B cell-activating factor (BAFF) enhances B-cell survival in vitro and is a regulator of the peripheral B-cell population. Overexpression of Baff in mice results in mature B-cell hyperplasia and symptoms of systemic lupus erythematosus (SLE). Also, some SLE patients have increased levels of BAFF in serum. Therefore, it has been proposed that abnormally high levels of BAFF may co... See more...

Aliases for TNFRSF13C Gene

Aliases for TNFRSF13C Gene

  • TNF Receptor Superfamily Member 13C 2 3 5
  • BAFFR 2 3 4
  • Tumor Necrosis Factor Receptor Superfamily Member 13C 3 4
  • BLyS Receptor 3 3 4
  • BAFF Receptor 3 4
  • BAFF-R 3 4
  • CD268 2 3
  • Tumor Necrosis Factor Receptor Superfamily, Member 13C 2
  • B Cell-Activating Factor Receptor 3
  • B-Cell-Activating Factor Receptor 4
  • CD268 Antigen 4
  • TNFRSF13C 5
  • Prolixin 3
  • BROMIX 3
  • CVID4 3
  • BR3 4

External Ids for TNFRSF13C Gene

Previous GeneCards Identifiers for TNFRSF13C Gene

  • GC22M038935
  • GC22M040564
  • GC22M040645
  • GC22M042321
  • GC22M025286
  • GC22M041927
  • GC22M042795
  • GC22M042909
  • GC22M042960
  • GC22M044570
  • GC22M042057
  • GC22M042064
  • GC22M042336
  • GC22M042682

Summaries for TNFRSF13C Gene

Entrez Gene Summary for TNFRSF13C Gene

  • B cell-activating factor (BAFF) enhances B-cell survival in vitro and is a regulator of the peripheral B-cell population. Overexpression of Baff in mice results in mature B-cell hyperplasia and symptoms of systemic lupus erythematosus (SLE). Also, some SLE patients have increased levels of BAFF in serum. Therefore, it has been proposed that abnormally high levels of BAFF may contribute to the pathogenesis of autoimmune diseases by enhancing the survival of autoreactive B cells. The protein encoded by this gene is a receptor for BAFF and is a type III transmembrane protein containing a single extracellular cysteine-rich domain. It is thought that this receptor is the principal receptor required for BAFF-mediated mature B-cell survival. [provided by RefSeq, Jul 2008]

GeneCards Summary for TNFRSF13C Gene

TNFRSF13C (TNF Receptor Superfamily Member 13C) is a Protein Coding gene. Diseases associated with TNFRSF13C include Immunodeficiency, Common Variable, 4 and Common Variable Immunodeficiency. Among its related pathways are NF-KappaB Family Pathway and TNF Superfamily - Human Ligand-Receptor Interactions and their Associated Functions. An important paralog of this gene is TNFRSF17.

UniProtKB/Swiss-Prot Summary for TNFRSF13C Gene

  • B-cell receptor specific for TNFSF13B/TALL1/BAFF/BLyS. Promotes the survival of mature B-cells and the B-cell response.

Gene Wiki entry for TNFRSF13C Gene

Additional gene information for TNFRSF13C Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for TNFRSF13C Gene

Genomics for TNFRSF13C Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for TNFRSF13C Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around TNFRSF13C on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for TNFRSF13C

Top Transcription factor binding sites by QIAGEN in the TNFRSF13C gene promoter:
  • AP-1
  • ATF-2
  • c-Jun
  • E47
  • p53
  • SEF-1 (1)
  • Sp1
  • USF-1
  • USF1

Genomic Locations for TNFRSF13C Gene

Genomic Locations for TNFRSF13C Gene
chr22:41,922,023-41,926,818
(GRCh38/hg38)
Size:
4,796 bases
Orientation:
Minus strand
chr22:42,321,036-42,322,822
(GRCh37/hg19)
Size:
1,787 bases
Orientation:
Minus strand

Genomic View for TNFRSF13C Gene

Genes around TNFRSF13C on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
TNFRSF13C Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for TNFRSF13C Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for TNFRSF13C Gene

Proteins for TNFRSF13C Gene

  • Protein details for TNFRSF13C Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q96RJ3-TR13C_HUMAN
    Recommended name:
    Tumor necrosis factor receptor superfamily member 13C
    Protein Accession:
    Q96RJ3

    Protein attributes for TNFRSF13C Gene

    Size:
    184 amino acids
    Molecular mass:
    18864 Da
    Quaternary structure:
    No Data Available

    Three dimensional structures from OCA and Proteopedia for TNFRSF13C Gene

    Alternative splice isoforms for TNFRSF13C Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for TNFRSF13C Gene

Post-translational modifications for TNFRSF13C Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for TNFRSF13C Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibody Products

No data available for DME Specific Peptides for TNFRSF13C Gene

Domains & Families for TNFRSF13C Gene

Gene Families for TNFRSF13C Gene

Protein Domains for TNFRSF13C Gene

InterPro:
Blocks:
  • TNFR/CD27/30/40/95 cysteine-rich region
ProtoNet:

