This gene encodes a member of the tumor necrosis factor receptor superfamily. The major ligands of this receptor include lymphotoxin alpha/beta and tumor necrosis factor ligand superfamily member 14. The encoded protein plays a role in signalling during the development of lymphoid and other organs, lipid metabolism, immune response, and programmed cell death. Activity of this r... See more...

Aliases for LTBR Gene

Aliases for LTBR Gene

  • Lymphotoxin Beta Receptor 2 3 5
  • TNFRSF3 2 3 4
  • TNFCR 2 3 4
  • Tumor Necrosis Factor Receptor Superfamily Member 3 3 4
  • Tumor Necrosis Factor Receptor 2-Related Protein 3 4
  • Tumor Necrosis Factor Receptor Type III 3 4
  • Tumor Necrosis Factor C Receptor 3 4
  • TNF-R-III 2 3
  • TNFR2-RP 2 3
  • D12S370 3 4
  • TNFR-RP 2 3
  • TNFR3 3 4
  • Lymphotoxin Beta Receptor (TNFR Superfamily, Member 3) 3
  • TNFR Superfamily, Member 3 2
  • Lymphotoxin-Beta Receptor 4
  • Lymphotoxin B Receptor 3
  • LT-BETA-R 3
  • TNF-RIII 4
  • TNFR-III 4
  • LTBR 5

External Ids for LTBR Gene

Previous HGNC Symbols for LTBR Gene

  • D12S370

Previous GeneCards Identifiers for LTBR Gene

  • GC12P006348
  • GC12P006467
  • GC12P006363
  • GC12P006347
  • GC12P006484

Summaries for LTBR Gene

Entrez Gene Summary for LTBR Gene

  • This gene encodes a member of the tumor necrosis factor receptor superfamily. The major ligands of this receptor include lymphotoxin alpha/beta and tumor necrosis factor ligand superfamily member 14. The encoded protein plays a role in signalling during the development of lymphoid and other organs, lipid metabolism, immune response, and programmed cell death. Activity of this receptor has also been linked to carcinogenesis. Alternatively spliced transcript variants encoding multiple isoforms have been observed. [provided by RefSeq, Aug 2012]

GeneCards Summary for LTBR Gene

LTBR (Lymphotoxin Beta Receptor) is a Protein Coding gene. Diseases associated with LTBR include Bronchiectasis With Or Without Elevated Sweat Chloride 2 and Cone-Rod Dystrophy 2. Among its related pathways are NF-KappaB Family Pathway and LT-BetaR Pathway. Gene Ontology (GO) annotations related to this gene include identical protein binding and ubiquitin protein ligase binding. An important paralog of this gene is TNFRSF21.

UniProtKB/Swiss-Prot Summary for LTBR Gene

  • Receptor for the heterotrimeric lymphotoxin containing LTA and LTB, and for TNFS14/LIGHT. Promotes apoptosis via TRAF3 and TRAF5. May play a role in the development of lymphoid organs.

Gene Wiki entry for LTBR Gene

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

Genomics for LTBR Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for LTBR 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 LTBR on the GeneHancer Hub at the UCSC Golden Path

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

Top Transcription factor binding sites by QIAGEN in the LTBR gene promoter:
  • AhR
  • AP-1
  • ATF-2
  • c-Jun
  • Chx10
  • GR
  • GR-alpha
  • GR-beta
  • NF-kappaB1
  • STAT3

Genomic Locations for LTBR Gene

Genomic Locations for LTBR Gene
chr12:6,375,045-6,391,571
(GRCh38/hg38)
Size:
16,527 bases
Orientation:
Plus strand
chr12:6,484,211-6,500,734
(GRCh37/hg19)
Size:
16,524 bases
Orientation:
Plus strand

Genomic View for LTBR Gene

Genes around LTBR on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for LTBR Gene

Proteins for LTBR Gene

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

    Protein Symbol:
    P36941-TNR3_HUMAN
    Recommended name:
    Tumor necrosis factor receptor superfamily member 3
    Protein Accession:
    P36941
    Secondary Accessions:
    • B7Z1D2
    • D3DUR2
    • F5GXE7

    Protein attributes for LTBR Gene

    Size:
    435 amino acids
    Molecular mass:
    46709 Da
    Quaternary structure:
    • Self-associates. Associates with TRAF3, TRAF4 and TRAF5.
    • (Microbial infection) Interacts with HCV core protein.

