LTB
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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
| Field | Value |
|---|---|
| HGNC ID | HGNC:6711 |
| Approved symbol | LTB |
| Name | lymphotoxin beta |
| Location | 6p21.33 |
| Locus type | gene with protein product |
| Status | Approved |
| Aliases | p33, TNFSF3 |
| Ensembl gene | ENSG00000227507 |
| Ensembl biotype | protein_coding |
| OMIM | 600978 |
| Entrez | 4050 |
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 ID | TPM avg | Samples expressed |
|---|---|---|
| 72748 | 18.6835 | 380 |
| 72747 | 2.9218 | 208 |
| 72746 | 0.3996 | 109 |
Top tissues by expression
133 total, by Bgee expression score (0-100, higher = more expressed):
| Tissue | Anatomy ID | Expression score | Quality |
|---|---|---|---|
| granulocyte | CL:0000094 | 99.17 | gold quality |
| spleen | UBERON:0002106 | 98.50 | gold quality |
| lymph node | UBERON:0000029 | 98.14 | gold quality |
| blood | UBERON:0000178 | 98.07 | gold quality |
| vermiform appendix | UBERON:0001154 | 97.29 | gold quality |
| leukocyte | CL:0000738 | 89.96 | gold quality |
| mucosa of transverse colon | UBERON:0004991 | 89.75 | gold quality |
| monocyte | CL:0000576 | 89.05 | gold quality |
| male germ line stem cell (sensu Vertebrata) in testis | CL:0000089 ∩ UBERON:0000473 | 87.44 | gold quality |
| bone marrow | UBERON:0002371 | 84.94 | gold quality |
| small intestine Peyer’s patch | UBERON:0003454 | 83.25 | gold quality |
| bone marrow cell | CL:0002092 | 82.58 | gold quality |
| small intestine | UBERON:0002108 | 82.42 | gold quality |
| duodenum | UBERON:0002114 | 81.89 | gold quality |
| metanephros cortex | UBERON:0010533 | 80.01 | gold quality |
| gall bladder | UBERON:0002110 | 77.27 | gold quality |
| tonsil | UBERON:0002372 | 76.89 | gold quality |
| rectum | UBERON:0001052 | 74.59 | gold quality |
| upper lobe of left lung | UBERON:0008952 | 74.35 | gold quality |
| right lobe of liver | UBERON:0001114 | 74.06 | gold quality |
| colonic epithelium | UBERON:0000397 | 73.48 | gold quality |
| lung | UBERON:0002048 | 72.75 | gold quality |
| cortex of kidney | UBERON:0001225 | 72.66 | gold quality |
| adult mammalian kidney | UBERON:0000082 | 72.44 | gold quality |
| liver | UBERON:0002107 | 71.29 | gold quality |
| intestine | UBERON:0000160 | 70.64 | gold quality |
| right lung | UBERON:0002167 | 70.35 | gold quality |
| right coronary artery | UBERON:0001625 | 69.43 | gold quality |
| kidney | UBERON:0002113 | 69.38 | gold quality |
| transverse colon | UBERON:0001157 | 69.17 | gold quality |
Single-cell (SCXA)
Detected in 41 experiment(s), a significant marker in 34.