Suggested Antigen Peptide Sequences for TNFRSF13C Gene

GenScript: Design optimal peptide antigens:
  • BAFF receptor (C8ZLJ6_HUMAN)
  • Tumor necrosis factor receptor superfamily, member 13C (Q5H8V1_HUMAN)
  • BLyS receptor 3 (TR13C_HUMAN)
genes like me logo Genes that share domains with TNFRSF13C: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for TNFRSF13C Gene

Function for TNFRSF13C Gene

Molecular function for TNFRSF13C Gene

UniProtKB/Swiss-Prot Function:
B-cell receptor specific for TNFSF13B/TALL1/BAFF/BLyS. Promotes the survival of mature B-cells and the B-cell response.

Phenotypes From GWAS Catalog for TNFRSF13C Gene

genes like me logo Genes that share phenotypes with TNFRSF13C: view

Human Phenotype Ontology for TNFRSF13C Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for TNFRSF13C Gene

MGI Knock Outs for TNFRSF13C:

Animal Model Products

CRISPR Products

miRNA for TNFRSF13C Gene

miRTarBase miRNAs that target TNFRSF13C

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for TNFRSF13C

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Transcription Factor Targets and HOMER Transcription for TNFRSF13C Gene

Localization for TNFRSF13C Gene

Subcellular locations from UniProtKB/Swiss-Prot for TNFRSF13C 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 TNFRSF13C gene
Compartment Confidence
plasma membrane 5
mitochondrion 3
nucleus 3
extracellular 2
cytoskeleton 2
cytosol 2
endoplasmic reticulum 1
endosome 1
lysosome 1
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for TNFRSF13C Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane TAS --
GO:0009897 external side of plasma membrane IBA 21873635
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with TNFRSF13C: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for TNFRSF13C Gene

Pathways & Interactions for TNFRSF13C Gene

PathCards logo

SuperPathways for TNFRSF13C Gene

SuperPathway Contained pathways
1 PEDF Induced Signaling
.51
.47
.43
2 Akt Signaling
.60
.60
.55
3 TGF-Beta Pathway
.60
.57
.51
4 RANK Signaling in Osteoclasts
.92
.39
5 Regulation of activated PAK-2p34 by proteasome mediated degradation
genes like me logo Genes that share pathways with TNFRSF13C: view

Pathways by source for TNFRSF13C Gene

14 Qiagen pathways for TNFRSF13C Gene
  • Akt Signaling
  • Antioxidant Action of Vitamin-C
  • BAFF in B-Cell Signaling
  • Glucocorticoid Receptor Signaling
  • JAK-STAT Pathway

SIGNOR curated interactions for TNFRSF13C Gene

Inactivates:
Is activated by:

Gene Ontology (GO) - Biological Process for TNFRSF13C Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001782 B cell homeostasis IEA --
GO:0002250 adaptive immune response IEA --
GO:0002376 immune system process IEA --
GO:0002636 positive regulation of germinal center formation IEA --
GO:0030890 positive regulation of B cell proliferation IBA 21873635
genes like me logo Genes that share ontologies with TNFRSF13C: view

Drugs & Compounds for TNFRSF13C Gene

(3) Drugs for TNFRSF13C 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 TNFRSF13C Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with TNFRSF13C: view

Transcripts for TNFRSF13C Gene

mRNA/cDNA for TNFRSF13C Gene

1 REFSEQ mRNAs :
5 NCBI additional mRNA sequence :
1 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for TNFRSF13C

Alternative Splicing Database (ASD) splice patterns (SP) for TNFRSF13C Gene

No ASD Table

Relevant External Links for TNFRSF13C Gene

GeneLoc Exon Structure for
TNFRSF13C

Expression for TNFRSF13C Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for TNFRSF13C Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for TNFRSF13C Gene

This gene is overexpressed in Spleen (x11.5) and Small Intestine - Terminal Ileum (x6.2).

Protein differential expression in normal tissues from HIPED for TNFRSF13C Gene

This gene is overexpressed in Blymphocyte (62.0) and Peripheral blood mononuclear cells (7.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for TNFRSF13C Gene



Protein tissue co-expression partners for TNFRSF13C Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for TNFRSF13C

SOURCE GeneReport for Unigene cluster for TNFRSF13C Gene:

Hs.344088

mRNA Expression by UniProt/SwissProt for TNFRSF13C Gene:

Q96RJ3-TR13C_HUMAN
Tissue specificity: Highly expressed in spleen and lymph node, and in resting B-cells. Detected at lower levels in activated B-cells, resting CD4+ T-cells, in thymus and peripheral blood leukocytes.

