LTBR (lymphotoxin beta receptor)

Gene

• Entrez ID: 4055
• Gene name: Lymphotoxin beta receptor
• Gene symbol: LTBR
• Synonyms (NCBI Gene): D12S370, LT-BETA-R, TNF-R-III, TNFCR, TNFR-RP, TNFR2-RP, TNFR3, TNFRSF3
• Chromosome: 12
• Chromosome location: 12p13.31
• Summary: 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 t

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT027696	hsa-miR-98-5p	Microarray	19088304
MIRT641725	hsa-miR-9500	HITS-CLIP	23824327
MIRT641724	hsa-miR-454-5p	HITS-CLIP	23824327
MIRT641723	hsa-miR-4533	HITS-CLIP	23824327
MIRT641722	hsa-miR-4747-5p	HITS-CLIP	23824327
MIRT641721	hsa-miR-5196-5p	HITS-CLIP	23824327
MIRT641720	hsa-miR-6883-3p	HITS-CLIP	23824327
MIRT734365	hsa-miR-29a-3p	Luciferase reporter assay, Western blotting	33602223
MIRT641725	hsa-miR-9500	HITS-CLIP	23824327
MIRT641724	hsa-miR-454-5p	HITS-CLIP	23824327
MIRT641723	hsa-miR-4533	HITS-CLIP	23824327
MIRT641722	hsa-miR-4747-5p	HITS-CLIP	23824327
MIRT641721	hsa-miR-5196-5p	HITS-CLIP	23824327
MIRT641720	hsa-miR-6883-3p	HITS-CLIP	23824327
MIRT1122183	hsa-miR-1182	CLIP-seq
MIRT1122184	hsa-miR-1255a	CLIP-seq
MIRT1122185	hsa-miR-1255b	CLIP-seq
MIRT1122186	hsa-miR-1273g	CLIP-seq
MIRT1122187	hsa-miR-127-5p	CLIP-seq
MIRT1122188	hsa-miR-1909	CLIP-seq
MIRT1122189	hsa-miR-2110	CLIP-seq
MIRT1122190	hsa-miR-29a	CLIP-seq
MIRT1122191	hsa-miR-29b	CLIP-seq
MIRT1122192	hsa-miR-29c	CLIP-seq
MIRT1122193	hsa-miR-3150a-3p	CLIP-seq
MIRT1122194	hsa-miR-3190	CLIP-seq
MIRT1122195	hsa-miR-338-5p	CLIP-seq
MIRT1122196	hsa-miR-3616-5p	CLIP-seq
MIRT1122197	hsa-miR-3647-5p	CLIP-seq
MIRT1122198	hsa-miR-3663-3p	CLIP-seq
MIRT1122199	hsa-miR-3911	CLIP-seq
MIRT1122200	hsa-miR-3921	CLIP-seq
MIRT1122201	hsa-miR-409-5p	CLIP-seq
MIRT1122202	hsa-miR-4450	CLIP-seq
MIRT1122203	hsa-miR-4453	CLIP-seq
MIRT1122204	hsa-miR-4538	CLIP-seq
MIRT1122205	hsa-miR-455-3p	CLIP-seq
MIRT1122206	hsa-miR-4653-5p	CLIP-seq
MIRT1122207	hsa-miR-4795-5p	CLIP-seq
MIRT1122208	hsa-miR-573	CLIP-seq
MIRT1122209	hsa-miR-593	CLIP-seq
MIRT1122210	hsa-miR-595	CLIP-seq
MIRT1122183	hsa-miR-1182	CLIP-seq
MIRT2034530	hsa-miR-1250	CLIP-seq
MIRT1122186	hsa-miR-1273g	CLIP-seq
MIRT1122188	hsa-miR-1909	CLIP-seq
MIRT2034531	hsa-miR-1910	CLIP-seq
MIRT1122195	hsa-miR-338-5p	CLIP-seq
MIRT1122201	hsa-miR-409-5p	CLIP-seq
MIRT2034532	hsa-miR-4264	CLIP-seq
MIRT2034533	hsa-miR-4469	CLIP-seq
MIRT1122205	hsa-miR-455-3p	CLIP-seq
MIRT2034534	hsa-miR-4655-3p	CLIP-seq
MIRT2034535	hsa-miR-4777-3p	CLIP-seq
MIRT1122195	hsa-miR-338-5p	CLIP-seq
MIRT2264990	hsa-miR-4659a-5p	CLIP-seq
MIRT2264991	hsa-miR-4659b-5p	CLIP-seq
MIRT2264992	hsa-miR-4776-3p	CLIP-seq
MIRT2390395	hsa-miR-1915	CLIP-seq
MIRT2390396	hsa-miR-4323	CLIP-seq

