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 metabo... See more...

Aliases for VDR Gene

Aliases for VDR Gene

  • Vitamin D Receptor 2 3 5
  • NR1I1 2 3 4
  • Vitamin D (1,25- Dihydroxyvitamin D3) Receptor 2 3
  • Protein Phosphatase 1, Regulatory Subunit 163 2 3
  • Nuclear Receptor Subfamily 1 Group I Member 1 3 4
  • 1,25-Dihydroxyvitamin D3 Receptor 3 4
  • Vitamin D3 Receptor 3 4
  • PPP1R163 2 3
  • Vitamin D Nuclear Receptor Variant 1 3
  • 1,25- Dihydroxyvitamin D3 Receptor 2
  • VDR 5

External Ids for VDR Gene

Previous GeneCards Identifiers for VDR Gene

  • GC12M048247
  • GC12M048134
  • GC12M047952
  • GC12M046521
  • GC12M045266

Summaries for VDR Gene

Entrez Gene Summary for VDR Gene

  • 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]

GeneCards Summary for VDR Gene

VDR (Vitamin D Receptor) is a Protein Coding gene. Diseases associated with VDR include Vitamin D-Dependent Rickets, Type 2A and Osteoporosis. Among its related pathways are Gene Expression and Development_Hedgehog and PTH signaling pathways in bone and cartilage development. Gene Ontology (GO) annotations related to this gene include DNA-binding transcription factor activity and steroid hormone receptor activity. An important paralog of this gene is NR1I2.

UniProtKB/Swiss-Prot Summary for VDR Gene

  • Nuclear receptor for calcitriol, the active form of vitamin D3 which mediates the action of this vitamin on cells (PubMed:28698609, PubMed:16913708, PubMed:15728261, PubMed:10678179). Enters the nucleus upon vitamin D3 binding where it forms heterodimers with the retinoid X receptor/RXR (PubMed:28698609). The VDR-RXR heterodimers bind to specific response elements on DNA and activate the transcription of vitamin D3-responsive target genes (PubMed:28698609). Plays a central role in calcium homeostasis (By similarity).

Tocris Summary for VDR Gene

  • Vitamin D receptors (VDRs) are members of the NR1I family, which also includes pregnane X receptors (PXR) and constitutive androstane receptors (CAR). They form heterodimers with retinoid X receptor family members, and are expressed in the intestine, thyroid and kidney.

Gene Wiki entry for VDR Gene

PharmGKB "VIP" Summary for VDR Gene

No data available for CIViC Summary , Rfam classification and piRNA Summary for VDR Gene

Genomics for VDR Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for VDR Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around VDR on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for VDR

Top Transcription factor binding sites by QIAGEN in the VDR gene promoter:
  • PPAR-alpha
  • PPAR-gamma1
  • PPAR-gamma2

Genomic Locations for VDR Gene

Latest Assembly
chr12:47,841,537-47,943,048
(GRCh38/hg38)
Size:
101,512 bases
Orientation:
Minus strand

Previous Assembly
chr12:48,235,320-48,298,777
(GRCh37/hg19 by Entrez Gene)
Size:
63,458 bases
Orientation:
Minus strand

chr12:48,235,320-48,336,831
(GRCh37/hg19 by Ensembl)
Size:
101,512 bases
Orientation:
Minus strand

Genomic View for VDR Gene

Genes around VDR on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
VDR Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for VDR Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for VDR Gene

Proteins for VDR Gene

  • Protein details for VDR Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P11473-VDR_HUMAN
    Recommended name:
    Vitamin D3 receptor
    Protein Accession:
    P11473
    Secondary Accessions:
    • B2R5Q1
    • G3V1V9
    • Q5PSV3

