VDR vitamin D receptor [Homo sapiens (human)] - Gene

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; AllianceGenome:HGNC:12679
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: mouse all
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Genomic context

Location:: 12q13.11

Exon count:: 12

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	12	NC_000012.12 (47841537..47904994, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	12	NC_060936.1 (47802918..47866398, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	12	NC_000012.11 (48235320..48298777, complement)

Chromosome 12 - NC_000012.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues 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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Association of Vitamin D receptor gene polymorphism with susceptibility and prognosis of Systemic Lupus Erythematosus in Chinese patients.
Title: Association of Vitamin D receptor gene polymorphism with susceptibility and prognosis of Systemic Lupus Erythematosus in Chinese patients.
Assessment of the contribution of VDR and VDBP/GC genes in the pathogenesis of celiac disease.
Title: Assessment of the contribution of VDR and VDBP/GC genes in the pathogenesis of celiac disease.
Prevalence and effects of Vitamin D receptor polymorphism on bone mineral density and metabolism in patients with systemic sclerosis: a preliminary study.
Title: Prevalence and effects of Vitamin D receptor polymorphism on bone mineral density and metabolism in patients with systemic sclerosis: a preliminary study.
Association of single nucleotide genetic polymorphisms of vitamin D receptor and calcium-sensitive receptor with calcium-containing kidney stones in Chinese Dai populations: a prospective multi-center study.
Title: Association of single nucleotide genetic polymorphisms of vitamin D receptor and calcium-sensitive receptor with calcium-containing kidney stones in Chinese Dai populations: a prospective multi-center study.
Molecular investigation of vitamin D receptor (VDR) genetic variants and their impact on VDR mRNA and serum vitamin D levels in allergic rhinitis in an Indian population: A case-control study.
Title: Molecular investigation of vitamin D receptor (VDR) genetic variants and their impact on VDR mRNA and serum vitamin D levels in allergic rhinitis in an Indian population: A case-control study.
Association of vitamin D receptor gene polymorphisms with caries risk in children: a systematic review and meta-analysis.
Title: Association of vitamin D receptor gene polymorphisms with caries risk in children: a systematic review and meta-analysis.
Role of Vitamin D Receptor (BsmI-VDR) and Insulin Receptor (NsiI-A/G) Gene Polymorphisms in Colorectal Adenoma Susceptibility.
Title: Role of Vitamin D Receptor (BsmI-VDR) and Insulin Receptor (NsiI-A/G) Gene Polymorphisms in Colorectal Adenoma Susceptibility.
The Impact of Vitamin D Receptor Gene Polymorphisms (FokI, ApaI, TaqI) in Correlation with Oxidative Stress and Hormonal and Dermatologic Manifestations in Polycystic Ovary Syndrome.
Title: The Impact of Vitamin D Receptor Gene Polymorphisms (FokI, ApaI, TaqI) in Correlation with Oxidative Stress and Hormonal and Dermatologic Manifestations in Polycystic Ovary Syndrome.
Vitamin D Status, Vitamin D Receptor Polymorphisms, and Risk of Type 2 Diabetes: A Prospective Cohort Study.
Title: Vitamin D Status, Vitamin D Receptor Polymorphisms, and Risk of Type 2 Diabetes: A Prospective Cohort Study.
Vitamin D receptor gene polymorphisms and multiple myeloma: a meta-analysis.
Title: Vitamin D receptor gene polymorphisms and multiple myeloma: a meta-analysis.

Submit: New GeneRIF Correction See all GeneRIFs (1950)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Vitamin D-dependent rickets type II with alopecia MedGen: C0342646 OMIM: 277440 GeneReviews: Not available	not available

EBI GWAS Catalog

Description
Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease. EBI GWAS Catalog EBI GWAS CatalogPubMed
Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

WI-17447 (e-PCR)
- UniSTS:55150

VDRU1 (e-PCR)
- UniSTS:463500

VDRU2 (e-PCR)
- UniSTS:463501

VDRU3 (e-PCR)
- UniSTS:463502

VDRU4 (e-PCR)
- UniSTS:463503

VDRU5 (e-PCR)
- UniSTS:463504

VDRU5-PoA (e-PCR)
- UniSTS:463505

VDR (e-PCR)
- UniSTS:503993

GDB:384887 (e-PCR)
- UniSTS:157116

RH17584 (e-PCR)
- UniSTS:5822

SHGC-142050 (e-PCR)
- UniSTS:171215

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
enables bile acid nuclear receptor activity	IDA Inferred from Direct Assay 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 nuclear receptor activity	IBA Inferred from Biological aspect of Ancestor more info
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 nuclear retinoid X receptor binding	IDA Inferred from Direct Assay more info	PubMed
enables nuclear retinoid X receptor binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein 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
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 apoptotic process involved in mammary gland involution	IEA Inferred from Electronic Annotation more info
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
involved_in cell morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in decidualization	IEP Inferred from Expression Pattern more info	PubMed
involved_in intestinal absorption	IEA Inferred from Electronic Annotation more info
involved_in intracellular calcium ion homeostasis	IEA Inferred from Electronic Annotation more info
involved_in lactation	IEA Inferred from Electronic Annotation more info
involved_in mRNA transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in mRNA transcription by RNA polymerase II	ISS Inferred from Sequence or Structural Similarity more info
involved_in mammary gland branching involved in pregnancy	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within negative regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of cell population proliferation	IDA Inferred from Direct Assay 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
involved_in negative regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in nuclear receptor-mediated bile acid signaling pathway	IDA Inferred from Direct Assay more info	PubMed
involved_in phosphate ion transmembrane transport	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 bone mineralization	NAS Non-traceable Author Statement more info	PubMed
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
involved_in positive regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay 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 transcription by RNA polymerase II	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of vitamin D 24-hydroxylase activity	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of vitamin D receptor signaling pathway	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of vitamin D receptor signaling pathway	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of calcidiol 1-monooxygenase activity	ISS Inferred from Sequence or Structural Similarity more info
involved_in response to bile acid	IDA Inferred from Direct Assay more info	PubMed
involved_in retinoic acid receptor signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
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
part_of RNA polymerase II transcription regulator complex	IPI Inferred from Physical Interaction more info	PubMed
part_of RNA polymerase II transcription regulator complex	ISS Inferred from Sequence or Structural Similarity more info
is_active_in chromatin	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
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
is_active_in nucleus	IDA Inferred from Direct Assay more info	PubMed
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