Transcription factors

Transcription factor	Regulation	Reference
WWTR1	Activation	22470139

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005515	Function	Protein binding	IPI	8995654, 12393901, 20732415, 26977880, 28514442, 29329668, 32296183, 33961781
GO:0005794	Component	Golgi apparatus	IDA
GO:0005886	Component	Plasma membrane	IEA
GO:0005886	Component	Plasma membrane	TAS
GO:0006915	Process	Apoptotic process	IEA
GO:0006955	Process	Immune response	IEA
GO:0007165	Process	Signal transduction	TAS	8171323
GO:0016020	Component	Membrane	IEA
GO:0031625	Function	Ubiquitin protein ligase binding	IBA
GO:0031625	Function	Ubiquitin protein ligase binding	IPI	11279055
GO:0042802	Function	Identical protein binding	IPI	20732415
GO:0043011	Process	Myeloid dendritic cell differentiation	IEA
GO:0043123	Process	Positive regulation of canonical NF-kappaB signal transduction	IBA
GO:0043123	Process	Positive regulation of canonical NF-kappaB signal transduction	IEA
GO:0043123	Process	Positive regulation of canonical NF-kappaB signal transduction	IEP	12761501
GO:0046330	Process	Positive regulation of JNK cascade	IMP	20732415
GO:0048534	Process	Hematopoietic or lymphoid organ development	IEA
GO:0071260	Process	Cellular response to mechanical stimulus	IEP
GO:2001238	Process	Positive regulation of extrinsic apoptotic signaling pathway	IMP	20732415

Other IDs

• MIM: 600979
• HGNC: 6718
• e!Ensembl: ENSG00000111321

Protein

• UniProt ID: P36941
• Protein name: Tumor necrosis factor receptor superfamily member 3 (Lymphotoxin-beta receptor) (Tumor necrosis factor C receptor) (Tumor necrosis factor receptor 2-related protein) (Tumor necrosis factor receptor type III) (TNF-RIII) (TNFR-III)
• Protein function: Receptor for the heterotrimeric lymphotoxin containing LTA and LTB, and for TNFS14/LIGHT (PubMed:24248355). Activates NF-kappa-B signaling pathway upon stimulation with lymphotoxin (LTA(1)-LTB(2)) (PubMed:24248355). Promotes apoptosis via TRAF3
• PDB: 1RF3, 4MXW
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00020	TNFR_c6	43 → 80	TNFR/NGFR cysteine-rich region	Domain
  PF00020	TNFR_c6	83 → 124	TNFR/NGFR cysteine-rich region	Domain
  PF00020	TNFR_c6	163 → 210	TNFR/NGFR cysteine-rich region	Domain

• Sequence:

  MLLPWATSAPGLAWGPLVLGLFGLLAASQPQAVPPYASENQTCRDQEKEYYEPQHRICCS
  RCPPGTYVSAKCSRIRDTVCATCAENSYNEHWNYLTICQLCRPCDPVMGLEEIAPCTSKR
  KTQCRCQPGMFCAAWALECTHCELLSDCPPGTEAELKDEVGKGNNHCVPCKAGHFQNTSS
  PSARCQPHTRCENQGLVEAAPGTAQSDTTCKNPLEPLPPEMSGTMLMLAVLLPLAFFLLL
  ATVFSCIWKSHPSLCRKLGSLLKRRPQGEGPNPVAGSWEPPKAHPYFPDLVQPLLPISGD
  VSPVSTGLPAAPVLEAGVPQQQSPLDLTREPQLEPGEQSQVAHGTNGIHVTGGSMTITGN
  IYIYNGPVLGGPPGPGDLPATPEPPYPIPEEGDPGPPGLSTPHQEDGKAWHLAETEHCGA
  TPSNRGPRNQFITHD

• Sequence length: 435

Pathways

KEGG:

Cytokine-cytokine receptor interaction
Viral protein interaction with cytokine and cytokine receptor
NF-kappa B signaling pathway
HIF-1 signaling pathway
Intestinal immune network for IgA production
Human T-cell leukemia virus 1 infection
Viral carcinogenesis

Reactome:

