Gene Gene information from NCBI Gene database.
Entrez ID 8600
Gene name TNF superfamily member 11
Gene symbol TNFSF11
Synonyms (NCBI Gene)
CD254ODFOPGLOPTB2RANKLTNLG6BTRANCEhRANKL2sOdf
Chromosome 13
Chromosome location 13q14.11
Summary This gene encodes a member of the tumor necrosis factor (TNF) cytokine family which is a ligand for osteoprotegerin and functions as a key factor for osteoclast differentiation and activation. This protein was shown to be a dentritic cell survival factor
SNPs SNP information provided by dbSNP.
3
SNP ID Visualize variation Clinical significance Consequence
rs121909072 T>A Pathogenic Missense variant, coding sequence variant
rs142756983 G>A Conflicting-interpretations-of-pathogenicity, uncertain-significance Missense variant, intron variant, upstream transcript variant, genic upstream transcript variant, coding sequence variant
rs863223288 CG>- Pathogenic Coding sequence variant, frameshift variant
miRNA miRNA information provided by mirtarbase database.
36
miRTarBase ID miRNA Experiments Reference
MIRT004387 hsa-miR-18a-5p MicroarrayNorthern blot 16331254
MIRT004387 hsa-miR-18a-5p Luciferase reporter assay 16331254
MIRT1443357 hsa-miR-3148 CLIP-seq
MIRT1443358 hsa-miR-3190 CLIP-seq
MIRT1443359 hsa-miR-4752 CLIP-seq
Transcription factors Transcription factors information provided by TRRUST V2 database.
3
Transcription factor Regulation Reference
DACH1 Repression 17891780
E2F1 Activation 18381203
HSF2 Activation 15731115
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
77
GO ID Ontology Definition Evidence Reference
GO:0000122 Process Negative regulation of transcription by RNA polymerase II IEA
GO:0001503 Process Ossification IEA
GO:0002158 Process Osteoclast proliferation IEA
GO:0002548 Process Monocyte chemotaxis IDA 15248232
GO:0005102 Function Signaling receptor binding IEA
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
602642 11926 ENSG00000120659
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
O14788
Protein name Tumor necrosis factor ligand superfamily member 11 (Osteoclast differentiation factor) (ODF) (Osteoprotegerin ligand) (OPGL) (Receptor activator of nuclear factor kappa-B ligand) (RANKL) (TNF-related activation-induced cytokine) (TRANCE) (CD antigen CD254
Protein function Cytokine that binds to TNFRSF11B/OPG and to TNFRSF11A/RANK. Osteoclast differentiation and activation factor. Augments the ability of dendritic cells to stimulate naive T-cell proliferation. May be an important regulator of interactions between
PDB 3URF , 5BNQ
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF00229 TNF 185 313 TNF(Tumour Necrosis Factor) family Domain
Tissue specificity TISSUE SPECIFICITY: Highest in the peripheral lymph nodes, weak in spleen, peripheral blood Leukocytes, bone marrow, heart, placenta, skeletal muscle, stomach and thyroid.
Sequence
MRRASRDYTKYLRGSEEMGGGPGAPHEGPLHAPPPPAPHQPPAASRSMFVALLGLGLGQV
VCSVALFFYFRAQMDPNRISEDGTHCIYRILRLHENADFQDTTLESQDTKLIPDSCRRIK
QAFQGAVQKELQHIVGSQHIRAEKAMVDGSWLDLAKRSKLEAQPFAHLTINATDIPSGSH
KVSLSSWYHDRGWAKISNMTFSNGKLIVNQDGFYYLYANICFRHHETSGDLATEYLQLMV
YVTKTSIKIPSSHTLMKGGSTKYWSGNSEFHFYSINVGGFFKLRSGEEISIEVSNPSLLD
PDQDATYFGAFKV
RDID
Sequence length 317
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
  KEGG  Reactome
  Cytokine-cytokine receptor interaction
NF-kappa B signaling pathway
Osteoclast differentiation
Prolactin signaling pathway
Parathyroid hormone synthesis, secretion and action
Chemical carcinogenesis - receptor activation
Breast cancer
Rheumatoid arthritis
  TNFR2 non-canonical NF-kB pathway
TNFs bind their physiological receptors
TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
26
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
Autosomal recessive osteopetrosis 2 Pathogenic; Likely pathogenic rs2137916719, rs2137905441, rs121909072, rs863223288, rs267603829 RCV002247768
RCV000007388
RCV000007389
RCV000007390
RCV002052073
★★★★★
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
AUTOSOMAL RECESSIVE OSTEOPETROSIS Disgenet
Disgenet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
BONE RESORPTION CTD
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
CHRONIC PERIODONTITIS CTD, Disgenet
CTD, Disgenet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
DESBUQUOIS SYNDROME CTD
★★☆☆☆
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 27615270, 28076786
★☆☆☆☆
Found in Text Mining only
Acromegaly Acromegaly BEFREE 29895074
★☆☆☆☆
Found in Text Mining only
Acromegaly Acromegaly Pubtator 39741885 Associate
★☆☆☆☆
Found in Text Mining only
Adenocarcinoma Adenocarcinoma LHGDN 18406448
★☆☆☆☆
Found in Text Mining only
Adenocarcinoma of prostate Prostate adenocarcinoma BEFREE 23096689
★☆☆☆☆
Found in Text Mining only
Adult Rickets Rickets BEFREE 21541994
★☆☆☆☆
Found in Text Mining only
Adult T-Cell Lymphoma/Leukemia T-Cell Lymphoma/Leukemia BEFREE 20050882, 20214446, 31578308
★☆☆☆☆
Found in Text Mining only
Alkaptonuria Alkaptonuria BEFREE 30343446
★☆☆☆☆
Found in Text Mining only
Allergic rhinitis (disorder) Allergic rhinitis BEFREE 30737962
★☆☆☆☆
Found in Text Mining only
Ameloblastoma Ameloblastoma LHGDN 15044512
★☆☆☆☆
Found in Text Mining only