| Experiment | Marker? | Max mean expression |
|---|---|---|
| E-MTAB-6505 | yes | 5821.42 |
| E-MTAB-9906 | yes | 3255.95 |
| E-MTAB-7407 | yes | 2768.33 |
| E-MTAB-8221 | yes | 2555.65 |
| E-CURD-112 | yes | 1973.65 |
| E-CURD-79 | yes | 1603.54 |
| E-MTAB-6701 | yes | 1586.27 |
| E-HCAD-10 | yes | 1535.66 |
| E-MTAB-9467 | yes | 1162.79 |
| E-HCAD-1 | yes | 1157.22 |
| E-HCAD-4 | yes | 1106.04 |
| E-GEOD-149689 | yes | 1086.78 |
| E-HCAD-36 | yes | 1048.52 |
| E-MTAB-7381 | yes | 1042.25 |
| E-HCAD-24 | yes | 985.99 |
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):
| miRNA | Max score | Avg score | miRNA target_count |
|---|---|---|---|
| HSA-MIR-8063 | 99.91 | 69.76 | 3146 |
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
| Organism | Symbol | Gene ID |
|---|---|---|
| mus_musculus | Ltb | ENSMUSG00000024399 |
| rattus_norvegicus | Ltb | ENSRNOG00000070531 |
Paralogs (8): CD40LG (ENSG00000102245), FASLG (ENSG00000117560), TNFSF11 (ENSG00000120659), TNFSF10 (ENSG00000121858), TNFSF14 (ENSG00000125735), TNFSF15 (ENSG00000181634), LTA (ENSG00000226979), TNF (ENSG00000232810)
Protein
Protein identifiers
Lymphotoxin-beta — Q06643 (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 ID | Names | Canonical? |
|---|---|---|
| Q06643-1 | 1 | yes |
| Q06643-2 | 2 |
RefSeq proteins (2): NP_002332, NP_033666 (=MANE)
Domains & families (InterPro)
| ID | Name | Type |
|---|---|---|
| IPR002961 | TNF_C | Family |
| IPR006052 | TNF_dom | Domain |
| IPR006053 | TNF | Family |
| IPR008983 | Tumour_necrosis_fac-like_dom | Homologous_superfamily |
| IPR021184 | TNF_CS | Conserved_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.
| PDB | Method | Resolution (Å) |
|---|---|---|
| 4MXW | X-RAY DIFFRACTION | 3.6 |
Predicted structure (AlphaFold)
| Model | pLDDT | Fraction very-high |
|---|---|---|
| AF-Q06643-F1 | 77.88 | 0.49 |
Antibody-complex structures (SAbDab): 1 — 4MXW
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):
| Position | Phenotype |
|---|---|
| 108 | in subunit 1; reduces binding of lta(1)-ltb(2) to ltbr and abolishes ltbr-mediated nf-kappa-b signaling activation; when |
| 109 | in subunit 1; reduces binding of lta(1)-ltb(2) to ltbr and abolishes ltbr-mediated nf-kappa-b signaling activation; when |
| 142 | in subunit 1; reduces binding of lta(1)-ltb(2) to ltbr and abolishes ltbr-mediated nf-kappa-b signaling activation; when |
| 170 | in 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
| ID | Pathway |
|---|---|
| R-HSA-5668541 | TNFR2 non-canonical NF-kB pathway |
| R-HSA-5676594 | TNF 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:
| Category | Pathways |
|---|---|
| Cytokine Signaling in Immune system | 1 |
| TNFR2 non-canonical NF-kB pathway | 1 |
GO top-level categories
Rollup of top GO terms by namespace:
| Category | Terms |
|---|---|
| cell communication | 2 |
| cellular process | 2 |
| signaling | 2 |
| immune system process | 1 |
| response to stimulus | 1 |
| regulation of cellular process | 1 |
| cellular response to stimulus | 1 |
| signal transduction | 1 |
| macromolecule biosynthetic process | 1 |
| positive regulation of cytokine production | 1 |
| interleukin-12 production | 1 |
| regulation of interleukin-12 production | 1 |
| canonical NF-kappaB signal transduction | 1 |
| regulation of canonical NF-kappaB signal transduction | 1 |
| positive regulation of intracellular signal transduction | 1 |
| animal organ development | 1 |
| hematopoietic or lymphoid organ development | 1 |
| extrinsic apoptotic signaling pathway | 1 |
| positive regulation of apoptotic signaling pathway | 1 |
| regulation of extrinsic apoptotic signaling pathway | 1 |
| regulation of biological process | 1 |
| protein binding | 1 |
| receptor ligand activity | 1 |
| tumor necrosis factor receptor superfamily binding | 1 |
| binding | 1 |
| membrane | 1 |
| cell periphery | 1 |
| cellular anatomical structure | 1 |
Protein interactions and networks
STRING
0 interactions, top by confidence (×1000):
IntAct
7 interactions, top by confidence:
| A | B | Type | Score |
|---|---|---|---|
| TNFSF14 | LTB | psi-mi:“MI:0915”(physical association) | 0.400 |
| FCN1 | LTB | psi-mi:“MI:0915”(physical association) | 0.370 |
| LTB | galK | psi-mi:“MI:0915”(physical association) | 0.000 |
| LTB | psi-mi:“MI:0915”(physical association) | 0.000 | |
| LTB | rapA | psi-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.
