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

    Gene ID: 4982, updated on 16-Apr-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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See TNFRSF11B in Genome Data Viewer
    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_000008.11Genomic 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
    not available

    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)

    NEW Try the new Transcript table

    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_2023_10

    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)