LTB

gene
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Also known as p33TNFSF3

Summary

LTB (lymphotoxin beta, HGNC:6711) is a protein-coding gene on chromosome 6p21.33, encoding Lymphotoxin-beta (Q06643). Cytokine that binds to LTBR/TNFRSF3.

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.

Source: NCBI Gene 4050 — RefSeq curated summary.

At a glance

  • GWAS associations: 22
  • Clinical variants (ClinVar): 25 total
  • Druggable target: yes
  • MANE Select transcript: NM_002341

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:6711
Approved symbolLTB
Namelymphotoxin beta
Location6p21.33
Locus typegene with protein product
StatusApproved
Aliasesp33, TNFSF3
Ensembl geneENSG00000227507
Ensembl biotypeprotein_coding
OMIM600978
Entrez4050

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 2 protein_coding, 1 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000429299, ENST00000446745, ENST00000482429, ENST00000483972

RefSeq mRNA: 2 — MANE Select: NM_002341 NM_002341, NM_009588

CCDS: CCDS4703, CCDS4704

Canonical transcript exons

ENST00000376117 — 0 exons

Expression profiles

Bgee: expression breadth ubiquitous, 130 present calls, max score 99.17.

FANTOM5 (CAGE): breadth broad, TPM avg 22.0049 / max 1652.0366, expressed in 431 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
7274818.6835380
727472.9218208
727460.3996109

Top tissues by expression

133 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
granulocyteCL:000009499.17gold quality
spleenUBERON:000210698.50gold quality
lymph nodeUBERON:000002998.14gold quality
bloodUBERON:000017898.07gold quality
vermiform appendixUBERON:000115497.29gold quality
leukocyteCL:000073889.96gold quality
mucosa of transverse colonUBERON:000499189.75gold quality
monocyteCL:000057689.05gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047387.44gold quality
bone marrowUBERON:000237184.94gold quality
small intestine Peyer’s patchUBERON:000345483.25gold quality
bone marrow cellCL:000209282.58gold quality
small intestineUBERON:000210882.42gold quality
duodenumUBERON:000211481.89gold quality
metanephros cortexUBERON:001053380.01gold quality
gall bladderUBERON:000211077.27gold quality
tonsilUBERON:000237276.89gold quality
rectumUBERON:000105274.59gold quality
upper lobe of left lungUBERON:000895274.35gold quality
right lobe of liverUBERON:000111474.06gold quality
colonic epitheliumUBERON:000039773.48gold quality
lungUBERON:000204872.75gold quality
cortex of kidneyUBERON:000122572.66gold quality
adult mammalian kidneyUBERON:000008272.44gold quality
liverUBERON:000210771.29gold quality
intestineUBERON:000016070.64gold quality
right lungUBERON:000216770.35gold quality
right coronary arteryUBERON:000162569.43gold quality
kidneyUBERON:000211369.38gold quality
transverse colonUBERON:000115769.17gold quality

Single-cell (SCXA)

Detected in 41 experiment(s), a significant marker in 34.

ExperimentMarker?Max mean expression
E-MTAB-6505yes5821.42
E-MTAB-9906yes3255.95
E-MTAB-7407yes2768.33
E-MTAB-8221yes2555.65
E-CURD-112yes1973.65
E-CURD-79yes1603.54
E-MTAB-6701yes1586.27
E-HCAD-10yes1535.66
E-MTAB-9467yes1162.79
E-HCAD-1yes1157.22
E-HCAD-4yes1106.04
E-GEOD-149689yes1086.78
E-HCAD-36yes1048.52
E-MTAB-7381yes1042.25
E-HCAD-24yes985.99

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): CREB1, CTCF, EGR1, ETS1, KLF3, MYC, NFAT5, NFKB1, NFKB, PAX3, RELA, SP1, YY1

miRNA regulators (miRDB)

1 targeting LTB, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-806399.9169.763146

Literature-anchored findings (GeneRIF, showing 18)

