Selected-GenAtlas references SOURCE GeneCards NCBI Gene Swiss-Prot Orphanet Ensembl
HGNC UniGene Nucleotide OMIM UCSC
Home Page
FLASH GENE
Symbol VDR contributors: mct/npt/pgu - updated : 01-10-2015
HGNC name vitamin D (1,25- dihydroxyvitamin D3) receptor
HGNC id 12679
Corresponding disease
VDDR2 vitamin D-dependent rickets, type II
VDRA rickets, vitamin D-dependent, type II, with alopecia
Location 12q13.11      Physical location : 48.235.321 - 48.298.814
Synonym name nuclear receptor subfamily 1 group I member 1
Synonym symbol(s) NR1I1, PPP1R163
DNA
TYPE functioning gene
STRUCTURE 63.49 kb     10 Exon(s)
10 Kb 5' upstream gene genomic sequence study
text structure 8 exons coding
MAPPING cloned Y linked   status confirmed
Map cen - (VDR ,COL2A1 ) - (PDDR ,ELA1 ,D12S15 ) - D12S4 - (D12S14 ,D12S17 ) - D12S6 - qter
Physical map
SLC38A4 12q12-q13 solute carrier family 38, member 4 LOC390310 12 similar to transient receptor protein 6 AMIGO2 12q13.11 amphoterin induced gene 2 MGC16044 12q13.11 hypothetical protein MGC16044 LOC387854 12 LOC387854 LOC387855 12 LOC387855 FLJ21908 12q13.11 hypothetical protein FLJ21908 P11 12q13.1 26 serine protease EPAC 12q13.1 Rap1 guanine-nucleotide-exchange factor directly activated by cAMP FLJ20489 12q13.11 hypothetical protein FLJ20489 HDAC7A 12q13.1 histone deacetylase 7A VDR 12q13.1 vitamin D (1,25- dihydroxyvitamin D3) receptor MGC5576 12q13.1 hypothetical protein MGC5576 COL2A1 12q13.1 collagen, type II, alpha 1 (primary osteoarthritis, spondyloepiphyseal dysplasia, congenital) LOC283389 12q13.12 hypothetical gene supported by BC029593 SENP1 12q12-q13 hypothetical gene supported by BC029593 PFKM 12q13.1 phosphofructokinase, muscle ASB8 12q13.12 ankyrin repeat and SOCS box-containing 8 LOC390311 12 similar to prohibitin LOC387856 12 similar to expressed sequence AI836003 LOC121275 12q13.12 similar to Olfactory receptor 10AD1 LOC341567 12q13.12 HANP1 FLJ31295 12q13.12 hypothetical protein FLJ31295 LOC390312 12 similar to olfactory receptor MOR160-1 ANP32D 12p11.1 acidic (leucine-rich) nuclear phosphoprotein 32 family, member D MGC35033 12q13.12 hypothetical protein MGC35033 LOC341568 12q13.12 similar to seven transmembrane helix receptor LOC390313 12 similar to seven transmembrane helix receptor LALBA 12q13.1 lactalbumin, alpha- LOC121270 12q13.12 similar to olfactory receptor MOR122-1 FLJ20436 12q13.12 hypothetical protein FLJ20436 CCNT1 12q13.1 cyclin T1 LOC255411 12q13.12 hypothetical LOC255411 ADCY6 12q12-q13 adenylate cyclase 6 LOC390314 12 similar to Protein C20orf27 CACNB3 12q13 calcium channel, voltage-dependent, beta 3 subunit DDX23 12q13.12 DEAD (Asp-Glu-Ala-Asp) box polypeptide 23 RHO6 12q12-q13 DEAD (Asp-Glu-Ala-Asp) box polypeptide 23 NYD-SP28 12q13.12 NYD-SP28 protein
RNA
TRANSCRIPTS type messenger
identificationnb exonstypebpproduct
ProteinkDaAAspecific expressionYearPubmed
10 - 4669 48 427 - 2011 21982773
11 - 4791 - 427 - 2011 21982773
10 - 5060 - 477 - 2011 21982773
EXPRESSION
Type widely
   expressed in (based on citations)
organ(s)
SystemOrgan level 1Organ level 2Organ level 3Organ level 4LevelPubmedSpeciesStageRna symbol
Cardiovascularheart    
Endocrineparathyroid   predominantly
Nervousbrainmidbrainsubstantia nigra   Homo sapiens
Reproductivefemale systemuteruscervix  
 female systemovary  highly
 male systemprostate   
Urinarykidney    
cells
SystemCellPubmedSpeciesStageRna symbol
Nervousdopaminergic neuron Homo sapiensFetal
cell lineage
cell lines
fluid/secretion
at STAGE
PROTEIN
PHYSICAL PROPERTIES
STRUCTURE
motifs/domains
  • N terminal DNA-binding domain (DBD), containing two zinc fingers that mediate VDR-DNA interactions
  • two zinc finger motifs
  • two short activation function domains, AF1 and AF2, important for nuclear co-modulator recruitment are found at the N and C termini respectively
  • a c terminal half containing a ligand-binding domain (LBD)
  • a hinge region made of a long alpha-helical structure, the loop between the alpha helix
  • the second zinc finger containing a short six residue region referred to as the T box and interacting with RXR*
  • mono polymer heteromer , dimer
    HOMOLOGY
    Homologene
    FAMILY
  • nuclear steroid/thyroid hormone receptor superfamily
  • NR1 subfamily
  • CATEGORY transcription factor , receptor
    SUBCELLULAR LOCALIZATION     intracellular
    intracellular,nucleus,nucleoplasm
    text
  • HR interacts with VDR and induces VDR relocalization in the nuclei
  • basic FUNCTION
  • mediating the action of vitamin D3 by controlling the expression of hormone sensitive genes
  • VDR and coactivators NCOA2 and NCOA3, which are also involved in other nuclear receptors as well, are critical for epidermis-specific sphingolipid production and barrier formation
