LTBR lymphotoxin beta receptor [Homo sapiens (human)] - Gene

Summary

Official Symbol: LTBRprovided by HGNC
Official Full Name: lymphotoxin beta receptorprovided by HGNC
Primary source: HGNC:HGNC:6718
See related: Ensembl:ENSG00000111321 MIM:600979; AllianceGenome:HGNC:6718
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: TNFCR; TNFR3; D12S370; TNFR-RP; TNFRSF3; TNFR2-RP; LT-BETA-R; TNF-R-III
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 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]
Expression: Ubiquitous expression in prostate (RPKM 23.4), placenta (RPKM 23.0) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 12p13.31

Exon count:: 13

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	12	NC_000012.12 (6375160..6391566)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	12	NC_060936.1 (6385218..6401631)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	12	NC_000012.11 (6484326..6500732)

Chromosome 12 - NC_000012.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Systematic analysis of the prognostic value and immunological function of LTBR in human cancer.
Title: Systematic analysis of the prognostic value and immunological function of LTBR in human cancer.
A LIGHT-HVEM/LTbetaR axis contributes to the fibrosis of intrauterine adhesion.
Title: A LIGHT-HVEM/LTβR axis contributes to the fibrosis of intrauterine adhesion.
LIGHT (TNFSF14) enhances osteogenesis of human bone marrow-derived mesenchymal stem cells.
Title: LIGHT (TNFSF14) enhances osteogenesis of human bone marrow-derived mesenchymal stem cells.
Clathrin- and dynamin-dependent endocytosis limits canonical NF-kappaB signaling triggered by lymphotoxin beta receptor.
Title: Clathrin- and dynamin-dependent endocytosis limits canonical NF-κB signaling triggered by lymphotoxin β receptor.
LIGHT/LTbetaR signaling regulates self-renewal and differentiation of hematopoietic and leukemia stem cells.
Title: LIGHT/LTβR signaling regulates self-renewal and differentiation of hematopoietic and leukemia stem cells.
Inhibition of LTbetaR signalling activates WNT-induced regeneration in lung.
Title: Inhibition of LTβR signalling activates WNT-induced regeneration in lung.
The Nuclear Protein HOXB13 Enhances Methylmercury Toxicity by Inducing Oncostatin M and Promoting Its Binding to TNFR3 in Cultured Cells.
Title: The Nuclear Protein HOXB13 Enhances Methylmercury Toxicity by Inducing Oncostatin M and Promoting Its Binding to TNFR3 in Cultured Cells.
Cutting Edge: The RNA-Binding Protein Ewing Sarcoma Is a Novel Modulator of Lymphotoxin beta Receptor Signaling.
Title: Cutting Edge: The RNA-Binding Protein Ewing Sarcoma Is a Novel Modulator of Lymphotoxin β Receptor Signaling.
These data provide the first evidence of overexpression of LIGHT and its receptors HVEM and LT beta receptor in systemic sclerosis and suggest that the LIGHT axis might contribute to the pathogenesis of systemic sclerosis.
Title: Increased expression of the TNF superfamily member LIGHT/TNFSF14 and its receptors (HVEM and LTßR) in patients with systemic sclerosis.
Authors found that knockdown of Rab7a or HOPS components led to sequestration of LTbetaR in intraluminal vesicles of endosomes, thus precluding NF-kappaB signaling. This was in contrast to the LTbetaR localization on the outer endosomal membrane that was seen after ESCRT depletion and was permissive for signaling.
Title: The topology of the lymphotoxin β receptor that accumulates upon endolysosomal dysfunction dictates the NF-κB signaling outcome.

Submit: New GeneRIF Correction See all GeneRIFs (49)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Tat	tat	HIV-1 Tat upregulates the expression of lymphotoxin beta receptor (TNFR superfamily, member 3, LTBR) gene in mammary epithelial cells	PubMed

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D8S2279 (e-PCR)
- UniSTS:473907

G16208 (e-PCR)
- UniSTS:61514

RH45015 (e-PCR)
- UniSTS:13133

D12S1911 (e-PCR)
- UniSTS:14505

LTBR_2435 (e-PCR)
- UniSTS:280831

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables identical protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables ubiquitin protein ligase binding	IBA Inferred from Biological aspect of Ancestor more info
enables ubiquitin protein ligase binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in apoptotic process	IEA Inferred from Electronic Annotation more info
involved_in cellular response to mechanical stimulus	IEP Inferred from Expression Pattern more info
involved_in hematopoietic or lymphoid organ development	IEA Inferred from Electronic Annotation more info
involved_in immune response	IEA Inferred from Electronic Annotation more info
involved_in myeloid dendritic cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of JNK cascade	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of canonical NF-kappaB signal transduction	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of canonical NF-kappaB signal transduction	IEP Inferred from Expression Pattern more info	PubMed
involved_in positive regulation of extrinsic apoptotic signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in signal transduction	TAS Traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
located_in Golgi apparatus	IDA Inferred from Direct Assay more info
located_in plasma membrane	TAS Traceable Author Statement more info

