Gene Gene information from NCBI Gene database.
Entrez ID 4982
Gene name TNF receptor superfamily member 11b
Gene symbol TNFRSF11B
Synonyms (NCBI Gene)
OCIFOPGPDB5TR1
Chromosome 8
Chromosome location 8q24.12
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 l
SNPs SNP information provided by dbSNP.
9
SNP ID Visualize variation Clinical significance Consequence
rs104894091 C>T Pathogenic Coding sequence variant, missense variant
rs104894092 A>G Pathogenic Coding sequence variant, missense variant
rs144654126 G>A Uncertain-significance, conflicting-interpretations-of-pathogenicity Coding sequence variant, synonymous variant
rs146450643 C>T Conflicting-interpretations-of-pathogenicity Coding sequence variant, synonymous variant
rs200071478 T>C,G Pathogenic Missense variant, coding sequence variant
miRNA miRNA information provided by mirtarbase database.
219
miRTarBase ID miRNA Experiments Reference
MIRT023202 hsa-miR-124-3p Microarray 18668037
MIRT031067 hsa-miR-21-5p Microarray 20371350
MIRT053664 hsa-miR-181a-5p Microarray 22942087
MIRT1442877 hsa-miR-135a CLIP-seq
MIRT1442878 hsa-miR-135b CLIP-seq
Transcription factors Transcription factors information provided by TRRUST V2 database.
4
Transcription factor Regulation Reference
CREB5 Repression 21132541
HOXC8 Unknown 11139569
PPARG Unknown 12056809
SMAD1 Unknown 11139569
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
20
GO ID Ontology Definition Evidence Reference
GO:0001501 Process Skeletal system development TAS 9108485
GO:0005125 Function Cytokine activity TAS 9168977
GO:0005515 Function Protein binding IPI 22664871, 32814053
GO:0005576 Component Extracellular region IEA
GO:0005576 Component Extracellular region NAS 22664871
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
602643 11909 ENSG00000164761
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
O00300
Protein name Tumor necrosis factor receptor superfamily member 11B (Osteoclastogenesis inhibitory factor) (Osteoprotegerin)
Protein function Acts as a decoy receptor for TNFSF11/RANKL and thereby neutralizes its function in osteoclastogenesis. Inhibits the activation of osteoclasts and promotes osteoclast apoptosis in vitro. Bone homeostasis seems to depend on the local ratio between
PDB 3URF
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF00020 TNFR_c6 25 62 TNFR/NGFR cysteine-rich region Domain
PF00020 TNFR_c6 65 105 TNFR/NGFR cysteine-rich region Domain
PF00020 TNFR_c6 107 142 TNFR/NGFR cysteine-rich region Domain
PF00531 Death 278 365 Death domain Domain
Tissue specificity TISSUE SPECIFICITY: Highly expressed in adult lung, heart, kidney, liver, spleen, thymus, prostate, ovary, small intestine, thyroid, lymph node, trachea, adrenal gland, testis, and bone marrow. Detected at very low levels in brain, placenta and skeletal m
Sequence
MNNLLCCALVFLDISIKWTTQETFPPKYLHYDEETSHQLLCDKCPPGTYLKQHCTAKWKT
VC
APCPDHYYTDSWHTSDECLYCSPVCKELQYVKQECNRTHNRVCECKEGRYLEIEFCLK
HRSCPPGFGVVQAGTPERNTVC
KRCPDGFFSNETSSKAPCRKHTNCSVFGLLLTQKGNAT
HDNICSGNSESTQKCGIDVTLCEEAFFRFAVPTKFTPNWLSVLVDNLPGTKVNAESVERI
KRQHSSQEQTFQLLKLWKHQNKDQDIVKKIIQDIDLCENSVQRHIGHANLTFEQLRSLME
SLPGKKVGAEDIEKTIKACKPSDQILKLLSLWRIKNGDQDTLKGLMHALKHSKTYHFPKT
VTQSL
KKTIRFLHSFTMYKLYQKLFLEMIGNQVQSVKISCL
Sequence length 401
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
  KEGG  Reactome
  Cytokine-cytokine receptor interaction
Osteoclast differentiation
  TNFs bind their physiological receptors
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
22
Evidence Score: ★☆☆☆☆  Gene-disease association found in Text Mining only ★★☆☆☆  Found in Text Mining and Unknown/Other Associations ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession Evidence Score
Hyperphosphatasemia with bone disease Pathogenic; Likely pathogenic rs200071478, rs796051868, rs104894091, rs2129878039, rs1355555142, rs1307942060 RCV000190837
RCV000007384
RCV000007385
RCV000007387
RCV003985152
View all (1 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Phenotype Name Clinical Significance Source Evidence Score
ARTHRITIS, EXPERIMENTAL CTD
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
ARTHRITIS, RHEUMATOID CTD
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
ASTHMA GWAS catalog
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
AUTOIMMUNE DISEASE GWAS catalog
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Associations from Text Mining Disease associations identified through text mining
Disease Name Disease (Merged) Source PMID Relationship Type Evidence Score
Abetalipoproteinemia Abetalipoproteinemia BEFREE 28674790
★☆☆☆☆
Found in Text Mining only
Acromegaly Acromegaly BEFREE 29895074
★☆☆☆☆
Found in Text Mining only
Acromegaly Acromegaly Pubtator 39741885 Associate
★☆☆☆☆
Found in Text Mining only
Acute Coronary Syndrome Coronary Syndrome LHGDN 18328262
★☆☆☆☆
Found in Text Mining only
Acute Coronary Syndrome Coronary Syndrome BEFREE 29330256
★☆☆☆☆
Found in Text Mining only
Acute Megakaryocytic Leukemias Megakaryocytic Leukemia BEFREE 15307108
★☆☆☆☆
Found in Text Mining only
Acute Megakaryocytic Leukemias Megakaryocytic Leukemia LHGDN 15307108
★☆☆☆☆
Found in Text Mining only
Adult T-Cell Lymphoma/Leukemia T-Cell Lymphoma/Leukemia BEFREE 19134004
★☆☆☆☆
Found in Text Mining only
Aggressive Periodontitis Aggressive Periodontitis BEFREE 16953816
★☆☆☆☆
Found in Text Mining only
Aggressive Periodontitis Aggressive Periodontitis LHGDN 18938269
★☆☆☆☆
Found in Text Mining only