    Protein attributes for VDR Gene

    Size:
    427 amino acids
    Molecular mass:
    48289 Da
    Quaternary structure:
    • Homodimer in the absence of bound vitamin D3 (PubMed:11980721). Heterodimer with RXRA after vitamin D3 binding (PubMed:15225774, PubMed:11980721, PubMed:10678179). Interacts with MED1, NCOA1, NCOA2, NCOA3 and NCOA6 coactivators, leading to a strong increase of transcription of target genes (PubMed:10866662, PubMed:15728261, PubMed:28698609, PubMed:9267036). Interacts with the corepressor NCOR1 (PubMed:28698609). Interacts with SNW1 (PubMed:9632709). Interacts with IRX4, the interaction does not affect its transactivation activity (PubMed:22323358). Interacts with CRY1 (By similarity). Interacts with CRY2 in a ligand-dependent manner (By similarity).
    SequenceCaution:
    • Sequence=AAH60832.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305}; Sequence=AAP88938.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for VDR Gene

    Alternative splice isoforms for VDR Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for VDR Gene

Post-translational modifications for VDR Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Antibodies for research

No data available for DME Specific Peptides for VDR Gene

Domains & Families for VDR Gene

Gene Families for VDR Gene

HGNC:
IUPHAR :
Human Protein Atlas (HPA):
  • Disease related genes
  • FDA approved drug targets
  • Nuclear receptors
  • Predicted intracellular proteins
  • Transcription factors
  • Transporters

Protein Domains for VDR Gene

InterPro:
Blocks:
  • Vitamin D receptor signature
  • Steroid hormone receptor signature

Suggested Antigen Peptide Sequences for VDR Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ51539, highly similar to Vitamin D3 receptor (B4DRV7_HUMAN)
  • Vitamin D (1,25-dihydroxyvitamin D3) receptor (B6ZGT0_HUMAN)
  • Vitamin D nuclear receptor variant 1 (F1D8P8_HUMAN)
  • Vitamin D receptor (Q6SZ90_HUMAN)
  • Vitamin D receptor (Q6T928_HUMAN)

Graphical View of Domain Structure for InterPro Entry

P11473

UniProtKB/Swiss-Prot:

VDR_HUMAN :
  • Composed of three domains: a modulating N-terminal domain, a DNA-binding domain and a C-terminal ligand-binding domain.
  • Belongs to the nuclear hormone receptor family. NR1 subfamily.
Domain:
  • Composed of three domains: a modulating N-terminal domain, a DNA-binding domain and a C-terminal ligand-binding domain.
  • The 9aaTAD motif is a transactivation domain present in a large number of yeast and animal transcription factors.
Family:
  • Belongs to the nuclear hormone receptor family. NR1 subfamily.
genes like me logo Genes that share domains with VDR: view

Function for VDR Gene

Molecular function for VDR Gene

UniProtKB/Swiss-Prot Function:
Nuclear receptor for calcitriol, the active form of vitamin D3 which mediates the action of this vitamin on cells (PubMed:28698609, PubMed:16913708, PubMed:15728261, PubMed:10678179). Enters the nucleus upon vitamin D3 binding where it forms heterodimers with the retinoid X receptor/RXR (PubMed:28698609). The VDR-RXR heterodimers bind to specific response elements on DNA and activate the transcription of vitamin D3-responsive target genes (PubMed:28698609). Plays a central role in calcium homeostasis (By similarity).
GENATLAS Biochemistry:
vitamin D (1,25-dihydroxyvitamin D3) receptor,48kDa,nuclear steroid/thyroid hormone receptor superfamily,heterodimerizing with retinoic acid X receptors RXR*

Phenotypes From GWAS Catalog for VDR Gene

Gene Ontology (GO) - Molecular Function for VDR Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000978 RNA polymerase II proximal promoter sequence-specific DNA binding IBA 21873635
GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific ISA --
GO:0003677 DNA binding IEA,IDA 11891224
GO:0003700 contributes_to DNA-binding transcription factor activity IEA,IDA 17426122
GO:0004879 nuclear receptor activity IEA,IMP 28698609
genes like me logo Genes that share ontologies with VDR: view
genes like me logo Genes that share phenotypes with VDR: view

