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VDR vitamin D (1,25- dihydroxyvitamin D3) receptor [ Homo sapiens (human) ]

Gene ID: 7421, updated on 7-Dec-2014
Official Symbol
VDRprovided by HGNC
Official Full Name
vitamin D (1,25- dihydroxyvitamin D3) receptorprovided by HGNC
Primary source
HGNC:HGNC:12679
See related
Ensembl:ENSG00000111424; HPRD:03463; MIM:601769; Vega:OTTHUMG00000169890
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
NR1I1; PPP1R163
Summary
This gene encodes the nuclear hormone receptor for vitamin D3. This receptor also functions as a receptor for the secondary bile acid lithocholic acid. The receptor belongs to the family of trans-acting transcriptional regulatory factors and shows sequence similarity to the steroid and thyroid hormone receptors. Downstream targets of this nuclear hormone receptor are principally involved in mineral metabolism though the receptor regulates a variety of other metabolic pathways, such as those involved in the immune response and cancer. Mutations in this gene are associated with type II vitamin D-resistant rickets. A single nucleotide polymorphism in the initiation codon results in an alternate translation start site three codons downstream. Alternative splicing results in multiple transcript variants encoding different proteins. [provided by RefSeq, Feb 2011]
Location:
12q13.11
Exon count:
11
Annotation release Status Assembly Chr Location
106 current GRCh38 (GCF_000001405.26) 12 NC_000012.12 (47841537..47905031, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (48235320..48298814, complement)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene Rap guanine nucleotide exchange factor (GEF) 3 Neighboring gene solute carrier family 48 (heme transporter), member 1 Neighboring gene histone deacetylase 7 Neighboring gene transmembrane protein 106C Neighboring gene collagen, type II, alpha 1

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Associated conditions

Description Tests
Osteoporosis
MedGen: C0029458 OMIM: 166710 GeneReviews: Not available
Compare labs
Vitamin D-dependent rickets, type 2
MedGen: C0268690 OMIM: 277440 GeneReviews: Not available
Compare labs

NHGRI GWAS Catalog

Description
Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
NHGRI GWA Catalog

Replication interactions

Interaction Pubs
Knockdown of vitamin D (1,25- dihydroxyvitamin D3) receptor (VDR) by siRNA inhibits HIV-1 replication in HeLa P4/R5 cells PubMed

Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp120 env HIV-1 gp160 and gp120 contain alpha-N-acetylgalactosaminidase (Nagalase) activity, which deglycosylates serum vitamin D3-binding protein (Gc protein) PubMed

