Lymphotoxin beta is a type II membrane protein of the TNF family. It anchors lymphotoxin-alpha to the cell surface through heterotrimer formation. The predominant form on the lymphocyte surface is the lymphotoxin-alpha 1/beta 2 complex (e.g. 1 molecule alpha/2 molecules beta) and this complex is the primary ligand for the lymphotoxin-beta receptor. The minor complex is lymphoto... See more...

Aliases for LTB Gene

Aliases for LTB Gene

  • Lymphotoxin Beta 2 3 5
  • TNFSF3 2 3 4
  • Tumor Necrosis Factor Ligand Superfamily Member 3 3 4
  • TNF Superfamily Member 3 2 3
  • Tumor Necrosis Factor C 3 4
  • Lymphotoxin-Beta 3 4
  • LT-Beta 3 4
  • TNF-C 3 4
  • TNFC 3 4
  • P33 2 3
  • Lymphotoxin Beta (TNF Superfamily, Member 3) 3
  • Tumor Necrosis Factor Ligand 1C 3
  • TNLG1C 3
  • LTB 5

External Ids for LTB Gene

Previous HGNC Symbols for LTB Gene

  • TNFC

Previous GeneCards Identifiers for LTB Gene

  • GC06M031611
  • GC06M031602
  • GC06M031319
  • GC06M031652
  • GC06M031656
  • GC06M031549
  • GC06M031335
  • GC06M031582
  • GC06M031583
  • GC06M032064
  • GC06M032132
  • GC06M032189
  • GC06M032353
  • GC06M031600
  • GC06M031767
  • GC06M031811
  • GC06M031835
  • GC06M031882
  • GC06M031918
  • GC06M031980
  • GC06M032015

Summaries for LTB Gene

Entrez Gene Summary for LTB Gene

  • Lymphotoxin beta is a type II membrane protein of the TNF family. It anchors lymphotoxin-alpha to the cell surface through heterotrimer formation. The predominant form on the lymphocyte surface is the lymphotoxin-alpha 1/beta 2 complex (e.g. 1 molecule alpha/2 molecules beta) and this complex is the primary ligand for the lymphotoxin-beta receptor. The minor complex is lymphotoxin-alpha 2/beta 1. LTB is an inducer of the inflammatory response system and involved in normal development of lymphoid tissue. Lymphotoxin-beta isoform b is unable to complex with lymphotoxin-alpha suggesting a function for lymphotoxin-beta which is independent of lympyhotoxin-alpha. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]

GeneCards Summary for LTB Gene

LTB (Lymphotoxin Beta) is a Protein Coding gene. Diseases associated with LTB include Synovitis and Myasthenic Syndrome, Congenital, 2C, Associated With Acetylcholine Receptor Deficiency. Among its related pathways are NF-KappaB Family Pathway and LT-BetaR Pathway. Gene Ontology (GO) annotations related to this gene include signaling receptor binding and tumor necrosis factor receptor binding. An important paralog of this gene is TNFSF14.

UniProtKB/Swiss-Prot Summary for LTB Gene

  • Cytokine that binds to LTBR/TNFRSF3. May play a specific role in immune response regulation. Provides the membrane anchor for the attachment of the heterotrimeric complex to the cell surface. Isoform 2 is probably non-functional.

Gene Wiki entry for LTB Gene

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

Genomics for LTB Gene

GeneHancer (GH) Regulatory Elements Pubs

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

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

Top Transcription factor binding sites by QIAGEN in the LTB gene promoter:
  • AP-1
  • ATF-2
  • c-Jun
  • COUP
  • COUP-TF
  • p53

Genomic Locations for LTB Gene

Genomic Locations for LTB Gene
chr6:31,580,525-31,582,522
(GRCh38/hg38)
Size:
1,998 bases
Orientation:
Minus strand
chr6:31,548,302-31,550,299
(GRCh37/hg19)
Size:
1,998 bases
Orientation:
Minus strand

Genomic View for LTB Gene

Genes around LTB on UCSC Golden Path with GeneCards custom track

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

Proteins for LTB Gene

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

    Protein Symbol:
    Q06643-TNFC_HUMAN
    Recommended name:
    Lymphotoxin-beta
    Protein Accession:
    Q06643
    Secondary Accessions:
    • P78370
    • Q52LU8
    • Q99761

    Protein attributes for LTB Gene

    Size:
    244 amino acids
    Molecular mass:
    25390 Da
    Quaternary structure:
    • Heterotrimer of either two LTB and one LTA subunits or (less prevalent) one LTB and two LTA subunits.

