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 (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
66
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
Rickets Likely pathogenic; Pathogenic rs121909796 RCV004798889
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
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
View all (19 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
AMYOTROPHIC LATERAL SCLEROSIS Disgenet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
ASTHMA Disgenet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
AUTISM SPECTRUM DISORDERS Disgenet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
AUTOIMMUNE CHRONIC HEPATITIS Disgenet
★★☆☆☆
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
Acne Acne BEFREE 30220112
★☆☆☆☆
Found in Text Mining only
Acne Vulgaris Acne BEFREE 30220112
★☆☆☆☆
Found in Text Mining only
Acromegaly Acromegaly BEFREE 25839036, 31616375
★☆☆☆☆
Found in Text Mining only
Acromegaly Acromegaly Pubtator 25839036 Associate
★☆☆☆☆
Found in Text Mining only
Actinic keratosis Actinic keratosis BEFREE 18647306, 30315595
★☆☆☆☆
Found in Text Mining only
Acute lymphocytic leukemia Lymphocytic Leukemia BEFREE 15459215, 18385010
★☆☆☆☆
Found in Text Mining only
Acute Megakaryocytic Leukemias Megakaryocytic Leukemia BEFREE 8639462
★☆☆☆☆
Found in Text Mining only
Acute monocytic leukemia Monocytic Leukemia BEFREE 12460926, 27144333, 28765039, 30074149
★☆☆☆☆
Found in Text Mining only
Acute monocytic leukemia Monocytic Leukemia LHGDN 15145445
★☆☆☆☆
Found in Text Mining only
Acute pancreatitis Pancreatitis BEFREE 29966312
★☆☆☆☆
Found in Text Mining only