    Three dimensional structures from OCA and Proteopedia for LTBR Gene

    Alternative splice isoforms for LTBR Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for LTBR Gene

Post-translational modifications for LTBR Gene

  • Glycosylation at Asn40 and Asn177
  • Modification sites at PhosphoSitePlus

Antibody Products

  • Abcam antibodies for LTBR

No data available for DME Specific Peptides for LTBR Gene

Domains & Families for LTBR Gene

Gene Families for LTBR Gene

HGNC:
IUPHAR :
Human Protein Atlas (HPA):
  • Cancer-related genes
  • Plasma proteins
  • Predicted intracellular proteins
  • Predicted membrane proteins

Protein Domains for LTBR Gene

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

Suggested Antigen Peptide Sequences for LTBR Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ38099 fis, clone D3OST1000238, highly similar to Tumor necrosis factor receptor superfamily member 3 (B3KTD9_HUMAN)
  • Lymphotoxin beta receptor (Q75UT6_HUMAN)
  • Tumor necrosis factor receptor type III (TNR3_HUMAN)
genes like me logo Genes that share domains with LTBR: view

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

Function for LTBR Gene

Molecular function for LTBR Gene

UniProtKB/Swiss-Prot Function:
Receptor for the heterotrimeric lymphotoxin containing LTA and LTB, and for TNFS14/LIGHT. Promotes apoptosis via TRAF3 and TRAF5. May play a role in the development of lymphoid organs.
GENATLAS Biochemistry:
lymphotoxin B receptor,(tumor necrosis factor receptor TNFR superfamily,member 3),expressed at the surface of most cell types,including cells of epithelial and myeloid lineages but not on T and B cells,involved in lymphoid organ development and apoptosis through interaction with TRAF3

Phenotypes From GWAS Catalog for LTBR Gene

Gene Ontology (GO) - Molecular Function for LTBR Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IEA,IPI 8995654
GO:0031625 ubiquitin protein ligase binding IPI 11279055
GO:0042802 identical protein binding IPI 20732415
genes like me logo Genes that share ontologies with LTBR: view
genes like me logo Genes that share phenotypes with LTBR: view

Animal Models for LTBR Gene

MGI Knock Outs for LTBR:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

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

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for LTBR Gene

Localization for LTBR Gene

Subcellular locations from UniProtKB/Swiss-Prot for LTBR Gene

Membrane. Single-pass type I 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 LTBR gene
Compartment Confidence
plasma membrane 5
golgi apparatus 4
extracellular 3
cytoskeleton 2
nucleus 2
cytosol 2
mitochondrion 1
endoplasmic reticulum 1
endosome 1
lysosome 1
peroxisome 0

Subcellular locations from the

Human Protein Atlas (HPA)
  • Golgi apparatus (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for LTBR Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005794 Golgi apparatus IDA --
GO:0005886 plasma membrane TAS --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with LTBR: view

Pathways & Interactions for LTBR Gene

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

Pathways by source for LTBR Gene

3 GeneGo (Thomson Reuters) pathways for LTBR Gene
  • Apoptosis and survival Apoptotic TNF-family pathways
  • Apoptosis and survival Lymphotoxin-beta receptor signaling
  • Transcription_NF-kB signaling pathway
3 Qiagen pathways for LTBR Gene
  • LT-BetaR Pathway
  • NF-KappaB Family Pathway
  • TNF Superfamily Pathway

SIGNOR curated interactions for LTBR Gene

Activates:
Is activated by:

Gene Ontology (GO) - Biological Process for LTBR Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006915 apoptotic process IEA --
GO:0006955 immune response IEA --
GO:0007165 signal transduction TAS 8171323
GO:0016032 viral process IEA --
GO:0033209 tumor necrosis factor-mediated signaling pathway TAS --
genes like me logo Genes that share ontologies with LTBR: view

Drugs & Compounds for LTBR Gene

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

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

(3) Additional Compounds for LTBR Gene - From: Novoseek

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

Transcripts for LTBR Gene

mRNA/cDNA for LTBR Gene

2 REFSEQ mRNAs :
10 NCBI additional mRNA sequence :
15 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 LTBR

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

ExUns: 1a · 1b · 1c · 1d · 1e ^ 2 ^ 3a · 3b · 3c · 3d ^ 4 ^ 5a · 5b · 5c ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11
SP1: - - -
SP2: - - - -
SP3: - -
SP4: - - - - - -
SP5: -
SP6: -
SP7:
SP8: - -

Relevant External Links for LTBR Gene

GeneLoc Exon Structure for
LTBR

Expression for LTBR Gene

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

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for LTBR Gene

This gene is overexpressed in Placenta (69.0).

