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TNFRSF11B TNF receptor superfamily member 11b [ Homo sapiens (human) ]

Gene ID: 4982, updated on 10-Dec-2024

Summary

Official Symbol
TNFRSF11Bprovided by HGNC
Official Full Name
TNF receptor superfamily member 11bprovided by HGNC
Primary source
HGNC:HGNC:11909
See related
Ensembl:ENSG00000164761 MIM:602643; AllianceGenome:HGNC:11909
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
OPG; TR1; OCIF; PDB5
Summary
The protein encoded by this gene is a member of the TNF-receptor superfamily. This protein is an osteoblast-secreted decoy receptor that functions as a negative regulator of bone resorption. This protein specifically binds to its ligand, osteoprotegerin ligand, both of which are key extracellular regulators of osteoclast development. Studies of the mouse counterpart also suggest that this protein and its ligand play a role in lymph-node organogenesis and vascular calcification. Alternatively spliced transcript variants of this gene have been reported, but their full length nature has not been determined. [provided by RefSeq, Jul 2008]
Expression
Biased expression in thyroid (RPKM 62.5), kidney (RPKM 16.2) and 7 other tissues See more
Orthologs
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Genomic context

See TNFRSF11B in Genome Data Viewer
Location:
8q24.12
Exon count:
5
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (118923557..118951885, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (120051990..120080310, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (119935796..119964124, complement)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105375723 Neighboring gene uncharacterized LOC124902008 Neighboring gene collectin subfamily member 10 Neighboring gene GABA type A receptor associated protein like 2 pseudogene Neighboring gene RNA, U6 small nuclear 12, pseudogene

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Hyperphosphatasemia with bone disease
MedGen: C0268414 OMIM: 239000 GeneReviews: Not available
Compare labs

EBI GWAS Catalog

Description
A genome-wide meta-analysis of six type 1 diabetes cohorts identifies multiple associated loci.
EBI GWAS Catalog
An integration of genome-wide association study and gene expression profiling to prioritize the discovery of novel susceptibility Loci for osteoporosis-related traits.
EBI GWAS Catalog
Bone mineral density, osteoporosis, and osteoporotic fractures: a genome-wide association study.
EBI GWAS Catalog
Genetic determinants of trabecular and cortical volumetric bone mineral densities and bone microstructure.
EBI GWAS Catalog
Genome-wide meta-analysis identifies 56 bone mineral density loci and reveals 14 loci associated with risk of fracture.
EBI GWAS Catalog
Meta-analysis of genome-wide association studies identifies two loci associated with circulating osteoprotegerin levels.
EBI GWAS Catalog
Multiple genetic loci for bone mineral density and fractures.
EBI GWAS Catalog
Multistage genome-wide association meta-analyses identified two new loci for bone mineral density.
EBI GWAS Catalog
Phenotypic dissection of bone mineral density reveals skeletal site specificity and facilitates the identification of novel loci in the genetic regulation of bone mass attainment.
EBI GWAS Catalog
Twenty bone-mineral-density loci identified by large-scale meta-analysis of genome-wide association studies.
EBI GWAS Catalog

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Clone Names

  • MGC29565

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables cytokine activity TAS
Traceable Author Statement
more info
PubMed 
enables heparan sulfate binding IEA
Inferred from Electronic Annotation
more info
 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables signaling receptor activity TAS
Traceable Author Statement
more info
PubMed 
Process Evidence Code Pubs
involved_in apoptotic process IEA
Inferred from Electronic Annotation
more info
 
involved_in extracellular matrix organization IEA
Inferred from Electronic Annotation
more info
 
involved_in negative regulation of bone resorption IEA
Inferred from Electronic Annotation
more info
 
involved_in negative regulation of odontogenesis of dentin-containing tooth IEA
Inferred from Electronic Annotation
more info
 
involved_in negative regulation of osteoclast differentiation ISO
Inferred from Sequence Orthology
more info
 
involved_in negative regulation of tumor necrosis factor-mediated signaling pathway IEA
Inferred from Electronic Annotation
more info
 
involved_in response to arsenic-containing substance IEA
Inferred from Electronic Annotation
more info
 
involved_in response to estrogen IEA
Inferred from Electronic Annotation
more info
 
involved_in response to magnesium ion IEA
Inferred from Electronic Annotation
more info
 
involved_in response to nutrient IEA
Inferred from Electronic Annotation
more info
 
involved_in response to xenobiotic stimulus IEA
Inferred from Electronic Annotation
more info
 
involved_in signal transduction IEA
Inferred from Electronic Annotation
more info
 
involved_in skeletal system development TAS
Traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
located_in extracellular matrix IEA
Inferred from Electronic Annotation
more info
 
located_in extracellular region NAS
Non-traceable Author Statement
more info
PubMed 
located_in extracellular space IDA
Inferred from Direct Assay
more info
PubMed 
located_in plasma membrane TAS
Traceable Author Statement
more info
 
part_of receptor complex IPI
Inferred from Physical Interaction
more info
PubMed 

General protein information

Preferred Names
tumor necrosis factor receptor superfamily member 11B
Names
osteoclastogenesis inhibitory factor
osteoprotegerin
tumor necrosis factor receptor superfamily, member 11b

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

  1. NG_012202.1 RefSeqGene

    Range
    5260..33588
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_002546.4NP_002537.3  tumor necrosis factor receptor superfamily member 11B precursor

    See identical proteins and their annotated locations for NP_002537.3

    Status: REVIEWED

    Source sequence(s)
    AK223155, CK903484, DA477521
    Consensus CDS
    CCDS6326.1
    UniProtKB/Swiss-Prot
    B2R9A8, O00300, O60236, Q53FX6, Q9UHP4
    Related
    ENSP00000297350.4, ENST00000297350.9
    Conserved Domains (4) summary
    cd00185
    Location:145186
    TNFRSF; CRD2 [structural motif]
    cd10581
    Location:6152
    TNFRSF11B; Tumor necrosis factor receptor superfamily member 11B (TNFRSF11B), also known as Osteoprotegerin (OPG)
    cl14633
    Location:278365
    DD; Death Domain Superfamily of protein-protein interaction domains
    cl22855
    Location:124187
    TNFRSF; Tumor necrosis factor receptor superfamily (TNFRSF)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000008.11 Reference GRCh38.p14 Primary Assembly

    Range
    118923557..118951885 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    120051990..120080310 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)