TNFR2 non-canonical NF-kB pathway
TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
ANKYLOSING SPONDYLITIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
BRONCHIECTASIS WITH OR WITHOUT ELEVATED SWEAT CHLORIDE 2	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CELIAC DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CHRONIC OBSTRUCTIVE PULMONARY DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CROHN'S DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DISORDER OF PHARYNX	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
INFLAMMATORY BOWEL DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of urinary bladder	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MULTIPLE SCLEROSIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OLIGOARTICULAR JUVENILE IDIOPATHIC ARTHRITIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
POLYARTICULAR JUVENILE IDIOPATHIC ARTHRITIS, RHEUMATOID FACTOR NEGATIVE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PRIMARY BILIARY CIRRHOSIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PSEUDOHYPOALDOSTERONISM, TYPE IB1, AUTOSOMAL RECESSIVE	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PSORIASIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
RESPIRATORY SYSTEM DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SCLEROSING CHOLANGITIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SYSTEMIC JUVENILE IDIOPATHIC ARTHRITIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TONSILLITIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ULCERATIVE COLITIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
UPPER RESPIRATORY TRACT DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Acute intermittent porphyria	Intermittent Porphyria	BEFREE	22863765, 24508087		★☆☆☆☆ Found in Text Mining only
Amyotrophic Lateral Sclerosis	Amyotrophic Lateral Sclerosis	BEFREE	21072055		★☆☆☆☆ Found in Text Mining only
Ankylosing spondylitis	Ankylosing Spondylitis	BEFREE	21743469		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ankylosing spondylitis	Ankylosing Spondylitis	GWASCAT_DG	23749187		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Arthritis Rheumatoid	Rheumatoid arthritis	Pubtator	18353171, 30159339	Associate	★☆☆☆☆ Found in Text Mining only
Asthma	Asthma	Pubtator	23804543	Associate	★☆☆☆☆ Found in Text Mining only
Autoimmune Diseases	Autoimmune Diseases	BEFREE	16272360		★☆☆☆☆ Found in Text Mining only
Autoimmune Diseases	Autoimmune disease	Pubtator	26782510, 30159339	Associate	★☆☆☆☆ Found in Text Mining only
Benign Prostatic Hyperplasia	Benign Prostatic Hyperplasia	BEFREE	26782510		★☆☆☆☆ Found in Text Mining only
Bladder Neoplasm	Bladder Neoplasm	BEFREE	25369740		★☆☆☆☆ Found in Text Mining only
Breast Carcinoma	Breast Carcinoma	BEFREE	26317411		★☆☆☆☆ Found in Text Mining only
Breast Neoplasms	Breast neoplasm	Pubtator	26317411	Associate	★☆☆☆☆ Found in Text Mining only
Carcinoma Hepatocellular	Hepatocellular carcinoma	Pubtator	37366426	Associate	★☆☆☆☆ Found in Text Mining only
Carcinoma of bladder	Bladder carcinoma	BEFREE	25369740		★☆☆☆☆ Found in Text Mining only
Celiac Disease	Celiac disease	BEFREE	31591516		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Celiac Disease	Celiac disease	Pubtator	31591516	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Colitis	Colitis	BEFREE	30524422		★☆☆☆☆ Found in Text Mining only
Colorectal Neoplasms	Colorectal neoplasm	Pubtator	34541005	Associate	★☆☆☆☆ Found in Text Mining only
Crohn Disease	Crohn Disease	GWASCAT_DG	26192919, 28067908		★☆☆☆☆ Found in Text Mining only
Cystitis	Cystitis	Pubtator	25369740	Stimulate	★☆☆☆☆ Found in Text Mining only
Delirium	Delirium	Pubtator	37156856	Associate	★☆☆☆☆ Found in Text Mining only
Diabetes	Diabetes	BEFREE	16934497		★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus	Diabetes Mellitus	BEFREE	16934497		★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus, Non-Insulin-Dependent	Diabetes Mellitus	BEFREE	27421726		★☆☆☆☆ Found in Text Mining only
Dyslipidemias	Dyslipidemias	BEFREE	17431181		★☆☆☆☆ Found in Text Mining only
Eosinophilia	Eosinophilia	BEFREE	21499267		★☆☆☆☆ Found in Text Mining only
Eosinophilic Esophagitis	Eosinophilia	Pubtator	32712105	Associate	★☆☆☆☆ Found in Text Mining only
Gastritis	Gastritis	BEFREE	27196595, 31065023		★☆☆☆☆ Found in Text Mining only
Glioblastoma	Glioblastoma	BEFREE	28404866		★☆☆☆☆ Found in Text Mining only
Glioblastoma Multiforme	Glioblastoma	BEFREE	28404866		★☆☆☆☆ Found in Text Mining only