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



Protein tissue co-expression partners for LTBR Gene

- Elite partner

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

SOURCE GeneReport for Unigene cluster for LTBR Gene:

Hs.1116

Evidence on tissue expression from TISSUES for LTBR Gene

  • Lung(4.7)
  • Liver(4.6)
  • Adrenal gland(4.4)
  • Nervous system(3.5)
  • Spleen(3.4)
  • Intestine(3.3)
  • Lymph node(3.2)
  • Blood(3.1)
  • Skin(3.1)
  • Kidney(2.9)
  • Heart(2.9)
  • Bone marrow(2.6)
  • Thyroid gland(2.5)
  • Stomach(2.5)
  • Pancreas(2.5)
  • Muscle(2.4)
genes like me logo Genes that share expression patterns with LTBR: view

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for LTBR Gene

Orthologs for LTBR Gene

This gene was present in the common ancestor of mammals.

Orthologs for LTBR Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia LTBR 30 31
  • 98.85 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia LTBR 30 31
  • 80.69 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia LTBR 30 31
  • 78.18 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Ltbr 30 17 31
  • 76.28 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Ltbr 30
  • 76.1 (n)
Oppossum
(Monodelphis domestica)
Mammalia LTBR 31
  • 56 (a)
OneToOne
Species where no ortholog for LTBR 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)
  • 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 LTBR Gene

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

Paralogs for LTBR Gene

Variants for LTBR Gene

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

SNP ID Clinical significance and condition Chr 12 pos Variation AA Info Type
710230 Benign: not provided 6,388,415(+) G/T MISSENSE_VARIANT
722300 Benign: not provided 6,386,133(+) C/T SYNONYMOUS_VARIANT
723535 Benign: not provided 6,385,291(+) G/A SYNONYMOUS_VARIANT
726797 Benign: not provided 6,384,579(+) C/T INTRON_VARIANT
771181 Benign: not provided 6,390,219(+) A/G SYNONYMOUS_VARIANT

Additional dbSNP identifiers (rs#s) for LTBR Gene

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

Variant ID Type Subtype PubMed ID
esv2759876 CNV gain 17122850
esv34325 CNV gain 17911159
nsv952790 CNV deletion 24416366

Variation tolerance for LTBR Gene

Residual Variation Intolerance Score: 39.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.07; 50.65% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LTBR Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
LTBR

SNP Genotyping and Copy Number Assay Products

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

Disorders for LTBR Gene

MalaCards: The human disease database

(2) MalaCards diseases for LTBR Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
bronchiectasis with or without elevated sweat chloride 2
  • cystic fibrosis-like syndrome
cone-rod dystrophy 2
  • cord2
- elite association - COSMIC cancer census association via MalaCards
Search LTBR in MalaCards View complete list of genes associated with diseases

Additional Disease Information for LTBR

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 LTBR: view

No data available for UniProtKB/Swiss-Prot and Genatlas for LTBR Gene

Publications for LTBR Gene

  1. A lymphotoxin-beta-specific receptor. (PMID: 8171323) Crowe PD … Smith CA (Science (New York, N.Y.) 1994) 2 3 4 23
  2. The lymphotoxin-beta receptor is necessary and sufficient for LIGHT-mediated apoptosis of tumor cells. (PMID: 10799510) Rooney IA … Ware CF (The Journal of biological chemistry 2000) 3 4 23
  3. The cytoplasmic domain of the lymphotoxin-beta receptor mediates cell death in HeLa cells. (PMID: 10207006) Wu MY … Hsieh SL (The Journal of biological chemistry 1999) 3 4 23
  4. Cloning and characterization of a cDNA encoding the human homolog of tumor necrosis factor receptor-associated factor 5 (TRAF5). (PMID: 9511754) Mizushima S … Inoue J (Gene 1998) 3 4 23
  5. TRAF-4 expression in epithelial progenitor cells. Analysis in normal adult, fetal, and tumor tissues. (PMID: 9626059) Krajewska M … Reed JC (The American journal of pathology 1998) 3 4 23

Products for LTBR Gene

Sources for LTBR Gene