    Three dimensional structures from OCA and Proteopedia for LTB Gene

    Alternative splice isoforms for LTB Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for LTB Gene

Post-translational modifications for LTB Gene

  • Glycosylation at Asn222
  • Modification sites at PhosphoSitePlus

Other Protein References for LTB Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for LTB Gene

Domains & Families for LTB Gene

Gene Families for LTB Gene

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

Protein Domains for LTB Gene

InterPro:
Blocks:
  • Tumor Necrosis Factor
  • Tumour necrosis factor family signature
  • Tumour necrosis factor c (lymphotoxin-beta) signature
ProtoNet:

Suggested Antigen Peptide Sequences for LTB Gene

GenScript: Design optimal peptide antigens:
  • cDNA, FLJ92499, Homo sapiens lymphotoxin beta (TNF superfamily, member 3) (LTB),transcript variant 2, mRNA (Q52LU8_HUMAN)
  • Lymphotoxin beta (TNF superfamily, member 3), isoform CRA_b (Q5STB2_HUMAN)
  • Tumor necrosis factor ligand superfamily member 3 (TNFC_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q06643

UniProtKB/Swiss-Prot:

TNFC_HUMAN :
  • Belongs to the tumor necrosis factor family.
Family:
  • Belongs to the tumor necrosis factor family.
genes like me logo Genes that share domains with LTB: view

Function for LTB Gene

Molecular function for LTB Gene

UniProtKB/Swiss-Prot Function:
Cytokine that binds to LTBR/TNFRSF3. May play a specific role in immune response regulation. Provides the membrane anchor for the attachment of the heterotrimeric complex to the cell surface. Isoform 2 is probably non-functional.
GENATLAS Biochemistry:
lymphotoxin beta,expressed in macrophages,,tumors necrosis factor (ligand) superfamily,member 3

Phenotypes From GWAS Catalog for LTB Gene

Gene Ontology (GO) - Molecular Function for LTB Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005102 signaling receptor binding TAS 7916655
GO:0005125 cytokine activity IEA --
GO:0005164 tumor necrosis factor receptor binding IEA --
GO:0005515 protein binding IEA --
genes like me logo Genes that share ontologies with LTB: view
genes like me logo Genes that share phenotypes with LTB: view

Animal Models for LTB Gene

MGI Knock Outs for LTB:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

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

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

Localization for LTB Gene

Subcellular locations from UniProtKB/Swiss-Prot for LTB Gene

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

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for LTB Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005575 cellular_component ND --
GO:0005615 extracellular space IEA --
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 LTB: view

Pathways & Interactions for LTB Gene

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

Pathways by source for LTB Gene

1 GeneGo (Thomson Reuters) pathway for LTB Gene
  • Apoptosis and survival Lymphotoxin-beta receptor signaling
4 Qiagen pathways for LTB Gene
  • LT-BetaR Pathway
  • NF-KappaB Family Pathway
  • OX40 Pathway
  • TNF Superfamily Pathway

SIGNOR curated interactions for LTB Gene

Activates:

Gene Ontology (GO) - Biological Process for LTB Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006955 immune response IEA --
GO:0007165 signal transduction TAS 7916655
GO:0007267 cell-cell signaling TAS 7916655
GO:0010467 gene expression IEA --
GO:0033209 tumor necrosis factor-mediated signaling pathway TAS --
genes like me logo Genes that share ontologies with LTB: view

Drugs & Compounds for LTB Gene

(13) Drugs for LTB Gene - From: PharmGKB, ClinicalTrials, DGIdb, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Abacavir Approved, Investigational Pharma 231
Isoniazid Approved, Investigational Pharma 215
Rifapentine Approved, Investigational Pharma 45
Simvastatin Approved Pharma Inhibitor, Competitive HMG-CoA reductase inhibitor 582
Baminercept Investigational Pharma 0

(1) Additional Compounds for LTB Gene - From: Novoseek

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

Transcripts for LTB Gene

mRNA/cDNA for LTB Gene

2 REFSEQ mRNAs :
9 NCBI additional mRNA sequence :
4 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 LTB

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

No ASD Table

Relevant External Links for LTB Gene

GeneLoc Exon Structure for
LTB

Expression for LTB Gene

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

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

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

This gene is overexpressed in Whole Blood (x26.2), Spleen (x14.1), and Small Intestine - Terminal Ileum (x4.5).

