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VDR vitamin D receptor [ Homo sapiens (human) ]

Gene ID: 7421, updated on 17-Oct-2021

Summary

Official Symbol
VDRprovided by HGNC
Official Full Name
vitamin D receptorprovided by HGNC
Primary source
HGNC:HGNC:12679
See related
Ensembl:ENSG00000111424 MIM:601769
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 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 vitamin D3 receptor are principally involved in mineral metabolism, though this receptor regulates a variety of other metabolic pathways, such as those involved in 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. Alternatively spliced transcript variants encoding different isoforms have been described for this gene. A recent study provided evidence for translational readthrough in this gene, and expression of an additional C-terminally extended isoform via the use of an alternative in-frame translation termination codon. [provided by RefSeq, Jun 2018]
Expression
Broad expression in small intestine (RPKM 24.6), duodenum (RPKM 24.1) and 14 other tissues See more
Orthologs
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Genomic context

See VDR in Genome Data Viewer
Location:
12q13.11
Exon count:
12
Annotation release Status Assembly Chr Location
109.20210514 current GRCh38.p13 (GCF_000001405.39) 12 NC_000012.12 (47841537..47905022, complement)
105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (48235320..48298777, complement)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene solute carrier family 48 member 1 Neighboring gene histone deacetylase 7 Neighboring gene long intergenic non-protein coding RNA 2354 Neighboring gene transmembrane protein 106C Neighboring gene uncharacterized LOC105369752 Neighboring gene collagen type II alpha 1 chain

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
GeneReviews: Not available
Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche.
GeneReviews: Not available
Vitamin D-dependent rickets type II with alopecia
MedGen: C0342646 OMIM: 277440 GeneReviews: Not available
Compare labs

HIV-1 interactions

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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
contributes_to DNA-binding transcription factor activity IDA
Inferred from Direct Assay
more info
PubMed 
enables DNA-binding transcription factor activity, RNA polymerase II-specific ISA
Inferred from Sequence Alignment
more info
 
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables calcitriol binding IDA
Inferred from Direct Assay
more info
PubMed 
enables calcitriol binding IMP
Inferred from Mutant Phenotype
more info
PubMed 
enables lithocholic acid binding IDA
Inferred from Direct Assay
more info
PubMed 
enables lithocholic acid receptor activity IDA
Inferred from Direct Assay
more info
PubMed 
enables nuclear receptor activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables nuclear receptor activity IDA
Inferred from Direct Assay
more info
PubMed 
enables nuclear receptor activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables retinoid X receptor binding IDA
Inferred from Direct Assay
more info
PubMed 
enables retinoid X receptor binding IPI
Inferred from Physical Interaction
more info
PubMed 
contributes_to vitamin D response element binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
contributes_to vitamin D response element binding IDA
Inferred from Direct Assay
more info
PubMed 
enables zinc ion binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
involved_in bile acid signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
involved_in calcium ion transport IEA
Inferred from Electronic Annotation
more info
 
involved_in cell differentiation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in cell morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in cellular calcium ion homeostasis IEA
Inferred from Electronic Annotation
more info
 
involved_in decidualization IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in intestinal absorption IEA
Inferred from Electronic Annotation
more info
 
involved_in lactation IEA
Inferred from Electronic Annotation
more info
 
involved_in mammary gland branching involved in pregnancy IEA
Inferred from Electronic Annotation
more info
 
involved_in multicellular organism development IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in negative regulation of cell population proliferation IDA
Inferred from Direct Assay
more info
PubMed 
acts_upstream_of_or_within negative regulation of gene expression IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in negative regulation of keratinocyte proliferation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in negative regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in negative regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
acts_upstream_of_or_within negative regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
involved_in positive regulation of apoptotic process involved in mammary gland involution IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of gene expression IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in positive regulation of keratinocyte differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in positive regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in positive regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in positive regulation of vitamin D 24-hydroxylase activity IDA
Inferred from Direct Assay
more info
PubMed 
involved_in regulation of calcidiol 1-monooxygenase activity ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in skeletal system development IEA
Inferred from Electronic Annotation
more info
 
