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

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: mouse all
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Genomic context

Location:: 8q24.12

Exon count:: 5

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	8	NC_000008.11 (118923557..118951885, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	8	NC_060932.1 (120051990..120080310, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	8	NC_000008.10 (119935796..119964124, complement)

Chromosome 8 - NC_000008.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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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?

Osteoprotegerin and receptor activator of the nuclear factor kappa B ligand (RANKL) in healthy pubertal girls - relationships with physical growth and classical bone turnover markers.
Title: Osteoprotegerin and receptor activator of the nuclear factor kappa B ligand (RANKL) in healthy pubertal girls - relationships with physical growth and classical bone turnover markers.
Osteopontin, osteoprotegerin and musculoskeletal ultrasound findings in first-degree relatives of rheumatoid arthritis: potential markers of preclinical disease.
Title: Osteopontin, osteoprotegerin and musculoskeletal ultrasound findings in first-degree relatives of rheumatoid arthritis: potential markers of preclinical disease.
Osteoprotegerin is associated with subclinical left ventricular systolic dysfunction in non-dipper hypertensive patients: a 2D speckle tracking echocardiographic study.
Title: Osteoprotegerin is associated with subclinical left ventricular systolic dysfunction in non-dipper hypertensive patients: a 2D speckle tracking echocardiographic study.
Circulating osteoprotegerin levels and cardiovascular outcomes in patients with pre-dialysis chronic kidney disease: results from the KNOW-CKD study.
Title: Circulating osteoprotegerin levels and cardiovascular outcomes in patients with pre-dialysis chronic kidney disease: results from the KNOW-CKD study.
Correlates of Circulating Osteoprotegerin in Women with a Pathogenic or Likely Pathogenic Variant in the BRCA1 Gene.
Title: Correlates of Circulating Osteoprotegerin in Women with a Pathogenic or Likely Pathogenic Variant in the BRCA1 Gene.
Downregulation of osteoprotegerin in colorectal cancer cells promotes liver metastasis via activating tumor-associated macrophage.
Title: Downregulation of osteoprotegerin in colorectal cancer cells promotes liver metastasis via activating tumor-associated macrophage.
Association of rs2073618 polymorphism and osteoprotegerin levels with hypertension and cardiovascular risks in patients with type 2 diabetes mellitus.
Title: Association of rs2073618 polymorphism and osteoprotegerin levels with hypertension and cardiovascular risks in patients with type 2 diabetes mellitus.
Identification and Association of Polymorphism rs2073618 of the <em>Osteoprotegerin </em>Gene in Type 2 Diabetics with and without Retinopathy.
Title: Identification and Association of Polymorphism rs2073618 of the <em>Osteoprotegerin </em>Gene in Type 2 Diabetics with and without Retinopathy.
Genetically predicted osteoprotegerin levels and the risk of cardiovascular diseases: A Mendelian randomization study.
Title: Genetically predicted osteoprotegerin levels and the risk of cardiovascular diseases: A Mendelian randomization study.
Bone mineral density in egyptian children with juvenile idiopathic arthritis: possible correlation to serum RANKL / osteoprotegerin (OPG) ratio and OPG gene polymorphisms.
Title: Bone mineral density in egyptian children with juvenile idiopathic arthritis: possible correlation to serum RANKL / osteoprotegerin (OPG) ratio and OPG gene polymorphisms.

Submit: New GeneRIF Correction See all GeneRIFs (743)

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

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 EBI GWAS CatalogPubMed
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 EBI GWAS CatalogPubMed
Bone mineral density, osteoporosis, and osteoporotic fractures: a genome-wide association study. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genetic determinants of trabecular and cortical volumetric bone mineral densities and bone microstructure. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide meta-analysis identifies 56 bone mineral density loci and reveals 14 loci associated with risk of fracture. EBI GWAS Catalog EBI GWAS CatalogPubMed
Meta-analysis of genome-wide association studies identifies two loci associated with circulating osteoprotegerin levels. EBI GWAS Catalog EBI GWAS CatalogPubMed
Multiple genetic loci for bone mineral density and fractures. EBI GWAS Catalog EBI GWAS CatalogPubMed
Multistage genome-wide association meta-analyses identified two new loci for bone mineral density. EBI GWAS Catalog EBI GWAS CatalogPubMed
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 EBI GWAS CatalogPubMed
Twenty bone-mineral-density loci identified by large-scale meta-analysis of genome-wide association studies. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

TNFRSF11B_1301 (e-PCR)
- UniSTS:277827

RH93303 (e-PCR)
- UniSTS:87881

PMC153764P1 (e-PCR)
- UniSTS:271270

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

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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

NG_012202.1 RefSeqGene

Range

5260..33588

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_002546.4 → NP_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:145 → 186

TNFRSF; CRD2 [structural motif]

cd10581
Location:6 → 152

TNFRSF11B; Tumor necrosis factor receptor superfamily member 11B (TNFRSF11B), also known as Osteoprotegerin (OPG)

cl14633
Location:278 → 365

DD; Death Domain Superfamily of protein-protein interaction domains

cl22855
Location:124 → 187

TNFRSF; Tumor necrosis factor receptor superfamily (TNFRSF)