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

SOURCE GeneReport for Unigene cluster for LTB Gene:

Hs.376208

mRNA Expression by UniProt/SwissProt for LTB Gene:

Q06643-TNFC_HUMAN
Tissue specificity: Spleen and thymus.

Evidence on tissue expression from TISSUES for LTB Gene

  • Spleen(4.7)
  • Intestine(4.6)
  • Blood(4.5)
  • Lung(2.3)
  • Lymph node(2.2)
genes like me logo Genes that share expression patterns with LTB: view

No data available for Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for LTB Gene

Orthologs for LTB Gene

This gene was present in the common ancestor of mammals.

Orthologs for LTB Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia LTB 30 31
  • 99.73 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia LTB 30 31
  • 84.56 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia LTB 30 31
  • 84.29 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Ltb 30
  • 80.83 (n)
Mouse
(Mus musculus)
Mammalia Ltb 30 17 31
  • 79.66 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia LTB 31
  • 52 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia -- 31
  • 44 (a)
OneToMany
-- 31
  • 38 (a)
OneToMany
Species where no ortholog for LTB 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)
  • 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 LTB Gene

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

Paralogs for LTB Gene

Paralogs for LTB Gene

(1) SIMAP similar genes for LTB Gene using alignment to 2 proteins:

  • TNFC_HUMAN
  • Q5STB2_HUMAN
genes like me logo Genes that share paralogs with LTB: view

Variants for LTB Gene

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

SNP ID Clinical significance and condition Chr 06 pos Variation AA Info Type
770169 Benign: not provided 31,581,079(-) G/A MISSENSE_VARIANT,THREE_PRIME_UTR_VARIANT
778228 Benign: not provided 31,581,580(-) G/A MISSENSE_VARIANT,SYNONYMOUS_VARIANT
rs2229699 - p.Ala122Asp
rs3093554 - p.Gly70Glu
rs3093555 - p.Ala111Pro

Additional dbSNP identifiers (rs#s) for LTB Gene

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

Variant ID Type Subtype PubMed ID
dgv10403n54 CNV loss 21841781
dgv10404n54 CNV loss 21841781
nsv1073969 CNV deletion 25765185
nsv1112900 CNV deletion 24896259
nsv1126749 CNV deletion 24896259
nsv830627 CNV loss 17160897

Variation tolerance for LTB Gene

Residual Variation Intolerance Score: 64.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.36; 41.97% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LTB Gene

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

SNP Genotyping and Copy Number Assay Products

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

Disorders for LTB Gene

MalaCards: The human disease database

(4) MalaCards diseases for LTB Gene - From: DISEASES, Novoseek, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search LTB in MalaCards View complete list of genes associated with diseases

Additional Disease Information for LTB

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 LTB: view

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

Publications for LTB Gene

  1. Variation in inflammation-related genes and risk of incident nonfatal myocardial infarction or ischemic stroke. (PMID: 17981284) Bis JC … Psaty BM (Atherosclerosis 2008) 3 23 41
  2. Haplotype analysis of a 100 kb region spanning TNF-LTA identifies a polymorphism in the LTA promoter region that is associated with atopic asthma susceptibility in Japan. (PMID: 15969671) Migita O … Arinami T (Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology 2005) 3 23 41
  3. Identification of two lymphotoxin beta isoforms expressed in human lymphoid cell lines and non-Hodgkin's lymphomas. (PMID: 9299492) Warzocha K … Salles G (Biochemical and biophysical research communications 1997) 3 4 23
  4. Lymphotoxin beta, a novel member of the TNF family that forms a heteromeric complex with lymphotoxin on the cell surface. (PMID: 7916655) Browning JL … Ware CF (Cell 1993) 2 3 4
  5. Lymphotoxin and an associated 33-kDa glycoprotein are expressed on the surface of an activated human T cell hybridoma. (PMID: 1714477) Browning JL … Ware CF (Journal of immunology (Baltimore, Md. : 1950) 1991) 2 3 23

Products for LTB Gene