Human Phenotype Ontology for VDR Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for VDR Gene

MGI Knock Outs for VDR:
  • Vdr Vdr<tm1Ska>
  • Vdr Vdr<tm1.2Sgcg>
  • Vdr Vdr<tm1.1Gcm>
  • Vdr Vdr<tm1.1Pcn>
  • Vdr Vdr<tm1Mbd>
  • Vdr Vdr<tm1Rge>
  • Vdr Vdr<tm1Tyam>

miRNA for VDR Gene

miRTarBase miRNAs that target VDR
Targeted motifs for VDR Gene
HOMER Transcription Factor Regulatory Elements motif VDR
  • Consensus sequence: NGAGGTCANNGAGTTCANNN Submotif: DR3 Cell Type: GM10855 GEO ID: GSE22484

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for VDR

No data available for Enzyme Numbers (IUBMB) and Transcription Factor Targets for VDR Gene

Localization for VDR Gene

Subcellular locations from UniProtKB/Swiss-Prot for VDR Gene

Nucleus. Cytoplasm. Note=Localizes mainly to the nucleus (PubMed:28698609, PubMed:12145331). Localization to the nucleus is enhanced by vitamin D3. {ECO:0000269 PubMed:12145331, ECO:0000269 PubMed:28698609}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for VDR gene
Compartment Confidence
nucleus 5
cytosol 5
extracellular 3
cytoskeleton 3
plasma membrane 2
mitochondrion 2
peroxisome 2
endoplasmic reticulum 2
lysosome 2
endosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoplasm (3)
  • Cytosol (2)
  • Intermediate filaments (1)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for VDR Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000785 chromatin ISA --
GO:0005634 nucleus IEA,IDA 15589699
GO:0005654 nucleoplasm IDA,TAS --
GO:0005737 cytoplasm IEA --
GO:0005829 cytosol IDA --
genes like me logo Genes that share ontologies with VDR: view

Pathways & Interactions for VDR Gene

genes like me logo Genes that share pathways with VDR: view

Pathways by source for VDR Gene

3 GeneGo (Thomson Reuters) pathways for VDR Gene
  • Development Role of Activin A in cell differentiation and proliferation
  • Development_Hedgehog and PTH signaling pathways in bone and cartilage development
  • Transcription_Role of VDR in regulation of genes involved in osteoporosis
1 Cell Signaling Technology pathway for VDR Gene

SIGNOR curated interactions for VDR Gene

Activates:
Inactivates:
Is activated by:
Is inactivated by:

Gene Ontology (GO) - Biological Process for VDR Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription by RNA polymerase II IDA 17426122
GO:0000902 cell morphogenesis IMP 17223341
GO:0001501 skeletal system development IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006367 transcription initiation from RNA polymerase II promoter TAS --
genes like me logo Genes that share ontologies with VDR: view

Drugs & Compounds for VDR Gene

(122) Drugs for VDR Gene - From: DrugBank, PharmGKB, ClinicalTrials, ApexBio, DGIdb, IUPHAR, HMDB, Tocris, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Calcipotriol Approved Pharma Agonist, Target, antagonist Vitamin D3 analog,regulates cell differentiation and proliferation 0
Calcitriol Approved Nutra Target, antagonist TNF-α and IL-1β production inhibitor, Vitamin D receptor (VDR) agonist 180
Doxercalciferol Approved Pharma Target, suppressor, antagonist Vitamin D receptor activator, Vitamin D2 analog, VDR agonist 0
Paricalcitol Approved, Investigational Pharma Target, agonist Analog of VD2 active form 0
Ergocalciferol Approved Nutra Target, agonist, antagonist 434

(47) Additional Compounds for VDR Gene - From: Novoseek, IUPHAR, and Tocris

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
EB 1089
134404-52-7
EB1089
Agonist
KH1060
Agonist
TEI-9647
Antagonist
TV-02H
Agonist