  • Heterotypic interaction between LTbeta-producing lymphocytes and responding fibroblast-like synoviocytes contributes to establishment of complex lymphoid microstructures. May be one element in susceptibility of synovial membrane to lymphoid organogenesis. (PMID:15248211)
  • The identification of IL-6 and IL-1beta as activators of LT-beta supports their involvement in LT-beta signaling in liver regeneration associated with chronic liver damage. (PMID:15910501)
  • Lymphotoxin (LT) beta receptor ligands LTalpha1 and -beta2 activate both the classical and noncanonical NF-kappa B pathways in human vascular endothelial cells and dermal microvascular endothelial cells in vitro. (PMID:18292573)
  • LT-Beta may play a role in rheumatoid arthritis disease pathogenesis by contributing to a more intense inflammatory reaction in the synovium (PMID:18379788)
  • blocking the lymphotoxin-beta receptor pathway results in ablation of the lymphoid organization in the NOD salivary glands and thus an improvement in salivary gland function. (PMID:19222863)
  • Overexpression of human TNF, lymphotoxin-alpha, and lymphotoxin-beta in mice (transgenic mice) resulted in thymic atropy. Chronic infections may promote thymic atrophy by upregulating lymphotoxin and TNF production. (PMID:19735075)
  • Sustained LT signaling represents a pathway involved in hepatitis-induced hepatocellular carcinoma. (PMID:19800575)
  • Soluble LTalphabeta in synovial fluid is associated with a proinflammatory cytokine milieu that contributes to synovitis in rheumatoid arthritis. (PMID:20356761)
  • Data show differential expression of interferon-gamma, TNFSF3, TNFSF10, TNFSF12 and PDGFbeta in CD8+, CD14+ and CD4+ cells. (PMID:21211989)
  • Findings provide evidence of additional complexity in the transcriptional regulation of LTB with implications for coordinate expression of genes in this important genomic locus. (PMID:21248773)
  • A strong association was found between several single nucleotide polymorphisms in the LTA/LTB/TNFalpha locus and Sjogren syndrome. (PMID:22294627)
  • The multifaceted character of lymphotoxin beta may be involved in inflammatory myopathies and muscular dystrophies. (PMID:22652080)
  • TNF is able to upregulate LT-beta expression in hepatic cells at the transcriptional level by the binding of NF-kappaB p50/p65 heterodimers and Ets1 to their respective sites in the LT-beta promoter. (PMID:22742857)
  • Combination of an EGFR tyrosine kinase inhibitor and a NF-kappaB inhibitor effectively suppressed cetuximab-resistant HNSCC and interfering with the EGFR-LTbeta interaction reverses resistance. (PMID:28196873)
  • Gastrointestinal Symptom Cluster is Associated With Epigenetic Regulation of Lymphotoxin Beta in Oncology Patients Receiving Chemotherapy. (PMID:35929442)
  • DNA methylation status of the SPHK1 and LTB genes underlies the clinicopathological diversity of non-alcoholic steatohepatitis-related hepatocellular carcinomas. (PMID:36348017)
  • Long Non-Coding RNA AL928768.3 Promotes Rheumatoid Arthritis Fibroblast-Like Synoviocytes Proliferation, Invasion and Inflammation, While Inhibits Apoptosis Via Activating Lymphotoxin Beta Mediated NF-kappaB Signaling Pathway. (PMID:37919527)
  • Lymphotoxin-beta promotes breast cancer bone metastasis colonization and osteolytic outgrowth. (PMID:39147874)

Cross-species orthologs

2 orthologs

OrganismSymbolGene ID
mus_musculusLtbENSMUSG00000024399
rattus_norvegicusLtbENSRNOG00000070531

Paralogs (8): CD40LG (ENSG00000102245), FASLG (ENSG00000117560), TNFSF11 (ENSG00000120659), TNFSF10 (ENSG00000121858), TNFSF14 (ENSG00000125735), TNFSF15 (ENSG00000181634), LTA (ENSG00000226979), TNF (ENSG00000232810)

Protein

Protein identifiers

Lymphotoxin-betaQ06643 (reviewed: Q06643)

Alternative names: Tumor necrosis factor C, Tumor necrosis factor ligand superfamily member 3

All UniProt accessions (2): Q06643, Q5STB2

UniProt curated annotations — full annotation on UniProt →

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.

Subunit / interactions. Heterotrimer of either two LTB and one LTA subunits or (less prevalent) one LTB and two LTA subunits.

Subcellular location. Membrane.

Tissue specificity. Spleen and thymus.

Similarity. Belongs to the tumor necrosis factor family.

