Gene
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.
7421
Gene name Gene Name - the full gene name approved by the HGNC.
Vitamin D receptor
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.
VDR
Synonyms (NCBI Gene) Gene synonyms aliases
NR1I1, PPP1R163
Chromosome Chromosome number
12
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.
12q13.11
Summary Summary of gene provided in NCBI Entrez Gene.
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.
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.
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 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 information of associated ontologies with gene provided by GO database.
GO ID Ontology Definition Evidence Reference
GO:0000122 Process Negative regulation of transcription by RNA polymerase II IBA 21873635
GO:0000122 Process Negative regulation of transcription by RNA polymerase II IDA 17426122
GO:0000785 Component Chromatin ISA
GO:0000902 Process Cell morphogenesis IMP 17223341
GO:0000978 Function RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA 21873635
Other IDs Other ids provides unique ids of gene in databases such as OMIM, HGNC, ENSEMBLE.
MIM HGNC e!Ensembl
601769 12679 ENSG00000111424
Protein
UniProt ID 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 information provided by ClinVar, GenCC, and GWAS databases.
Causal
Disease term Disease name dbSNP ID References
Breast cancer Malignant neoplasm of breast rs587776547, rs1137887, rs137853007, rs587776650, rs80359351, rs80359714, rs121917783, rs104886456, rs121964878, rs80359874, rs80357868, rs80357508, rs387906843, rs80357569, rs80358158
View all (309 more)
22892281, 16280049
Breast carcinoma Breast Carcinoma rs80359671, rs11540652, rs28934575, rs28897672, rs137886232, rs193922376, rs80357783, rs80359306, rs80359405, rs80359507, rs80359598, rs80358429, rs397507683, rs397515636, rs80359451
View all (71 more)
16280049, 22892281
Epilepsy Epilepsy, Temporal Lobe, Uncinate Epilepsy, Epilepsy, Benign Psychomotor, Childhood, Epilepsy, Lateral Temporal rs113994140, rs28937874, rs1589762127, rs104894166, rs28939075, rs2134001459, rs104894167, rs119488099, rs119488100, rs387906420, rs121917752, rs121918622, rs281865564, rs387907313, rs397514670
View all (165 more)
18534255
Hyperparathyroidism Hyperparathyroidism, Hyperparathyroidism, Secondary rs28942098, rs121434262, rs80356649, rs121434264, rs587776558, rs587776559, rs121909259, rs104893689, rs28936684, rs104893690, rs869320729, rs104893700, rs104893705, rs104893707, rs104893709
View all (14 more)
Unknown
Disease term Disease name Evidence References Source
Cerebral infarction Cerebral Infarction 25498546 ClinVar
Rickets vitamin D-dependent rickets, type 2 GenCC
Gout Gout GWAS
Carcinoma Carcinoma GWAS
Associations from Text Mining
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