involved_in vitamin D receptor signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
involved_in vitamin D receptor signaling pathway IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
part_of RNA polymerase II transcription regulator complex IDA
Inferred from Direct Assay
more info
PubMed 
located_in chromatin ISA
Inferred from Sequence Alignment
more info
 
located_in cytosol IDA
Inferred from Direct Assay
more info
 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
 
located_in nucleoplasm TAS
Traceable Author Statement
more info
 
located_in nucleus IDA
Inferred from Direct Assay
more info
PubMed 
part_of receptor complex IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

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 (1,25- dihydroxyvitamin D3) receptor
vitamin D nuclear receptor variant 1
vitamin D3 receptor isoform VDRA

NCBI Reference Sequences (RefSeq)

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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_000376.3NP_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) represents the predominant transcript and encodes two isoforms, which result from the use of alternative in-frame translation termination codons. The shorter isoform (VDRA, also known as VDR) results from translation termination at the upstream UGA stop codon, while the longer isoform (VDRAx, also known as VDRx) results from UGA stop codon readthrough to the downstream UGA termination codon. This RefSeq represents the shorter isoform (VDRA). Variants 1 and 2 encode the same isoform.
    Source sequence(s)
    AC004466, BC060832, BM908433, BQ002808, CF138099, J03258
    Consensus CDS
    CCDS8757.1
    UniProtKB/Swiss-Prot
    P11473
    UniProtKB/TrEMBL
    F1D8P8
    Related
    ENSP00000449573.2, ENST00000549336.6
    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_001017535.2NP_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) contains an additional 5' non-coding exon compared to variant 1. Variants 1 and 2 encode the same isoform (VDRA).
    Source sequence(s)
    AC004466, AC121338
    Consensus CDS
    CCDS8757.1
    UniProtKB/Swiss-Prot
    P11473
    UniProtKB/TrEMBL
    F1D8P8
    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_001017536.2NP_001017536.1  vitamin D3 receptor isoform VDRB1

    See identical proteins and their annotated locations for NP_001017536.1

    Status: REVIEWED

    Source sequence(s)
    AC004466, BC060832, BM685276
    Consensus CDS
    CCDS55820.1
    UniProtKB/Swiss-Prot
    P11473
    Related
    ENSP00000447173.1, ENST00000550325.5
    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
  4. NM_001364085.2NP_001351014.1  vitamin D3 receptor isoform VDRAx

    Status: REVIEWED

    Source sequence(s)
    AC004466, AC121338
    Related
    ENSP00000229022.5, ENST00000229022.9
    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
  5. NM_001374661.1NP_001361590.1  vitamin D3 receptor isoform VDRA

    Status: REVIEWED

    Source sequence(s)
    AC004466, AC121338
    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
  6. NM_001374662.1NP_001361591.1  vitamin D3 receptor isoform VDRA

    Status: REVIEWED

    Source sequence(s)
    AC004466, AC121338
    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

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20210514

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p13 Primary Assembly

    Range
    47841537..47905022 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011538720.2XP_011537022.1  vitamin D3 receptor isoform X2

    See identical proteins and their annotated locations for XP_011537022.1

    UniProtKB/Swiss-Prot
    P11473
    UniProtKB/TrEMBL
    F1D8P8
    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_024449178.1XP_024304946.1  vitamin D3 receptor isoform X1

    Conserved Domains (2) summary
    cd06933
    Location:147449
    NR_LBD_VDR; The ligand binding domain of vitamin D receptors, a member of the nuclear receptor superfamily
    cd06955
    Location:39145
    NR_DBD_VDR; DNA-binding domain of vitamin D receptors (VDR) is composed of two C4-type zinc fingers
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