Isoforms (2)

UniProt IDNamesCanonical?
Q06643-11yes
Q06643-22

RefSeq proteins (2): NP_002332, NP_033666 (=MANE)

Domains & families (InterPro)

IDNameType
IPR002961TNF_CFamily
IPR006052TNF_domDomain
IPR006053TNFFamily
IPR008983Tumour_necrosis_fac-like_domHomologous_superfamily
IPR021184TNF_CSConserved_site

Pfam: PF00229

UniProt features (18 total): sequence variant 5, mutagenesis site 4, topological domain 2, splice variant 2, chain 1, sequence conflict 1, transmembrane region 1, domain 1, glycosylation site 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
4MXWX-RAY DIFFRACTION3.6

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q06643-F177.880.49

Antibody-complex structures (SAbDab): 14MXW

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Glycosylation sites (1): 222

Mutagenesis-validated functional residues (4):

PositionPhenotype
108in subunit 1; reduces binding of lta(1)-ltb(2) to ltbr and abolishes ltbr-mediated nf-kappa-b signaling activation; when
109in subunit 1; reduces binding of lta(1)-ltb(2) to ltbr and abolishes ltbr-mediated nf-kappa-b signaling activation; when
142in subunit 1; reduces binding of lta(1)-ltb(2) to ltbr and abolishes ltbr-mediated nf-kappa-b signaling activation; when
170in subunit 2; no significant effect on binding of lta(1)-ltb(2) to ltbr and ltbr-mediated nf-kappa-b signaling activatio

Function

Pathways and Gene Ontology

Reactome pathways

2 pathways

IDPathway
R-HSA-5668541TNFR2 non-canonical NF-kB pathway
R-HSA-5676594TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway

MSigDB gene sets: 410 (showing top): CREL_01, MODULE_92, MCLACHLAN_DENTAL_CARIES_UP, GOBP_REGULATION_OF_PHOSPHORYLATION, REACTOME_CYTOKINE_SIGNALING_IN_IMMUNE_SYSTEM, TGCTGCT_MIR15A_MIR16_MIR15B_MIR195_MIR424_MIR497, MODULE_45, MODULE_64, GOBP_CANONICAL_NF_KAPPAB_SIGNAL_TRANSDUCTION, GOBP_ACTIVATION_OF_NF_KAPPAB_INDUCING_KINASE_ACTIVITY, GOBP_LYMPH_NODE_DEVELOPMENT, THEILGAARD_NEUTROPHIL_AT_SKIN_WOUND_DN, GOBP_EXTRINSIC_APOPTOTIC_SIGNALING_PATHWAY, GOBP_REGULATION_OF_TRANSFERASE_ACTIVITY, GOBP_POSITIVE_REGULATION_OF_CYTOKINE_PRODUCTION

GO Biological Process (12): immune response (GO:0006955), signal transduction (GO:0007165), cell surface receptor signaling pathway (GO:0007166), cell-cell signaling (GO:0007267), gene expression (GO:0010467), positive regulation of interleukin-12 production (GO:0032735), positive regulation of canonical NF-kappaB signal transduction (GO:0043123), skin development (GO:0043588), lymph node development (GO:0048535), positive regulation of extrinsic apoptotic signaling pathway (GO:2001238), cell communication (GO:0007154), signaling (GO:0023052)

GO Molecular Function (4): signaling receptor binding (GO:0005102), cytokine activity (GO:0005125), tumor necrosis factor receptor binding (GO:0005164), protein binding (GO:0005515)

GO Cellular Component (3): obsolete extracellular space (GO:0005615), plasma membrane (GO:0005886), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-2 pathways:

CategoryPathways
Cytokine Signaling in Immune system1
TNFR2 non-canonical NF-kB pathway1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cell communication2
cellular process2
signaling2
immune system process1
response to stimulus1
regulation of cellular process1
cellular response to stimulus1
signal transduction1
macromolecule biosynthetic process1
positive regulation of cytokine production1
interleukin-12 production1
regulation of interleukin-12 production1
canonical NF-kappaB signal transduction1
regulation of canonical NF-kappaB signal transduction1
positive regulation of intracellular signal transduction1
animal organ development1
hematopoietic or lymphoid organ development1
extrinsic apoptotic signaling pathway1
positive regulation of apoptotic signaling pathway1
regulation of extrinsic apoptotic signaling pathway1
regulation of biological process1
protein binding1
receptor ligand activity1
tumor necrosis factor receptor superfamily binding1
binding1
membrane1
cell periphery1
cellular anatomical structure1

Protein interactions and networks

STRING

0 interactions, top by confidence (×1000):