| A | Effect | B | Mechanism |
|---|---|---|---|
| LTB | “up-regulates activity” | LTBR | binding |
Disease & clinical
Cancer significance
Clinical variants and AI predictions
ClinVar
25 variants total. Per-class counts are floors (≥ shown; pagination cap):
| Classification | Count (floor) |
|---|---|
| Pathogenic | 0 |
| Likely pathogenic | 0 |
| Uncertain significance | 12 |
| Likely benign | 5 |
| Benign | 2 |
Top pathogenic / likely-pathogenic (0)
SpliceAI
363 predictions. Top by Δscore:
| Variant | Effect | Δscore |
|---|---|---|
| 6:31581628:ACC:A | acceptor_gain | 0.9900 |
| 6:31581629:CC:C | acceptor_gain | 0.9900 |
| 6:31581629:CCC:C | acceptor_gain | 0.9900 |
| 6:31581630:CC:C | acceptor_gain | 0.9900 |
| 6:31581630:CCTGG:C | acceptor_loss | 0.9900 |
| 6:31581631:C:A | acceptor_loss | 0.9900 |
| 6:31581631:C:CC | acceptor_gain | 0.9800 |
| 6:31581631:C:T | acceptor_gain | 0.9800 |
| 6:31581627:AACC:A | acceptor_gain | 0.9700 |
| 6:31581626:AAACC:A | acceptor_gain | 0.9600 |
| 6:31581808:TCTTA:T | donor_loss | 0.9500 |
| 6:31581810:TTA:T | donor_loss | 0.9500 |
| 6:31581811:TAC:T | donor_loss | 0.9500 |
| 6:31581812:AC:A | donor_gain | 0.9500 |
| 6:31581813:CC:C | donor_gain | 0.9500 |
| 6:31582248:CCACT:C | donor_loss | 0.9500 |
| 6:31582249:CACTC:C | donor_loss | 0.9500 |
| 6:31582250:ACTC:A | donor_loss | 0.9500 |
| 6:31582251:CT:C | donor_loss | 0.9500 |
| 6:31582252:T:TC | donor_loss | 0.9500 |
| 6:31582253:CAC:C | donor_loss | 0.9500 |
| 6:31582254:A:AT | donor_loss | 0.9500 |
| 6:31582255:CCAGT:C | donor_gain | 0.9500 |
| 6:31581807:CTCTT:C | donor_loss | 0.9400 |
| 6:31582247:GCCAC:G | donor_loss | 0.9400 |
| 6:31582254:A:AC | donor_gain | 0.9400 |
| 6:31582255:C:CC | donor_gain | 0.9400 |
| 6:31581812:A:AC | donor_gain | 0.9300 |
| 6:31581813:C:CC | donor_gain | 0.9300 |
| 6:31581161:CGC:C | acceptor_gain | 0.9200 |
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):
| Study | Trait | p-value |
|---|---|---|
| GCST000308_1 | AIDS progression | 3.000000e-19 |
| GCST000738_5 | Neonatal lupus | 5.000000e-10 |
| GCST000879_24 | Crohn’s disease | 4.000000e-11 |
| GCST004131_25 | Inflammatory bowel disease | 2.000000e-31 |
| GCST004133_79 | Ulcerative colitis | 5.000000e-65 |
| GCST004521_114 | Autism spectrum disorder or schizophrenia | 3.000000e-17 |
| GCST004521_117 | Autism spectrum disorder or schizophrenia | 3.000000e-15 |
| GCST004521_126 | Autism spectrum disorder or schizophrenia | 2.000000e-10 |
| GCST004521_209 | Autism spectrum disorder or schizophrenia | 5.000000e-16 |
| GCST004521_211 | Autism spectrum disorder or schizophrenia | 5.000000e-15 |
| GCST004521_213 | Autism spectrum disorder or schizophrenia | 5.000000e-13 |
| GCST004521_265 | Autism spectrum disorder or schizophrenia | 7.000000e-14 |
| GCST004521_3 | Autism spectrum disorder or schizophrenia | 2.000000e-15 |
| GCST004521_70 | Autism spectrum disorder or schizophrenia | 8.000000e-20 |
| GCST004521_81 | Autism spectrum disorder or schizophrenia | 1.000000e-14 |