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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

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

NG_008731.1 RefSeqGene

Range

5038..68495

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_000376.3 → NP_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

B2R5Q1, G3V1V9, P11473, Q5PSV3

UniProtKB/TrEMBL

B6ZGT0, F1D8P8

Related

ENSP00000449573.2, ENST00000549336.6

Conserved Domains (2) summary

cd06933
Location:124 → 426

NR_LBD_VDR; The ligand binding domain of vitamin D receptors, a member of the nuclear receptor superfamily

cd06955
Location:16 → 122

NR_DBD_VDR; DNA-binding domain of vitamin D receptors (VDR) is composed of two C4-type zinc fingers
NM_001017535.2 → NP_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

B2R5Q1, G3V1V9, P11473, Q5PSV3

UniProtKB/TrEMBL

B6ZGT0, F1D8P8

Conserved Domains (2) summary

cd06933
Location:124 → 426

NR_LBD_VDR; The ligand binding domain of vitamin D receptors, a member of the nuclear receptor superfamily

cd06955
Location:16 → 122

NR_DBD_VDR; DNA-binding domain of vitamin D receptors (VDR) is composed of two C4-type zinc fingers
NM_001017536.2 → NP_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/TrEMBL

B6ZGT0

Related

ENSP00000447173.1, ENST00000550325.5

Conserved Domains (2) summary

cd06933
Location:174 → 476

NR_LBD_VDR; The ligand binding domain of vitamin D receptors, a member of the nuclear receptor superfamily

cd06955
Location:66 → 172

NR_DBD_VDR; DNA-binding domain of vitamin D receptors (VDR) is composed of two C4-type zinc fingers
NM_001364085.2 → NP_001351014.1 vitamin D3 receptor isoform VDRAx

Status: REVIEWED

Source sequence(s)

AC004466, AC121338

Consensus CDS

CCDS91689.1

UniProtKB/TrEMBL

A0A5K1VW50, B6ZGT0

Related

ENSP00000229022.5, ENST00000229022.9

Conserved Domains (2) summary

cd06933
Location:124 → 426

NR_LBD_VDR; The ligand binding domain of vitamin D receptors, a member of the nuclear receptor superfamily

cd06955
Location:16 → 122

NR_DBD_VDR; DNA-binding domain of vitamin D receptors (VDR) is composed of two C4-type zinc fingers
NM_001374661.1 → NP_001361590.1 vitamin D3 receptor isoform VDRA

Status: REVIEWED

Source sequence(s)

AC004466, AC121338

Consensus CDS

CCDS8757.1

UniProtKB/Swiss-Prot

B2R5Q1, G3V1V9, P11473, Q5PSV3

UniProtKB/TrEMBL

B6ZGT0, F1D8P8

Conserved Domains (2) summary

cd06933
Location:124 → 426

NR_LBD_VDR; The ligand binding domain of vitamin D receptors, a member of the nuclear receptor superfamily

cd06955
Location:16 → 122

NR_DBD_VDR; DNA-binding domain of vitamin D receptors (VDR) is composed of two C4-type zinc fingers
NM_001374662.1 → NP_001361591.1 vitamin D3 receptor isoform VDRA

Status: REVIEWED

Source sequence(s)

AC004466, AC121338

Consensus CDS

CCDS8757.1

UniProtKB/Swiss-Prot

B2R5Q1, G3V1V9, P11473, Q5PSV3

UniProtKB/TrEMBL

B6ZGT0, F1D8P8

Conserved Domains (2) summary

cd06933
Location:124 → 426

NR_LBD_VDR; The ligand binding domain of vitamin D receptors, a member of the nuclear receptor superfamily

cd06955
Location:16 → 122

NR_DBD_VDR; DNA-binding domain of vitamin D receptors (VDR) is composed of two C4-type zinc fingers

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000012.12 Reference GRCh38.p14 Primary Assembly

Range

47841537..47904994 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047429500.1 → XP_047285456.1 vitamin D3 receptor isoform X2

UniProtKB/Swiss-Prot

B2R5Q1, G3V1V9, P11473, Q5PSV3

UniProtKB/TrEMBL

F1D8P8
XM_024449178.2 → XP_024304946.1 vitamin D3 receptor isoform X1

UniProtKB/TrEMBL

B6ZGT0

Conserved Domains (2) summary

cd06933
Location:147 → 449

NR_LBD_VDR; The ligand binding domain of vitamin D receptors, a member of the nuclear receptor superfamily

cd06955
Location:39 → 145

NR_DBD_VDR; DNA-binding domain of vitamin D receptors (VDR) is composed of two C4-type zinc fingers