IntAct

7 interactions, top by confidence:

ABTypeScore
TNFSF14LTBpsi-mi:“MI:0915”(physical association)0.400
FCN1LTBpsi-mi:“MI:0915”(physical association)0.370
LTBgalKpsi-mi:“MI:0915”(physical association)0.000
LTBpsi-mi:“MI:0915”(physical association)0.000
LTBrapApsi-mi:“MI:0915”(physical association)0.000

BioGRID (5): LTB (Reconstituted Complex), LTB (Reconstituted Complex), LTB (Affinity Capture-Western), LTA (Reconstituted Complex), TNFRSF1A (Reconstituted Complex)

ESM2 similar proteins: A4FV98, A5D7B1, A5PK51, A6QLN9, A8MUP2, D3ZVU9, O15527, O35595, O75078, O95848, P57775, Q05B60, Q06643, Q14728, Q14CX5, Q1LZB9, Q27HK4, Q2T9T5, Q2TBS1, Q3UGX3, Q4R3I0, Q4V892, Q58CT4, Q5E9H2, Q5RCI5, Q5SUV1, Q5TM22, Q642A6, Q6IA17, Q6PCB0, Q6XQN6, Q862Z7, Q8N8L6, Q8R2R5, Q8R2Z5, Q8R366, Q8WUG5, Q95JH0, Q95JH2, Q969P0

Diamond homologs: O43557, O95150, P01374, P04924, P09225, P10154, P13296, P23383, P26445, P29553, P36939, P36940, P41047, P48023, P51743, P59684, P59693, P59694, P61125, P63306, P63307, P63308, Q06332, Q06599, Q06600, Q06643, Q19LH4, Q2MH05, Q5TM20, Q5TM22, Q5UBV8, Q5WR07, Q75N23, Q861W5, Q862Z7, Q8JFG3, Q8K3Y7, Q8MKG8, Q8WNR1, Q9BDN1

SIGNOR signaling

1 interactions.

AEffectBMechanism
LTB“up-regulates activity”LTBRbinding

Disease & clinical

Cancer significance

Clinical variants and AI predictions

ClinVar

25 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance12
Likely benign5
Benign2

Top pathogenic / likely-pathogenic (0)

SpliceAI

363 predictions. Top by Δscore:

VariantEffectΔscore
6:31581628:ACC:Aacceptor_gain0.9900
6:31581629:CC:Cacceptor_gain0.9900
6:31581629:CCC:Cacceptor_gain0.9900
6:31581630:CC:Cacceptor_gain0.9900
6:31581630:CCTGG:Cacceptor_loss0.9900
6:31581631:C:Aacceptor_loss0.9900
6:31581631:C:CCacceptor_gain0.9800
6:31581631:C:Tacceptor_gain0.9800
6:31581627:AACC:Aacceptor_gain0.9700
6:31581626:AAACC:Aacceptor_gain0.9600
6:31581808:TCTTA:Tdonor_loss0.9500
6:31581810:TTA:Tdonor_loss0.9500
6:31581811:TAC:Tdonor_loss0.9500
6:31581812:AC:Adonor_gain0.9500
6:31581813:CC:Cdonor_gain0.9500
6:31582248:CCACT:Cdonor_loss0.9500
6:31582249:CACTC:Cdonor_loss0.9500
6:31582250:ACTC:Adonor_loss0.9500
6:31582251:CT:Cdonor_loss0.9500
6:31582252:T:TCdonor_loss0.9500
6:31582253:CAC:Cdonor_loss0.9500
6:31582254:A:ATdonor_loss0.9500
6:31582255:CCAGT:Cdonor_gain0.9500
6:31581807:CTCTT:Cdonor_loss0.9400
6:31582247:GCCAC:Gdonor_loss0.9400
6:31582254:A:ACdonor_gain0.9400
6:31582255:C:CCdonor_gain0.9400
6:31581812:A:ACdonor_gain0.9300
6:31581813:C:CCdonor_gain0.9300
6:31581161:CGC:Cacceptor_gain0.9200

