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

Gene ID: 4982, updated on 27-Sep-2020

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
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

Genomic context

See TNFRSF11B in Genome Data Viewer
Location:
8q24.12
Exon count:
5
Annotation release Status Assembly Chr Location
109.20200815 current GRCh38.p13 (GCF_000001405.39) 8 NC_000008.11 (118923557..118951885, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (119935796..119964383, complement)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene ribosomal protein S26 pseudogene 35 Neighboring gene uncharacterized LOC105375723 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
A genome-wide meta-analysis of six type 1 diabetes cohorts identifies multiple associated loci.
GeneReviews: Not available
An integration of genome-wide association study and gene expression profiling to prioritize the discovery of novel susceptibility Loci for osteoporosis-related traits.
GeneReviews: Not available
Bone mineral density, osteoporosis, and osteoporotic fractures: a genome-wide association study.
GeneReviews: Not available
Genetic determinants of trabecular and cortical volumetric bone mineral densities and bone microstructure.
GeneReviews: Not available
Genome-wide meta-analysis identifies 56 bone mineral density loci and reveals 14 loci associated with risk of fracture.
GeneReviews: Not available
Hyperphosphatasemia with bone disease
MedGen: C0268414 OMIM: 239000 GeneReviews: Not available
Compare labs
Meta-analysis of genome-wide association studies identifies two loci associated with circulating osteoprotegerin levels.
GeneReviews: Not available
Multiple genetic loci for bone mineral density and fractures.
GeneReviews: Not available
Multistage genome-wide association meta-analyses identified two new loci for bone mineral density.
GeneReviews: Not available
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.
GeneReviews: Not available
Twenty bone-mineral-density loci identified by large-scale meta-analysis of genome-wide association studies.
GeneReviews: Not available

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC29565

Gene Ontology Provided by GOA

Function Evidence Code Pubs
cytokine activity TAS
Traceable Author Statement
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
signaling receptor activity TAS
Traceable Author Statement
more info
PubMed 
Process Evidence Code Pubs
apoptotic process IEA
Inferred from Electronic Annotation
more info
 
extracellular matrix organization IEA
Inferred from Electronic Annotation
more info
 
negative regulation of bone resorption IEA
Inferred from Electronic Annotation
more info
 
negative regulation of odontogenesis of dentin-containing tooth IEA
Inferred from Electronic Annotation
more info
 
response to arsenic-containing substance IEA
Inferred from Electronic Annotation
more info
 
response to drug IEA
Inferred from Electronic Annotation
more info
 
response to estrogen IEA
Inferred from Electronic Annotation
more info
 
response to magnesium ion IEA
Inferred from Electronic Annotation
more info
 
response to nutrient IEA
Inferred from Electronic Annotation
more info
 
signal transduction TAS
Traceable Author Statement
more info
PubMed 
skeletal system development TAS
Traceable Author Statement
more info
PubMed 
tumor necrosis factor-mediated signaling pathway TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
extracellular matrix IEA
Inferred from Electronic Annotation
more info
 
extracellular region TAS
Traceable Author Statement
more info
PubMed 
extracellular space IDA
Inferred from Direct Assay
more info
PubMed 
plasma membrane TAS
Traceable Author Statement
more info
 

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)

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
    O00300
    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: Homo sapiens Updated Annotation Release 109.20200815

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000008.11 Reference GRCh38.p13 Primary Assembly

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