Evidence on tissue expression from TISSUES for TNFRSF13C Gene

  • Lymph node(3.7)
  • Spleen(3.5)
  • Blood(3.1)
  • Bone marrow(3)
  • Intestine(2.4)
  • Kidney(2.2)
  • Nervous system(2.1)
  • Skin(2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for TNFRSF13C 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 TNFRSF13C: view

Orthologs for TNFRSF13C Gene

This gene was present in the common ancestor of mammals.

Orthologs for TNFRSF13C Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia TNFRSF13C 30 31
  • 98.56 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia TNFRSF13C 31
  • 67 (a)
OneToOne
Mouse
(Mus musculus)
Mammalia Tnfrsf13c 30 17 31
  • 66.67 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Tnfrsf13c 30
  • 66.08 (n)
Cow
(Bos Taurus)
Mammalia TNFRSF13C 31
  • 59 (a)
OneToOne
Species where no ortholog for TNFRSF13C was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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)
  • Chicken (Gallus gallus)
  • 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)
  • Lizard (Anolis carolinensis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Oppossum (Monodelphis domestica)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Platypus (Ornithorhynchus anatinus)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (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 TNFRSF13C Gene

ENSEMBL:
Gene Tree for TNFRSF13C (if available)
TreeFam:
Gene Tree for TNFRSF13C (if available)
Aminode:
Evolutionary constrained regions (ECRs) for TNFRSF13C: view image

Paralogs for TNFRSF13C Gene

Paralogs for TNFRSF13C Gene

genes like me logo Genes that share paralogs with TNFRSF13C: view

Variants for TNFRSF13C Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for TNFRSF13C Gene

SNP ID Clinical significance and condition Chr 22 pos Variation AA Info Type
647889 Uncertain Significance: Common variable immunodeficiency 4 41,926,295(-) T/A MISSENSE_VARIANT
657280 Uncertain Significance: Common variable immunodeficiency 4 41,926,143(-) G/A MISSENSE_VARIANT
659163 Uncertain Significance: Common variable immunodeficiency 4 41,925,437(-) G/A MISSENSE_VARIANT
660119 Uncertain Significance: Common variable immunodeficiency 4 41,925,379(-) AGGGCCGGCC/CCTGC FRAMESHIFT_VARIANT
717071 Conflicting Interpretations: Common variable immunodeficiency 4 41,925,486(-) G/A MISSENSE_VARIANT

Additional dbSNP identifiers (rs#s) for TNFRSF13C Gene

Structural Variations from Database of Genomic Variants (DGV) for TNFRSF13C Gene

Variant ID Type Subtype PubMed ID
nsv1057208 CNV gain 25217958
nsv508736 CNV insertion 20534489
nsv589053 CNV loss 21841781
nsv955162 CNV deletion 24416366

Variation tolerance for TNFRSF13C Gene

Residual Variation Intolerance Score: 60.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.17; 51.80% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for TNFRSF13C Gene

Human Gene Mutation Database (HGMD)
TNFRSF13C
SNPedia medical, phenotypic, and genealogical associations of SNPs for
TNFRSF13C

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for TNFRSF13C Gene

Disorders for TNFRSF13C Gene

MalaCards: The human disease database

(27) MalaCards diseases for TNFRSF13C Gene - From: OMIM, ClinVar, GTR, Orphanet, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
immunodeficiency, common variable, 4
  • cvid4
common variable immunodeficiency
  • acquired agammaglobulinemia
immunodeficiency, common variable, 2
  • cvid2
primary agammaglobulinemia
  • antibody deficiency
b cell deficiency
  • b cell deficiencies
- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

TR13C_HUMAN
  • Immunodeficiency, common variable, 4 (CVID4) [MIM:613494]: 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:19666484}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for TNFRSF13C

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with TNFRSF13C: view

No data available for Genatlas for TNFRSF13C Gene

Publications for TNFRSF13C Gene

  1. Mutational analysis of human BAFF receptor TNFRSF13C (BAFF-R) in patients with common variable immunodeficiency. (PMID: 16160919) Losi CG … Plebani A (Journal of clinical immunology 2005) 3 4 23 41
  2. B-cell activating factor receptor deficiency is associated with an adult-onset antibody deficiency syndrome in humans. (PMID: 19666484) Warnatz K … Eibel H (Proceedings of the National Academy of Sciences of the United States of America 2009) 3 4 23
  3. Ligand-receptor binding revealed by the TNF family member TALL-1. (PMID: 12721620) Liu Y … Zhang G (Nature 2003) 3 4 23
  4. Crystal structure of the BAFF-BAFF-R complex and its implications for receptor activation. (PMID: 12715002) Kim HM … Lee JO (Nature structural biology 2003) 3 4 23
  5. BAFF/BLyS receptor 3 comprises a minimal TNF receptor-like module that encodes a highly focused ligand-binding site. (PMID: 12755599) Gordon NC … Starovasnik MA (Biochemistry 2003) 3 4 23

Products for TNFRSF13C Gene

Sources for TNFRSF13C Gene