Go to the HIV-1, Human Interaction Database

  • Direct p53 effectors, organism-specific biosystem (from Pathway Interaction Database)
    Direct p53 effectors, organism-specific biosystem
    Direct p53 effectors
  • Drug Induction of Bile Acid Pathway, organism-specific biosystem (from WikiPathways)
    Drug Induction of Bile Acid Pathway, organism-specific biosystem
    Drug Induction of Bile Acid Pathway
  • Endocrine and other factor-regulated calcium reabsorption, organism-specific biosystem (from KEGG)
    Endocrine and other factor-regulated calcium reabsorption, organism-specific biosystemCalcium (Ca2+) is essential for numerous physiological functions including intracellular signalling processes, neuronal excitability, muscle contraction and bone formation. Therefore, its homeostasis...
  • Endocrine and other factor-regulated calcium reabsorption, conserved biosystem (from KEGG)
    Endocrine and other factor-regulated calcium reabsorption, conserved biosystemCalcium (Ca2+) is essential for numerous physiological functions including intracellular signalling processes, neuronal excitability, muscle contraction and bone formation. Therefore, its homeostasis...
  • Gene Expression, organism-specific biosystem (from REACTOME)
    Gene Expression, organism-specific biosystemGene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are process...
  • Generic Transcription Pathway, organism-specific biosystem (from REACTOME)
    Generic Transcription Pathway, organism-specific biosystemOVERVIEW OF TRANSCRIPTION REGULATION: Detailed studies of gene transcription regulation in a wide variety of eukaryotic systems has revealed the general principles and mechanisms by which cell- or t...
  • Mineral absorption, organism-specific biosystem (from KEGG)
    Mineral absorption, organism-specific biosystemMinerals are one of the five fundamental groups of nutrients needed to sustain life. Of the minerals, calcium plays innumerable roles in our bodies, serving as a main component of bone as well as an ...
  • Mineral absorption, conserved biosystem (from KEGG)
    Mineral absorption, conserved biosystemMinerals are one of the five fundamental groups of nutrients needed to sustain life. Of the minerals, calcium plays innumerable roles in our bodies, serving as a main component of bone as well as an ...
  • Nuclear Receptor transcription pathway, organism-specific biosystem (from REACTOME)
    Nuclear Receptor transcription pathway, organism-specific biosystemA classic example of bifunctional transcription factors is the family of Nuclear Receptor (NR) proteins. These are DNA-binding transcription factors that bind certain hormones, vitamins, and other s...
  • Nuclear Receptors, organism-specific biosystem (from WikiPathways)
    Nuclear Receptors, organism-specific biosystemNuclear receptors are a class of proteins found within the interior of cells that are responsible for sensing the presence of steroid and thyroid hormones and certain other molecules. In response, th...
  • Nuclear receptors in lipid metabolism and toxicity, organism-specific biosystem (from WikiPathways)
    Nuclear receptors in lipid metabolism and toxicity, organism-specific biosystemNuclear receptors are transcription factors that are activated upon binding to its ligands. Initially, they had been classified as classic endocrine nuclear hormone receptors and orphan receptors. Ho...
  • Ovarian Infertility Genes, organism-specific biosystem (from WikiPathways)
    Ovarian Infertility Genes, organism-specific biosystemOvarian bottleneck genes associated with infertility. A valuable approach to the study of infertility is the comparison of mutations of individual human and mouse genes associated with infertility ph...
  • RXR and RAR heterodimerization with other nuclear receptor, organism-specific biosystem (from Pathway Interaction Database)
    RXR and RAR heterodimerization with other nuclear receptor, organism-specific biosystem
    RXR and RAR heterodimerization with other nuclear receptor
  • Regulation of nuclear SMAD2/3 signaling, organism-specific biosystem (from Pathway Interaction Database)
    Regulation of nuclear SMAD2/3 signaling, organism-specific biosystem
    Regulation of nuclear SMAD2/3 signaling
  • Retinoic acid receptors-mediated signaling, organism-specific biosystem (from Pathway Interaction Database)
    Retinoic acid receptors-mediated signaling, organism-specific biosystem
    Retinoic acid receptors-mediated signaling
  • TGF-beta Receptor Signaling Pathway, organism-specific biosystem (from WikiPathways)
    TGF-beta Receptor Signaling Pathway, organism-specific biosystem"The TGF beta receptors TGFBR1 and TGFBR2 belong to a subfamily of membrane-bound serine/threonine kinases which are designated as Type I or II based on their structural and functional properties. Th...
  • Tuberculosis, organism-specific biosystem (from KEGG)
    Tuberculosis, organism-specific biosystemTuberculosis, or TB, is an infectious disease caused by Mycobacterium tuberculosis. One third of the world's population is thought to be infected with TB. About 90% of those infected result in latent...
  • Tuberculosis, conserved biosystem (from KEGG)
    Tuberculosis, conserved biosystemTuberculosis, or TB, is an infectious disease caused by Mycobacterium tuberculosis. One third of the world's population is thought to be infected with TB. About 90% of those infected result in latent...
  • Vitamin D synthesis, organism-specific biosystem (from WikiPathways)
    Vitamin D synthesis, organism-specific biosystemPhotochemical synthesis of vitamin D3 (cholecalciferol, D3) occurs cutaneously where pro-vitamin D3 (7-dehydrocholesterol) is converted to pre-vitamin D3 (pre-D3) in response to ultraviolet B (sunlig...
Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
calcitriol binding IDA
Inferred from Direct Assay
more info
PubMed 
calcitriol receptor activity IDA
Inferred from Direct Assay
more info
PubMed 
lithocholic acid binding IDA
Inferred from Direct Assay
more info
PubMed 
lithocholic acid receptor activity IDA
Inferred from Direct Assay
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
retinoid X receptor binding IPI
Inferred from Physical Interaction
more info
PubMed 
sequence-specific DNA binding IEA
Inferred from Electronic Annotation
more info
 
contributes_to sequence-specific DNA binding transcription factor activity IDA
Inferred from Direct Assay
more info
PubMed 
steroid hormone receptor activity IEA
Inferred from Electronic Annotation
more info
 
contributes_to vitamin D response element binding IDA
Inferred from Direct Assay
more info
PubMed 
zinc ion binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
bile acid signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
calcium ion transport IEA
Inferred from Electronic Annotation
more info
 
cell morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
cellular calcium ion homeostasis IEA
Inferred from Electronic Annotation
more info
 
decidualization IEP
Inferred from Expression Pattern
more info
PubMed 
gene expression TAS
Traceable Author Statement
more info
 
intestinal absorption IEA
Inferred from Electronic Annotation
more info
 
lactation IEA
Inferred from Electronic Annotation
more info
 
mammary gland branching involved in pregnancy IEA
Inferred from Electronic Annotation
more info
 
negative regulation of cell proliferation IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of keratinocyte proliferation IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of transcription from RNA polymerase II promoter IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of apoptotic process involved in mammary gland involution IEA
Inferred from Electronic Annotation
more info
 
