conflicting-interpretations-of-pathogenicity, likely-benign, Common variable immunodeficiency 2, Common Variable Immune Deficiency, Dominant, Immunodeficiency, common variable, 2 (CVID2) [MIM:240500] 16,940,352(-) C/T coding_sequence_variant, missense_variant
rs104894650 pathogenic, not provided, Common variable immunodeficiency 2 16,948,752(-) G/A/C/T coding_sequence_variant, missense_variant, stop_gained
rs11078355 benign, not specified, Common Variable Immune Deficiency, Dominant 16,939,598(-) A/G/T coding_sequence_variant, missense_variant, synonymous_variant

Structural Variations from Database of Genomic Variants (DGV) for TNFRSF13B Gene

Variant ID Type Subtype PubMed ID
esv2662060 CNV deletion 23128226
esv2666300 CNV deletion 23128226
esv275147 CNV gain+loss 21479260
esv2761948 CNV loss 21179565
esv3640119 CNV loss 21293372
esv3640120 CNV loss 21293372
nsv1055688 CNV gain 25217958
nsv155 OTHER inversion 15895083
nsv499114 OTHER inversion 21111241
nsv524738 CNV loss 19592680
nsv833379 CNV gain 17160897

Variation tolerance for TNFRSF13B Gene

Residual Variation Intolerance Score: 92% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.15; 69.42% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for TNFRSF13B Gene

Human Gene Mutation Database (HGMD)
TNFRSF13B
SNPedia medical, phenotypic, and genealogical associations of SNPs for
TNFRSF13B

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for TNFRSF13B Gene

Disorders for TNFRSF13B Gene

MalaCards: The human disease database

(12) MalaCards diseases for TNFRSF13B Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

TR13B_HUMAN
  • Immunodeficiency, common variable, 2 (CVID2) [MIM:240500]: 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. {ECO:0000269 PubMed:16007086}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • 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. {ECO:0000269 PubMed:16007086}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for TNFRSF13B

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with TNFRSF13B: view

No data available for Genatlas for TNFRSF13B Gene

Publications for TNFRSF13B Gene

  1. Phenotypic and clinical heterogeneity associated with monoallelic TNFRSF13B-A181E mutations in common variable immunodeficiency. (PMID: 20156508) Dong X … Abraham RS (Human immunology 2010) 3 22 44 58
  2. Lymphocyte characteristics in children with common variable immunodeficiency. (PMID: 20006554) van de Ven AA … van Montfrans JM (Clinical immunology (Orlando, Fla.) 2010) 3 22 44 58
  3. Role of polymorphisms in the TNFRSF13B (TACI) gene in Spanish patients with immunoglobulin A deficiency. (PMID: 19392801) López-Mejías R … Núñez C (Tissue antigens 2009) 3 22 44 58
  4. An evolutionary approach to the medical implications of the tumor necrosis factor receptor superfamily member 13B (TNFRSF13B) gene. (PMID: 19494827) Sazzini M … Luiselli D (Genes and immunity 2009) 3 22 44 58
  5. Novel mutations in TACI (TNFRSF13B) causing common variable immunodeficiency. (PMID: 19629655) Mohammadi J … Hammarström L (Journal of clinical immunology 2009) 3 22 44 58

Products for TNFRSF13B Gene

Sources for TNFRSF13B Gene

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