(4) Tocris Compounds for VDR Gene

Compound Action Cas Number
Calcitriol Vitamin D receptor (VDR) agonist 32222-06-3
Doxercalciferol Vitamin D2 analog, VDR agonist 54573-75-0
EB 1089 Vitamin D receptor (VDR) agonist 134404-52-7
Ercalcitriol Active metabolite of vitamin D2 60133-18-8

(18) ApexBio Compounds for VDR Gene

Compound Action Cas Number
1alpha, 25-Dihydroxy VD2-D6 216244-04-1
24, 25-Dihydroxy VD3 Vitamin D analogue 40013-87-4
Alfacalcidol Bone resorption inhibitor 41294-56-8
Calcifediol Major circulating form of vitamin D3 19356-17-3
Calcifediol monohydrate Prehormone;vitamin D3 metabolite 63283-36-3
Calcipotriol Vitamin D3 analog,regulates cell differentiation and proliferation 112965-21-6
Calcitriol TNF-α and IL-1β production inhibitor 32222-06-3
Doxercalciferol Vitamin D receptor activator 54573-75-0
Ercalcidiol Vitamin D2 metabolite,ligand of VDR-like receptors 21343-40-8
Ercalcitriol Active metabolite of vitamin D2 60133-18-8
Lithocholic Acid Activator of vitamin D receptor,PXR and FXR 434-13-9
Maxacalcitol Non-calcemic vitamin D3 analog and VDR ligand. 103909-75-7
MC 1046 Vitamin D3 analog 126860-83-1
Paricalcitol Analog of VD2 active form 131918-61-1
Seocalcitol Vitamin D receptor agonist 134404-52-7
Tacalcitol Promotes normal bone development by regulating calcium 57333-96-7
vitamin D binding protein precursor (353-363) [Homo sapiens] Highly polymorphic serum glycoprotein
Vitamin D3 Fat-soluble secosteroids 67-97-0
genes like me logo Genes that share compounds with VDR: view

Drug products for research

Transcripts for VDR Gene

mRNA/cDNA for VDR Gene

6 REFSEQ mRNAs :
18 NCBI additional mRNA sequence :
8 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for VDR

Alternative Splicing Database (ASD) splice patterns (SP) for VDR Gene

ExUns: 1a · 1b · 1c · 1d ^ 2a · 2b ^ 3 ^ 4 ^ 5a · 5b ^ 6a · 6b ^ 7 ^ 8 ^ 9 ^ 10
SP1: - -
SP2: -
SP3: - - -
SP4:

Relevant External Links for VDR Gene

GeneLoc Exon Structure for
VDR

Expression for VDR Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for VDR Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for VDR Gene

This gene is overexpressed in Colon - Transverse (x6.5) and Skin - Not Sun Exposed (Suprapubic) (x4.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for VDR Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for VDR

SOURCE GeneReport for Unigene cluster for VDR Gene:

Hs.524368

Evidence on tissue expression from TISSUES for VDR Gene

  • Blood(4.5)
  • Eye(4.3)
  • Thyroid gland(3.8)
  • Kidney(3.1)
  • Intestine(3)
  • Skin(2.8)
  • Bone(2.4)
  • Lung(2.3)
  • Heart(2.3)
  • Muscle(2.3)
  • Spleen(2.3)
  • Lymph node(2.3)
  • Liver(2.2)
  • Pancreas(2.1)
  • Bone marrow(2.1)
  • Nervous system(2.1)
  • Adrenal gland(2)
  • Gall bladder(2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for VDR Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • endocrine
  • immune
  • integumentary
  • nervous
  • respiratory
  • skeletal muscle
  • skeleton
  • urinary
Regions:
Head and neck:
  • brain
  • ear
  • eye
  • face
  • forehead
  • head
  • jaw
  • larynx
  • mandible
  • maxilla
  • mouth
  • neck
  • parathyroid
  • skull
  • thyroid
  • tooth
Thorax:
  • chest wall
  • clavicle
  • diaphragm
  • esophagus
  • heart
  • rib
  • rib cage
  • scapula
  • sternum
Abdomen:
  • abdominal wall
  • biliary tract
  • intestine
  • kidney
  • large intestine
  • liver
  • small intestine
  • stomach
Pelvis:
  • pelvis
  • ureter
Limb:
  • ankle
  • arm
  • digit
  • elbow
  • femur
  • fibula
  • finger
  • foot
  • forearm
  • hand
  • hip
  • humerus
  • knee
  • lower limb
  • radius
  • shin
  • shoulder
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
  • wrist
General:
  • blood
  • blood vessel
  • hair
  • peripheral nerve
  • peripheral nervous system
  • red blood cell
  • skin
  • spinal column
  • vertebrae
  • white blood cell
genes like me logo Genes that share expression patterns with VDR: view