Granulomatous Disease Chronic	Granulomatous disease	Pubtator	12000723	Associate	★☆☆☆☆ Found in Text Mining only
Head and Neck Carcinoma	Head And Neck Carcinoma	BEFREE	30488488		★☆☆☆☆ Found in Text Mining only
Head and Neck Neoplasms	Head and neck neoplasm	Pubtator	30488488	Associate	★☆☆☆☆ Found in Text Mining only
Hyperglycemia	Hyperglycemia	BEFREE	29330151		★☆☆☆☆ Found in Text Mining only
Hypopigmentation disorder	Hypopigmentation Disorder	BEFREE	29730385		★☆☆☆☆ Found in Text Mining only
IGA Glomerulonephritis	Glomerulonephritis	BEFREE	22417320		★☆☆☆☆ Found in Text Mining only
Intestinal Diseases	Intestinal Diseases	BEFREE	15944326		★☆☆☆☆ Found in Text Mining only
Juvenile pauciarticular chronic arthritis	Pauciarticular chronic arthritis	GWASCAT_DG	23603761		★☆☆☆☆ Found in Text Mining only
Juvenile-Onset Still Disease	Still Disease	GWASCAT_DG	23603761		★☆☆☆☆ Found in Text Mining only
Leukemia	Leukemia	Pubtator	37951201	Associate	★☆☆☆☆ Found in Text Mining only
Leukemia Myeloid Acute	Myeloid leukemia	Pubtator	11264180	Associate	★☆☆☆☆ Found in Text Mining only
Liver carcinoma	Liver carcinoma	BEFREE	28575727		★☆☆☆☆ Found in Text Mining only
Lung Neoplasms	Lung neoplasms	Pubtator	9817170	Associate	★☆☆☆☆ Found in Text Mining only
Lupus Erythematosus Systemic	Systemic lupus erythematosus	Pubtator	30159339	Associate	★☆☆☆☆ Found in Text Mining only
Lymphatic Metastasis	Lymphatic metastasis	Pubtator	25369740	Associate	★☆☆☆☆ Found in Text Mining only
Malignant Head and Neck Neoplasm	Head and neck cancer	BEFREE	30488488		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of breast	Breast Cancer	BEFREE	26317411		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of prostate	Prostate cancer	BEFREE	20603617		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of urinary bladder	Urinary bladder cancer	BEFREE	25369740		★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	19701890, 20117833, 24014111, 30488488, 30837284		★☆☆☆☆ Found in Text Mining only
melanoma	Melanoma	LHGDN	18347013		★☆☆☆☆ Found in Text Mining only
Melanoma	Melanoma	Pubtator	18347013	Associate	★☆☆☆☆ Found in Text Mining only
Multiple Myeloma	Multiple myeloma	Pubtator	17692805	Associate	★☆☆☆☆ Found in Text Mining only
Multiple Sclerosis	Multiple sclerosis	Pubtator	30479356	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MYD88 Deficiency	MYD88 Deficiency	BEFREE	30250175		★☆☆☆☆ Found in Text Mining only
Nasopharyngeal carcinoma	Nasopharyngeal Carcinoma	BEFREE	19718711		★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	19701890, 19718711, 20460520, 27196595, 28404866		★☆☆☆☆ Found in Text Mining only
Non-Small Cell Lung Carcinoma	Lung carcinoma	BEFREE	31137630		★☆☆☆☆ Found in Text Mining only
Oligoarticular Juvenile Idiopathic Arthritis	Oligoarticular Arthritis	GWASCAT_DG	23603761		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Osteosarcoma	Osteosarcoma	Pubtator	10849374	Associate	★☆☆☆☆ Found in Text Mining only
Polyarticular Juvenile Idiopathic Arthritis, Rheumatoid Factor Negative	Seronegative polyarthritis	GWASCAT_DG	23603761		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Precursor T-Cell Lymphoblastic Leukemia-Lymphoma	Lymphoblastic Leukemia	BEFREE	26456771		★☆☆☆☆ Found in Text Mining only
Primary biliary cirrhosis	Biliary Cirrhosis	GWASCAT_DG	22961000		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Prostate carcinoma	Prostate cancer	BEFREE	20603617		★☆☆☆☆ Found in Text Mining only
Prostatic Hyperplasia	Prostatic hyperplasia	Pubtator	26782510	Associate	★☆☆☆☆ Found in Text Mining only
Pulmonary Fibrosis	Pulmonary Fibrosis	BEFREE	21499267		★☆☆☆☆ Found in Text Mining only
Renal fibrosis	Renal fibrosis	BEFREE	29997302		★☆☆☆☆ Found in Text Mining only
Rheumatoid Arthritis	Rheumatoid arthritis	LHGDN	18412315		★☆☆☆☆ Found in Text Mining only
Rheumatoid Arthritis, Systemic Juvenile	Rheumatoid arthritis	GWASCAT_DG	23603761		★☆☆☆☆ Found in Text Mining only
Sjogren's Syndrome	Sjogren syndrome	Pubtator	30159339	Associate	★☆☆☆☆ Found in Text Mining only
Spondylitis Ankylosing	Ankylosing spondylitis	Pubtator	21743469	Associate	★☆☆☆☆ Found in Text Mining only
Squamous Cell Carcinoma of Head and Neck	Squamous cell carcinoma	Pubtator	30488488	Associate	★☆☆☆☆ Found in Text Mining only
Systemic onset juvenile chronic arthritis	Arthritis	GWASCAT_DG	23603761		★☆☆☆☆ Found in Text Mining only
Urinary Bladder Neoplasms	Urinary bladder neoplasms	Pubtator	25369740	Stimulate	★☆☆☆☆ Found in Text Mining only