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

    Gene ID: 7421, updated on 5-Jul-2015
    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]
    Orthologs
    Location:
    12q13.11
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    107 current GRCh38.p2 (GCF_000001405.28) 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 uncharacterized LOC105369748 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 uncharacterized LOC105369749 Neighboring gene uncharacterized LOC105369752 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
    Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche.
    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)
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    • 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)
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    • Nuclear receptors in lipid metabolism and toxicity, organism-specific biosystem (from WikiPathways)
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    • 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
    1,25-dihydroxyvitamin D3 receptor
    nuclear receptor subfamily 1 group I member 1
    protein phosphatase 1, regulatory subunit 163
    vitamin D nuclear receptor variant 1

    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 RefSeqGene

      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 identical proteins and their annotated locations for 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 identical proteins and their annotated locations for 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 identical proteins and their annotated locations for 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 107

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

    Reference GRCh38.p2 Primary Assembly

    Genomic

    1. NC_000012.12 Reference GRCh38.p2 Primary Assembly

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

    mRNA and Protein(s)

    1. XM_006719587.2XP_006719650.1  

      See identical proteins and their annotated locations for XP_006719650.1

      UniProtKB/TrEMBL
      F1D8P8
      UniProtKB/Swiss-Prot
      P11473
      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. XM_011538720.1XP_011537022.1  

      See identical proteins and their annotated locations for XP_011537022.1

      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 Alternate CHM1_1.1

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