No data available for Protein differential expression in normal tissues , Protein tissue co-expression partners and mRNA Expression by UniProt/SwissProt for VDR Gene

Orthologs for VDR Gene

This gene was present in the common ancestor of animals.

Orthologs for VDR Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia VDR 29
  • 93.1 (n)
Dog
(Canis familiaris)
Mammalia VDR 29 30
  • 91.1 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia VDR 29 30
  • 89.49 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Vdr 29
  • 87.16 (n)
Mouse
(Mus musculus)
Mammalia Vdr 29 16 30
  • 86.1 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia VDR 30
  • 75 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia VDR 30
  • 45 (a)
OneToOne
Chicken
(Gallus gallus)
Aves VDR 29 30
  • 76.83 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia VDR 30
  • 74 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia vdr 29
  • 67.54 (n)
African clawed frog
(Xenopus laevis)
Amphibia vdr-A 29
Zebrafish
(Danio rerio)
Actinopterygii vdrb 30
  • 71 (a)
OneToMany
vdra 29
  • 70.32 (n)
VDR (1 of 2) 30
  • 67 (a)
OneToMany
vdr 29
Rainbow Trout
(Oncorhynchus mykiss)
Actinopterygii Omy.668 29
Fruit Fly
(Drosophila melanogaster)
Insecta EcR 30
  • 14 (a)
OneToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 30
  • 23 (a)
OneToMany
Species where no ortholog for VDR was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for VDR Gene

ENSEMBL:
Gene Tree for VDR (if available)
TreeFam:
Gene Tree for VDR (if available)
Aminode:
Evolutionary constrained regions (ECRs) for VDR: view image
Alliance of Genome Resources:
Additional Orthologs for VDR

Paralogs for VDR Gene

(63) SIMAP similar genes for VDR Gene using alignment to 11 proteins:

  • VDR_HUMAN
  • B4DRV7_HUMAN
  • F8VPF8_HUMAN
  • F8VRJ4_HUMAN
  • F8VVY8_HUMAN
  • F8VXQ9_HUMAN
  • Q6SZ90_HUMAN
  • Q6T928_HUMAN
  • T1WRW3_HUMAN
  • T1WSH6_HUMAN
  • T1WSQ6_HUMAN
genes like me logo Genes that share paralogs with VDR: view

Variants for VDR Gene

Polymorphic Variants from UniProtKB/Swiss-Prot for VDR Gene

VDR_HUMAN-P11473
Genetic variations in VDR may determine Mycobacterium tuberculosis susceptibility [MIM:607948].