  • Vitamin D and VDR are important regulators of inflammation in the lungs
  • potentially playing a vital role in lung development, function and extracellular matrix remodeling
  • important regulator of mineral ion homeostasis
  • through its interactions with LEF1, contributes potentially to regulation of the canonical Wnt and Hedgehog signaling pathways in the epidermis
  • HR and the vitamin D receptor (VDR) play a critical role in the maintenance of hair growth
  • plays a critical role in epidermal homeostasis
  • vitamin D and VDR regulate the MYC/MXD1 network to suppress MYC function, providing a molecular basis for cancer preventive actions of vitamin D
  • transcription factor that mediates the genomic effects of (1,25(OH)2D3)
  • contribution of VDR and SOST, as well as 1,25-dihydroxyvitamin D, to increase bone resorption in idiopathic hypercalciuria
  • CELLULAR PROCESS nucleotide, transcription
    PHYSIOLOGICAL PROCESS
    PATHWAY
    metabolism metal
    signaling
    calcium
    a component
  • heterodimerizing with retinoic acid X receptors RXR
  • RIPK1 also formed a complex with VDR, and RIPK1 increased VDR retention in the cytoplasm, which may account for its inhibition of VDR transcriptional activity
  • INTERACTION
    DNA
    RNA
    small molecule
    protein
  • retinoic acid receptors RXR*
  • interacting with SNAI1 (correlation between low expression of VDR with poor differentiation of the tumors, and overexpression of SNAI1 and vascular invasion)
  • interacting with TCF8 and SNAI1 in colorectal cancer (loss of VDR and TCF8 and presence of SNAI1 is predictor of poor clinical prognosis)
  • interacting with NCOR2 (role of helix 12 of VDR in NCOR2 corepressor interaction)
  • interaction between VDR and the C-terminus of NUP214 containing a cluster of the phenylalanine-glycine (FG) repeat
  • COL1A1
  • interaction between VDR and CAV3 (providing that VDR plays a role in regulation of heart structure and function)
  • interaction between VDR and LEF1 that is mediated by the DNA-binding domain of the VDR and that is required for normal canonical Wnt signaling in keratinocytes
  • VDR physically interacts with IKBKB to block NFKB1 activation
  • overexpression of IGFBP3 suppresses osteoblastic differentiation regulated by VDR in the presence of 1,25-(OH)2D3
  • VDR-mediated control of DKKL1, SOSTDC1, and HR gene expression in keratinocytes
  • activation of the VDR represses hepatic NR0B2 to increase levels on CYP7A1 and reduce cholesterol
  • is a negative regulator of TGFB1/SMAD signalling, and regulates TGFB1 signalling in systemic sclerosis
  • activated CD4+ T cells can produce 1,25(OH)2D3, and 1,25(OH)2D3 induces a 2-fold up-regulation of the VDR protein expression in activated CD4+ T cells by protecting the VDR against proteasomal degradation
  • regulation of ELOVL3 expression is mediated by ligand-dependent VDR occupancy of a negative-response element in the promoter proximal region of the ELOVL3 gene
  • cell & other
    REGULATION
    Other phosphorylation of by CSNK2A1 at Ser-208 specifically modulates its transcriptional capacity, suggesting that this covalent modification alters the conformation of VDR to potentiate its interaction with the machinery for DNA transcription
    ASSOCIATED DISORDERS
    corresponding disease(s) VDRA , VDDR2
    Other morbid association(s)
    TypeGene ModificationChromosome rearrangementProtein expressionProtein Function
    tumoral     --low  
    in colorectal cancer with poor differentiation
    constitutional     --low  
    in lungs of patients with chronic obstructive pulmonary disease (COPD)
    constitutional   deletion    
    leads to premature emphysema/COPD by increased matrix metalloproteinases and lymphoid aggregates formation
    Susceptibility
  • to osteoporosis
  • to higher adult height
  • to lower circulating vitamin D and lower height in adolescent girl
  • to idiopathic short stature
  • Variant & Polymorphism SNP , other
  • A>G at intron 8 associated with higher adult height
  • T>C at exon 9 associated with higher adult height
  • homozygous 1521C/1012G associated with lower circulating vitamin D and lower height in adolescent girl
  • SNP associated to idiopathic short stature
  • Candidate gene
    Marker
    Therapy target
    SystemTypeDisorderPubmed
    cancerdigestivecolon
    therapy target for colorectal cancer
    immunologyautoimmune 
    VDR/MED1 interaction is of potential therapeutic interest
    ANIMAL & CELL MODELS
  • VDR null mice exhibit abnormal cutaneous barrier function with altered lipid composition
  • significant increase in infiltration of macrophages into the lung interstitium of VDR-/- mice, but not in WT