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1001191370 (6:31580937 G>A), RS1001470507 (6:31580302 C>T), RS1002865202 (6:31582561 T>G), RS1005203493 (6:31583963 C>T), RS1005671968 (6:31583514 C>G), RS1006622188 (6:31582134 A>G,T), RS1007933816 (6:31583669 G>A), RS1011274938 (6:31582953 T>G), RS1011723204 (6:31583279 A>G), RS1011927853 (6:31581399 T>A,C,G), RS1012527826 (6:31584150 A>G), RS1013185586 (6:31582927 C>G), RS1013486390 (6:31582580 G>A), RS1013789569 (6:31582295 C>G), RS1014107548 (6:31580777 T>C)

Disease associations

OMIM: gene MIM:600978 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

22 associations (top):

StudyTraitp-value
GCST000308_1AIDS progression3.000000e-19
GCST000738_5Neonatal lupus5.000000e-10
GCST000879_24Crohn’s disease4.000000e-11
GCST004131_25Inflammatory bowel disease2.000000e-31
GCST004133_79Ulcerative colitis5.000000e-65
GCST004521_114Autism spectrum disorder or schizophrenia3.000000e-17
GCST004521_117Autism spectrum disorder or schizophrenia3.000000e-15
GCST004521_126Autism spectrum disorder or schizophrenia2.000000e-10
GCST004521_209Autism spectrum disorder or schizophrenia5.000000e-16
GCST004521_211Autism spectrum disorder or schizophrenia5.000000e-15
GCST004521_213Autism spectrum disorder or schizophrenia5.000000e-13
GCST004521_265Autism spectrum disorder or schizophrenia7.000000e-14
GCST004521_3Autism spectrum disorder or schizophrenia2.000000e-15
GCST004521_70Autism spectrum disorder or schizophrenia8.000000e-20
GCST004521_81Autism spectrum disorder or schizophrenia1.000000e-14
GCST008916_111Asthma2.000000e-14
GCST008916_114Asthma1.000000e-09
GCST008916_30Asthma1.000000e-09
GCST008917_2Asthma (childhood onset)4.000000e-07
GCST008921_1Asthma and major depressive disorder2.000000e-16
GCST010725_43Malaria5.000000e-07
GCST010725_62Malaria3.000000e-06

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (2): CHEMBL3713022 (SINGLE PROTEIN), CHEMBL3833421 (PROTEIN COMPLEX)

PharmGKB: 1 entry (VIP=true, CPIC=false)

PharmGKB clinical annotations

1 annotations.

VariantTypeLevelDrugsPhenotypes
rs3093726Toxicity3abacavirDrug Hypersensitivity

PharmGKB variants

1 variants.

VariantGenesLevelScore#Clin annotsDrugs
rs3093726LST1, LTA, LTB, TNF30.001abacavir

CTD chemical–gene interactions

70 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Benzo(a)pyrenedecreases expression, increases expression, increases methylation4
trichostatin Aaffects cotreatment, increases expression3
1-nitropyreneincreases expression2
Air Pollutantsincreases abundance, increases expression, decreases expression2
Arsenicaffects expression, affects cotreatment, decreases expression2
Lipopolysaccharidesaffects cotreatment, increases expression2
Silicon Dioxideincreases expression2
Particulate Matterincreases abundance, increases expression, decreases expression2
GSK-J4decreases expression1
triphenyl phosphateaffects expression1
sanguinarineaffects cotreatment, increases expression1
ethyl-p-hydroxybenzoateincreases expression1
nickel chlorideincreases expression1
3,4,5,3’,4’-pentachlorobiphenylincreases expression1
perfluorooctanoic aciddecreases expression1
3-nitrofluorantheneincreases expression1
cobalt oxidedecreases expression1
di-n-butylphosphoric acidaffects expression1
perfluorooctane sulfonic aciddecreases expression1
perfluoro-n-nonanoic aciddecreases expression1
lipopolysaccharide, E. coli O26-B6increases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression1
perfluorohexanesulfonic aciddecreases expression1
beta-hydroxy simvastatin aciddecreases expression1
ICG 001increases expression1
ormosilaffects binding, decreases expression1
dorsomorphinaffects cotreatment, increases expression1
PF 3758309increases expression1
(+)-JQ1 compounddecreases expression1
Aripiprazoleaffects cotreatment, increases expression1

ChEMBL screening assays

1 unique, capped per target: 1 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL4688320BindingInhibition of LTbeta (unknown origin)Biologic-like In Vivo Efficacy with Small Molecule Inhibitors of TNFα Identified Using Scaffold Hopping and Structure-Based Drug Design Approaches. — J Med Chem

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.

  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): AIDS, neonatal lupus erythematosus