TNFSF11 (TNF superfamily member 11)

Gene
Gene SNPs miRNA Transcription factors Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.
8600
Gene name Gene Name - the full gene name approved by the HGNC.
TNF superfamily member 11
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.
TNFSF11
Synonyms (NCBI Gene) Gene synonyms aliases
CD254, ODF, OPGL, OPTB2, RANKL, TNLG6B, TRANCE, hRANKL2, sOdf
Chromosome Chromosome number
13
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.
13q14.11
Summary Summary of gene provided in NCBI Entrez Gene.
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.
Gene SNPs miRNA Transcription factors Gene ontology Other IDs Protein Pathways Associated diseases
Show/Hide all(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.
Gene SNPs miRNA Transcription factors Gene ontology Other IDs Protein Pathways Associated diseases
Show/Hide all(36)
miRTarBase ID miRNA Experiments Reference
MIRT004387 hsa-miR-18a-5p Microarray, Northern 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
Gene SNPs miRNA Transcription factors Gene ontology Other IDs Protein Pathways Associated diseases
Show/Hide all(3)
Transcription factor Regulation Reference
DACH1 Repression 17891780
E2F1 Activation 18381203
HSF2 Activation 15731115
Gene ontology (GO) Gene ontology information of associated ontologies with gene provided by GO database.
Gene SNPs miRNA Transcription factors Gene ontology Other IDs Protein Pathways Associated diseases
Show/Hide all(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 ids of gene in databases such as OMIM, HGNC, ENSEMBLE.
Gene SNPs miRNA Transcription factors Gene ontology Other IDs Protein Pathways Associated diseases
MIM HGNC e!Ensembl
602642 11926 ENSG00000120659
Protein
Gene SNPs miRNA Transcription factors Gene ontology Other IDs Protein Pathways Associated diseases
UniProt ID 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
PDQDATYFGAFKVRDID
Sequence length 317
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
Gene SNPs miRNA Transcription factors Gene ontology Other IDs Protein Pathways Associated diseases
  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
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Associated diseases Disease associations categorized as Causal (pathogenic variants), Unknown (uncertain genetic evidence), or Text Mining (literature-based associations)
Gene SNPs miRNA Transcription factors Gene ontology Other IDs Protein Pathways Associated diseases
Show/Hide Causal Diseases (1)
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
Disease merge term Disease name dbSNP ID References
Osteopetrosis Autosomal recessive osteopetrosis 2 rs2137905441, rs121909072, rs863223288, rs267603829 N/A
Show/Hide Unknown Diseases (6)
Unknown Includes: (1) ClinVar NON-pathogenic variants (Uncertain, Benign, Conflicting, VUS), (2) GenCC associations, (3) GWAS associations, (4) CBGDA evidence-based associations. NOTE: Diseases with pathogenic evidence are excluded to avoid conflicts.
Disease merge term Disease name Evidence References Source
Biliary Cirrhosis Primary biliary cirrhosis N/A N/A GWAS
Hypothyroidism Hypothyroidism N/A N/A GWAS
Osteoporosis Osteoporosis N/A N/A GWAS
Otosclerosis Otosclerosis N/A N/A GWAS
Show/Hide Text Mining Associations (259)
Associations from Text Mining Disease associations identified through Pubtator
Disease Name Relationship Type References
abc disease Associate 24438319
Acro Osteolysis Stimulate 12393684
Acro Osteolysis Associate 29680857, 36174298
Acromegaly Associate 39741885
Adamantinoma Associate 21983933
Addison Disease Associate 23388484
Adenocarcinoma Associate 34818353
Adenocarcinoma of Lung Associate 32508318, 34229638, 37021520, 39198460
Alveolar Bone Loss Associate 22437688
Ameloblastoma Associate 21643971, 30151060, 31017256