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for VDR Gene

SNP ID Clinical significance and condition Chr 12 pos Variation AA Info Type
1006650 Uncertain Significance: not provided 47,857,249(-) G/T
NM_000376.3(VDR):c.463C>A (p.Pro155Thr)
MISSENSE
1009301 Uncertain Significance: not provided 47,865,124(-) C/T
NM_000376.3(VDR):c.200G>A (p.Arg67His)
MISSENSE
1017357 Uncertain Significance: not provided 47,844,925(-) AG/CT
NM_000376.3(VDR):c.1104_1105inv (p.Cys369Gly)
MISSENSE
1028945 Pathogenic: Vitamin D-dependent rickets type II with alopecia 47,878,966(-) A/T
NM_000376.3(VDR):c.146+2T>A
SPLICE_DONOR
1032542 Pathogenic: Postmenopausal osteoporosis 47,879,111(-) C/T
NM_000376.3(VDR):c.3G>A (p.Met1Ile)
INITIATIOR_CODON_VARIANT,MISSENSE

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for VDR Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for VDR Gene

Variant ID Type Subtype PubMed ID
esv8233 CNV gain 19470904
nsv975483 CNV duplication 23825009

Variation tolerance for VDR Gene

Residual Variation Intolerance Score: 42.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.50; 29.20% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for VDR Gene

Human Gene Mutation Database (HGMD)
VDR
SNPedia medical, phenotypic, and genealogical associations of SNPs for
VDR
Leiden Open Variation Database (LOVD)
VDR

SNP Genotyping and Copy Number Assays for research

Disorders for VDR Gene

MalaCards: The human disease database

(110) MalaCards diseases for VDR Gene - From: OMI, CVR, ORP, SWI, COP, and GCD

Disorder Aliases PubMed IDs
vitamin d-dependent rickets, type 2a
  • vddr2a
osteoporosis
  • bone mineral density quantitative trait locus; bmnd
rickets
  • active rickets
secondary hyperparathyroidism
  • hyperparathyroidism secondary
vitamin d-dependent rickets
  • vddr
- elite association - COSMIC cancer census association via MalaCards
Search VDR in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

VDR_HUMAN
  • Rickets vitamin D-dependent 2A (VDDR2A) [MIM:277440]: A disorder of vitamin D metabolism resulting in severe rickets, hypocalcemia and secondary hyperparathyroidism. Most patients have total alopecia in addition to rickets. {ECO:0000269 PubMed:1652893, ECO:0000269 PubMed:17970811, ECO:0000269 PubMed:2177843, ECO:0000269 PubMed:2849209, ECO:0000269 PubMed:28698609, ECO:0000269 PubMed:7828346, ECO:0000269 PubMed:8106618, ECO:0000269 PubMed:8381803, ECO:0000269 PubMed:8392085, ECO:0000269 PubMed:8675579, ECO:0000269 PubMed:8961271, ECO:0000269 PubMed:9005998}. Note=The disease is caused by variants affecting the gene represented in this entry.

Genatlas disease for VDR Gene

rickets,vitamin D-dependent,type II,with alopecia

Additional Disease Information for VDR

Human Genome Epidemiology Navigator
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Publications for VDR Gene

  1. Vitamin D receptor (VDR) gene polymorphisms and haplotypes, interactions with plasma 25-hydroxyvitamin D and 1,25-dihydroxyvitamin D, and prostate cancer risk. (PMID: 17440943) Mikhak B … Giovannucci E (The Prostate 2007) 3 22 25 40
  2. Vitamin d pathway genes, diet, and risk of renal cell carcinoma. (PMID: 20049159) Karami S … Moore LE (International journal of endocrinology 2010) 3 22 40
  3. Genetic variation in the vitamin D receptor (VDR) and the vitamin D-binding protein (GC) and risk for colorectal cancer: results from the Colon Cancer Family Registry. (PMID: 20086113) Poynter JN … Haile RW (Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology 2010) 3 22 40
  4. Maternal serum 25-hydroxyvitamin D concentrations are associated with small-for-gestational age births in white women. (PMID: 20200114) Bodnar LM … Simhan HN (The Journal of nutrition 2010) 3 22 40
  5. Influence of vitamin D receptor haplotypes on blood lead concentrations in environmentally exposed children of Uygur and Han populations. (PMID: 20100036) Chen Y … Tian W (Biomarkers : biochemical indicators of exposure, response, and susceptibility to chemicals 2010) 3 22 40

Products for VDR Gene