Gene Gene information from NCBI Gene database.
Entrez ID 7421
Gene name Vitamin D receptor
Gene symbol VDR
Synonyms (NCBI Gene)
NR1I1PPP1R163
Chromosome 12
Chromosome location 12q13.11
Summary This gene encodes vitamin D3 receptor, which is a member of the nuclear hormone receptor superfamily of ligand-inducible transcription factors. This receptor also functions as a receptor for the secondary bile acid, lithocholic acid. Downstream targets of
SNPs SNP information provided by dbSNP.
18
SNP ID Visualize variation Clinical significance Consequence
rs2228570 A>C,G,T Benign, drug-response Coding sequence variant, initiator codon variant, missense variant
rs121909790 C>G,T Pathogenic Coding sequence variant, missense variant
rs121909791 C>T Pathogenic, uncertain-significance Coding sequence variant, missense variant
rs121909792 G>T Pathogenic Coding sequence variant, stop gained
rs121909793 C>T Pathogenic Coding sequence variant, missense variant
miRNA miRNA information provided by mirtarbase database.
635
miRTarBase ID miRNA Experiments Reference
MIRT002080 hsa-let-7a-5p Luciferase reporter assay 17890240
MIRT002080 hsa-let-7a-5p Luciferase reporter assay 17890240
MIRT002080 hsa-let-7a-5p Luciferase reporter assay 17890240
MIRT002080 hsa-let-7a-5p Luciferase reporter assay 17890240
MIRT002080 hsa-let-7a-5p Luciferase reporter assay 17890240
Transcription factors Transcription factors information provided by TRRUST V2 database.
19
Transcription factor Regulation Reference
CDX2 Unknown 11450701;16604479;16883525;19960008
EZH2 Unknown 23424038
JUN Activation 15930183
KLF4 Repression 22677193
MED1 Unknown 17229570
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
82
GO ID Ontology Definition Evidence Reference
GO:0000122 Process Negative regulation of transcription by RNA polymerase II IBA
GO:0000122 Process Negative regulation of transcription by RNA polymerase II IDA 17426122
GO:0000785 Component Chromatin IDA 12016314
GO:0000785 Component Chromatin ISA
GO:0000902 Process Cell morphogenesis IMP 17223341
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
601769 12679 ENSG00000111424
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
P11473
Protein name Vitamin D3 receptor (VDR) (1,25-dihydroxyvitamin D3 receptor) (Nuclear receptor subfamily 1 group I member 1)
Protein function Nuclear receptor for calcitriol, the active form of vitamin D3 which mediates the action of this vitamin on cells (PubMed:10678179, PubMed:15728261, PubMed:16913708, PubMed:28698609, PubMed:37478846). Enters the nucleus upon vitamin D3 binding w
PDB 1DB1 , 1IE8 , 1IE9 , 1KB2 , 1KB4 , 1KB6 , 1S0Z , 1S19 , 1TXI , 1YNW , 2HAM , 2HAR , 2HAS , 2HB7 , 2HB8 , 3A2I , 3A2J , 3A3Z , 3A40 , 3A78 , 3AUQ , 3AUR , 3AX8 , 3AZ1 , 3AZ2 , 3AZ3 , 3B0T , 3CS4 , 3CS6 , 3KPZ , 3M7R , 3OGT , 3P8X , 3TKC , 3VHW , 3W0A , 3W0C , 3W0Y , 3WGP , 3WWR , 3X31 , 3X36 , 4G2I , 4ITE , 4ITF , 5GT4 , 5V39 , 5YSY , 5YT2 , 7QPP , 8IQN
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF00105 zf-C4 22 91 Zinc finger, C4 type (two domains) Domain
PF00104 Hormone_recep 216 406 Ligand-binding domain of nuclear hormone receptor Domain
Sequence
Sequence length 427
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
  KEGG  Reactome
  Parathyroid hormone synthesis, secretion and action
Endocrine and other factor-regulated calcium reabsorption
Mineral absorption
Tuberculosis
Chemical carcinogenesis - receptor activation
  Vitamin D (calciferol) metabolism
Nuclear Receptor transcription pathway
SUMOylation of intracellular receptors
Associated diseases Disease associations from ClinVar categorized as Causal (Pathogenic/Likely Pathogenic) or Unknown.
239
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession
Rickets Likely pathogenic; Pathogenic rs121909796 RCV004798889
Vitamin D-dependent rickets type II with alopecia Pathogenic; Likely pathogenic rs201106427, rs752414831, rs980041568, rs776088779, rs121909790, rs121909791, rs121909792, rs121909802, rs121909794, rs121909795, rs121909796, rs121909797, rs121909798, rs121909800, rs121909801
View all (7 more)
RCV001843694
RCV001843695
RCV002246806
RCV004796759
RCV000008186
RCV000008187
RCV000008188
RCV000008189
RCV000008191
RCV000008192
RCV000008193
RCV000008194
RCV000008195
RCV000008197
RCV000008198
RCV000008199
RCV000008200
RCV003134705
RCV000243398
RCV000251590
RCV003236657
RCV003486511
RCV004689734
RCV001843570
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession
Familial adenomatous polyposis 2 Conflicting classifications of pathogenicity rs1164008328 RCV001507088
Hepatocellular carcinoma Conflicting classifications of pathogenicity; Benign rs7975232, rs1544410, rs731236 RCV002274199
RCV002274200
RCV002274013
Periodontitis Conflicting classifications of pathogenicity; Benign rs7975232, rs1544410, rs9729, rs3847987, rs731236, rs2228570, rs739837 RCV003992537
RCV003992539
RCV003992269
RCV003992270
RCV003992272
RCV003992273
RCV003992271
Squamous cell lung carcinoma Uncertain significance rs756376013 RCV005924050
Associations from Text MiningDisease associations identified through Pubtator
Disease Name Relationship Type References
Abortion Missed Associate 31532316, 34937516
Acidosis Inhibit 32900990
Acne Vulgaris Associate 39336541
Acromegaly Associate 25839036
ACTH Secreting Pituitary Adenoma Associate 35960046
Adenocarcinoma Associate 11789558, 22546272, 25910066, 28212604, 31275989, 34651346
Adenocarcinoma of Lung Associate 22564539
Adenoma Associate 16097046, 27978548, 39201651
Adenoma Stimulate 22511602
Adenoma Islet Cell Associate 22960018, 29061729