| GCST008916_111 | Asthma | 2.000000e-14 |
| GCST008916_114 | Asthma | 1.000000e-09 |
| GCST008916_30 | Asthma | 1.000000e-09 |
| GCST008917_2 | Asthma (childhood onset) | 4.000000e-07 |
| GCST008921_1 | Asthma and major depressive disorder | 2.000000e-16 |
| GCST010725_43 | Malaria | 5.000000e-07 |
| GCST010725_62 | Malaria | 3.000000e-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.
| Variant | Type | Level | Drugs | Phenotypes |
|---|---|---|---|---|
| rs3093726 | Toxicity | 3 | abacavir | Drug Hypersensitivity |
PharmGKB variants
1 variants.
| Variant | Genes | Level | Score | #Clin annots | Drugs |
|---|---|---|---|---|---|
| rs3093726 | LST1, LTA, LTB, TNF | 3 | 0.00 | 1 | abacavir |
CTD chemical–gene interactions
70 total (human), top 30 by PubMed support.
| Chemical | Actions (top 5) | PubMed papers |
|---|---|---|
| Benzo(a)pyrene | decreases expression, increases expression, increases methylation | 4 |
| trichostatin A | affects cotreatment, increases expression | 3 |
| 1-nitropyrene | increases expression | 2 |
| Air Pollutants | increases abundance, increases expression, decreases expression | 2 |
| Arsenic | affects expression, affects cotreatment, decreases expression | 2 |
| Lipopolysaccharides | affects cotreatment, increases expression | 2 |
| Silicon Dioxide | increases expression | 2 |
| Particulate Matter | increases abundance, increases expression, decreases expression | 2 |
| GSK-J4 | decreases expression | 1 |
| triphenyl phosphate | affects expression | 1 |
| sanguinarine | affects cotreatment, increases expression | 1 |
| ethyl-p-hydroxybenzoate | increases expression | 1 |
| nickel chloride | increases expression | 1 |
| 3,4,5,3’,4’-pentachlorobiphenyl | increases expression | 1 |
| perfluorooctanoic acid | decreases expression | 1 |
| 3-nitrofluoranthene | increases expression | 1 |
| cobalt oxide | decreases expression | 1 |
| di-n-butylphosphoric acid | affects expression | 1 |
| perfluorooctane sulfonic acid | decreases expression | 1 |
| perfluoro-n-nonanoic acid | decreases expression | 1 |
| lipopolysaccharide, E. coli O26-B6 | increases expression | 1 |
| 4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide | affects cotreatment, increases expression | 1 |
| perfluorohexanesulfonic acid | decreases expression | 1 |
| beta-hydroxy simvastatin acid | decreases expression | 1 |
| ICG 001 | increases expression | 1 |
| ormosil | affects binding, decreases expression | 1 |
| dorsomorphin | affects cotreatment, increases expression | 1 |
| PF 3758309 | increases expression | 1 |
| (+)-JQ1 compound | decreases expression | 1 |
| Aripiprazole | affects cotreatment, increases expression | 1 |
ChEMBL screening assays
1 unique, capped per target: 1 binding
Representative assays (with source publication via chembl_document):
| Assay ID | Type | Description | Source paper |
|---|---|---|---|
| CHEMBL4688320 | Binding | Inhibition 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.
Related Atlas pages
- 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