positive regulation of gene expression IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of keratinocyte differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of transcription from RNA polymerase II promoter IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of vitamin D 24-hydroxylase activity IDA
Inferred from Direct Assay
more info
PubMed 
regulation of calcidiol 1-monooxygenase activity ISS
Inferred from Sequence or Structural Similarity
more info
 
signal transduction TAS
Traceable Author Statement
more info
PubMed 
skeletal system development IEA
Inferred from Electronic Annotation
more info
 
steroid hormone mediated signaling pathway IEA
Inferred from Electronic Annotation
more info
 
transcription initiation from RNA polymerase II promoter TAS
Traceable Author Statement
more info
 
vitamin D receptor signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
RNA polymerase II transcription factor complex IDA
Inferred from Direct Assay
more info
PubMed 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
receptor complex IDA
Inferred from Direct Assay
more info
PubMed 
Preferred Names
vitamin D3 receptor
Names
vitamin D3 receptor
1,25-dihydroxyvitamin D3 receptor
vitamin D nuclear receptor variant 1
nuclear receptor subfamily 1 group I member 1
protein phosphatase 1, regulatory subunit 163

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_008731.1 

    Range
    5001..68495
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_000376.2NP_000367.1  vitamin D3 receptor isoform VDRA

    See proteins identical to NP_000367.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) differs in the 5' UTR and coding sequence compared to variant 3. The resulting isoform (VDRA) is shorter at the N-terminus compared to isoform VDRB1. Variants 1 and 2 encode the same protein.
    Source sequence(s)
    AC004466, AC121338, BC060832, BM908433, BQ002808, CF138099, J03258
    Consensus CDS
    CCDS8757.1
    UniProtKB/TrEMBL
    F1D8P8
    UniProtKB/Swiss-Prot
    P11473
    Related
    ENSP00000449573, OTTHUMP00000242392, ENST00000549336, OTTHUMT00000406434
    Conserved Domains (2) summary
    cd06933
    Location:124426
    NR_LBD_VDR; The ligand binding domain of vitamin D receptors, a member of the nuclear receptor superfamily
    cd06955
    Location:16122
    NR_DBD_VDR; DNA-binding domain of vitamin D receptors (VDR) is composed of two C4-type zinc fingers
  2. NM_001017535.1NP_001017535.1  vitamin D3 receptor isoform VDRA

    See proteins identical to NP_001017535.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and coding sequence compared to variant 3. The resulting isoform (VDRA) is shorter at the N-terminus compared to isoform VDRB1. Variants 1 and 2 encode the same protein.
    Source sequence(s)
    AC004466, AC121338, BC060832, BM908433, BQ002808, BX355584, CF138099, J03258
    Consensus CDS
    CCDS8757.1
    UniProtKB/TrEMBL
    F1D8P8
    UniProtKB/Swiss-Prot
    P11473
    Related
    ENSP00000229022, ENST00000229022
    Conserved Domains (2) summary
    cd06933
    Location:124426
    NR_LBD_VDR; The ligand binding domain of vitamin D receptors, a member of the nuclear receptor superfamily
    cd06955
    Location:16122
    NR_DBD_VDR; DNA-binding domain of vitamin D receptors (VDR) is composed of two C4-type zinc fingers
  3. NM_001017536.1NP_001017536.1  vitamin D3 receptor isoform VDRB1

    See proteins identical to NP_001017536.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) represents the longest transcript and encodes the longer isoform (VDRB1).
    Source sequence(s)
    AC004466, BC060832, BM685276, DA721726
    Consensus CDS
    CCDS55820.1
    UniProtKB/Swiss-Prot
    P11473
    Conserved Domains (2) summary
    cd06933
    Location:174476
    NR_LBD_VDR; The ligand binding domain of vitamin D receptors, a member of the nuclear receptor superfamily
    cd06955
    Location:66172
    NR_DBD_VDR; DNA-binding domain of vitamin D receptors (VDR) is composed of two C4-type zinc fingers

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 106

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38 Primary Assembly

Genomic

  1. NC_000012.12 

    Range
    47841537..47905031
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006719587.1XP_006719650.1  

    See proteins identical to XP_006719650.1

    UniProtKB/TrEMBL
    F1D8P8
    UniProtKB/Swiss-Prot
    P11473
    Related
    ENSP00000447173, OTTHUMP00000242393, ENST00000550325, OTTHUMT00000406435
    Conserved Domains (2) summary
    cd06933
    Location:124426
    NR_LBD_VDR; The ligand binding domain of vitamin D receptors, a member of the nuclear receptor superfamily
    cd06955
    Location:16122
    NR_DBD_VDR; DNA-binding domain of vitamin D receptors (VDR) is composed of two C4-type zinc fingers

Alternate CHM1_1.1

Genomic

  1. NC_018923.2 

    Range
    48201212..48264704
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate HuRef

Genomic

  1. AC_000144.1 

    Range
    45266368..45330677
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)