General protein information

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Preferred Names: tumor necrosis factor receptor superfamily member 3

Names: lymphotoxin B receptor; lymphotoxin beta receptor (TNFR superfamily, member 3); tumor necrosis factor C receptor; tumor necrosis factor receptor 2-related protein; tumor necrosis factor receptor type III

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_033039.2 RefSeqGene

Range

13795..21199

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001270987.2 → NP_001257916.1 tumor necrosis factor receptor superfamily member 3 isoform 2

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (2) has a distinct N-terminus and is shorter than isoform 1.

Source sequence(s)

AC005840, AK027080, AK293187, BC026262, DC424721

Consensus CDS

CCDS59233.1

UniProtKB/Swiss-Prot

P36941

Related

ENSP00000440875.1, ENST00000539925.5

Conserved Domains (3) summary

cd00185
Location:151 → 191

TNFRSF; CRD2 [structural motif]

cd10578
Location:4 → 149

TNFRSF3; Tumor necrosis factor receptor superfamily member 3 (TNFRSF3), also known as lymphotoxin beta receptor (LTBR)

cl22855
Location:129 → 191

TNFRSF; Tumor necrosis factor receptor superfamily (TNFRSF)
NM_001414303.1 → NP_001401232.1 tumor necrosis factor receptor superfamily member 3 isoform 3 precursor

Status: REVIEWED

Source sequence(s)

AC005840
NM_001414304.1 → NP_001401233.1 tumor necrosis factor receptor superfamily member 3 isoform 4 precursor

Status: REVIEWED

Source sequence(s)

AC005840
NM_001414305.1 → NP_001401234.1 tumor necrosis factor receptor superfamily member 3 isoform 5 precursor

Status: REVIEWED

Source sequence(s)

AC005840
NM_001414306.1 → NP_001401235.1 tumor necrosis factor receptor superfamily member 3 isoform 6 precursor

Status: REVIEWED

Source sequence(s)

AC005840
NM_001414307.1 → NP_001401236.1 tumor necrosis factor receptor superfamily member 3 isoform 7 precursor

Status: REVIEWED

Source sequence(s)

AC005840
NM_001414308.1 → NP_001401237.1 tumor necrosis factor receptor superfamily member 3 isoform 8 precursor

Status: REVIEWED

Source sequence(s)

AC005840
NM_001414309.1 → NP_001401238.1 tumor necrosis factor receptor superfamily member 3 isoform 9

Status: REVIEWED

Source sequence(s)

AC005840
NM_001414310.1 → NP_001401239.1 tumor necrosis factor receptor superfamily member 3 isoform 10 precursor

Status: REVIEWED

Source sequence(s)

AC005840
NM_001414311.1 → NP_001401240.1 tumor necrosis factor receptor superfamily member 3 isoform 11 precursor

Status: REVIEWED

Source sequence(s)

AC005840
NM_001414312.1 → NP_001401241.1 tumor necrosis factor receptor superfamily member 3 isoform 12 precursor

Status: REVIEWED

Source sequence(s)

AC005840
NM_002342.3 → NP_002333.1 tumor necrosis factor receptor superfamily member 3 isoform 1 precursor

See identical proteins and their annotated locations for NP_002333.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes isoform 1.

Source sequence(s)

AK027080, BC026262, DA679291, L04270

Consensus CDS

CCDS8544.1

UniProtKB/Swiss-Prot

B7Z1D2, D3DUR2, F5GXE7, P36941

Related

ENSP00000228918.4, ENST00000228918.9

Conserved Domains (4) summary

cd00185
Location:170 → 210

TNFRSF; CRD2 [structural motif]

cd10578
Location:11 → 168

TNFRSF3; Tumor necrosis factor receptor superfamily member 3 (TNFRSF3), also known as lymphotoxin beta receptor (LTBR)

cl22855
Location:148 → 210

TNFRSF; Tumor necrosis factor receptor superfamily (TNFRSF)

cl27169
Location:264 → 342

ZipA; ZipA C-terminal domain. ZipA, a membrane-anchored protein, is one of at least nine essential gene products necessary for assembly of the septal ring which mediates cell division in E.coli. ZipA and FtsA directly bind FtsZ, a homolog of eukaryotic ...