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Gene id

7421

Gene Summary SNPs Protein Summary Gene ontology KEGG pathways Diseases PubMed references

Gene Summary

Gene Symbol

VDR Gene UCSC Ensembl

Aliases

NR1I1, PPP1R163

Gene name

vitamin D (1,25- dihydroxyvitamin D3) receptor

Alternate names

vitamin D3 receptor, 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, vitamin D receptor,

Gene location

12q13.11 (47905030: 47841536) Exons: 11 NC_000012.12

Gene summary(Entrez)

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]

OMIM

601769

SNPs

rs1544410

Strand:    Allele origin:   Allele change: A/C/G/T   Mutation type: snp

CM000674.2   g.47846052C>A
CM000674.2   g.47846052C>G
CM000674.2   g.47846052C>T
NC_000012.11   g.48239835C>T
NC_000012.12   g.47846052C>A
NC_000012.12   g.47846052C>G
NC_000012.12   g.47846052C>T
NG_008731.1   g.63980G>A
NG_008731.1   g.63980G>C
NG_008731.1   g.63980G>T
NM_000376.2   c.1024+283G>A
NM_000376.2   c.1024+283G>C
NM_000376.2   c.1024+283G>T
NM_001017535.1   c.1024+283G>A
NM_001017535.1   c.1024+283G>C
NM_001017535.1   c.1024+283G>T
NM_001017536.1   c.1174+283G>A
NM_001017536.1   c.1174+283G>C
NM_001017536.1   c.1174+283G>T
rs2228570

Strand: -   Allele origin: unknown  Allele change: A/C/G/T   Mutation type: snp


NC_000012.11   g.48272895A>G
NG_008731.1   g.30920T>C
NC_000012.12   g.47879112A>G
NM_000376.2   c.2T>C
NM_001017535.1   c.2T>C
NM_001017536.1   c.152T>C
NP_000367.1   p.Met1Thr
NP_001017536.1   p.Met51Thr
NP_001017535.1   p.Met1Thr
XM_006719587.3   c.2T>C
XM_011538720.2   c.
Clinical Significance: Benign

rs731236

Strand:    Allele origin:   Allele change: C/T   Mutation type: snp

CM000674.2   g.47844974A>G
NC_000012.11   g.48238757A>G
NC_000012.12   g.47844974A>G
NG_008731.1   g.65058T>C
NM_000376.2   c.1056T>C
NM_001017535.1   c.1056T>C
NM_001017536.1   c.1206T>C
NP_000367.1   p.Ile352=
NP_001017535.1   p.Ile352=
NP_001017536.1   p.Ile402=
XP_006719650.1   p.Ile352=
XP_011537022.1   p.Ile352=
Clinical Significance: Likely benign

rs7975232

Strand:    Allele origin:   Allele change: A/C   Mutation type: snp

CM000674.2   g.47845054C>A
NC_000012.11   g.48238837C>A
NC_000012.12   g.47845054C>A
NG_008731.1   g.64978G>T
NM_000376.2   c.1025-49G>T
NM_001017535.1   c.1025-49G>T
NM_001017536.1   c.1175-49G>T

Protein Summary

Protein general information

P11473

Name: Vitamin D3 receptor (VDR) (1,25 dihydroxyvitamin D3 receptor) (Nuclear receptor subfamily 1 group I member 1)

Length: 427 Mass: 48,289

Sequence

MEAMAASTSLPDPGDFDRNVPRICGVCGDRATGFHFNAMTCEGCKGFFRRSMKRKALFTCPFNGDCRITKDNRRH
CQACRLKRCVDIGMMKEFILTDEEVQRKREMILKRKEEEALKDSLRPKLSEEQQRIIAILLDAHHKTYDPTYSDF
CQFRPPVRVNDGGGSHPSRPNSRHTPSFSGDSSSSCSDHCITSSDMMDSSSFSNLDLSEEDSDDPSVTLELSQLS
MLPHLADLVSYSIQKVIGFAKMIPGFRDLTSEDQIVLLKSSAIEVIMLRSNESFTMDDMSWTCGNQDYKYRVSDV
TKAGHSLELIEPLIKFQVGLKKLNLHEEEHVLLMAICIVSPDRPGVQDAALIEAIQDRLSNTLQTYIRCRHPPPG
SHLLYAKMIQKLADLRSLNEEHSKQYRCLSFQPECSMKLTPLVLEVFGNEIS

Structural information

Interpro:	IPR000536 IPR001723 IPR000324 IPR001628 IPR013088
Prosite:	PS00031 PS51030
Pfam:	PF00104 PF00105
PDB:	1DB1 1IE8 1IE9 1KB2 1KB4 1KB6 1S0Z 1S19 1TXI 1YNW 2HAM 2HAR 2HAS 2HB7 2HB8 3A2I 3A2J 3A3Z 3A40 3A78 3AUQ 3AUR 3AX8 3AZ1 3AZ2 3AZ3 3B0T 3CS4 3CS6 3KPZ 3M7R 3OGT 3P8X 3TKC 3VHW 3W0A 3W0C 3W0Y 3WGP 3WWR 3X31 3X36 4G2I 4ITE 4ITF 5GT4
PDBsum:	1DB1 1IE8 1IE9 1KB2 1KB4 1KB6 1S0Z 1S19 1TXI 1YNW 2HAM 2HAR 2HAS 2HB7 2HB8 3A2I 3A2J 3A3Z 3A40 3A78 3AUQ 3AUR 3AX8 3AZ1 3AZ2 3AZ3 3B0T 3CS4 3CS6 3KPZ 3M7R 3OGT 3P8X 3TKC 3VHW 3W0A 3W0C 3W0Y 3WGP 3WWR 3X31 3X36 4G2I 4ITE 4ITF 5GT4
DIP:	32624
MINT:	236408
STRING:	ENSP00000447173;

Other Databases

GeneCards: VDR; Malacards: VDR

Gene ontology

GO accession	Term name	Evidence code	Go category
GO:0000122	negative regulation of tr anscription from RNA poly merase II promoter	IDA	biological_process
GO:0000902	cell morphogenesis	IMP	biological_process
GO:0001501	skeletal system developme nt	IEA	biological_process
GO:0003677	DNA binding	IDA	molecular_function
GO:0003707	steroid hormone receptor activity	IEA	molecular_function
GO:0005515	protein binding	IPI	molecular_function
GO:0005515	protein binding	IPI	molecular_function
GO:0005515	protein binding	IPI	molecular_function
GO:0005515	protein binding	IPI	molecular_function
GO:0005515	protein binding	IPI	molecular_function
GO:0005515	protein binding	IPI	molecular_function
GO:0005515	protein binding	IPI	molecular_function
GO:0005515	protein binding	IPI	molecular_function
GO:0005515	protein binding	IPI	molecular_function
GO:0005515	protein binding	IPI	molecular_function
GO:0005515	protein binding	IPI	molecular_function
GO:0005515	protein binding	IPI	molecular_function
GO:0005515	protein binding	IPI	molecular_function
GO:0005515	protein binding	IPI	molecular_function
GO:0005634	nucleus	IDA	cellular_component
GO:0005634	nucleus	IDA	cellular_component
GO:0005654	nucleoplasm	IDA	cellular_component
GO:0005654	nucleoplasm	TAS	cellular_component
GO:0006367	transcription initiation from RNA polymerase II pr omoter	TAS	biological_process
GO:0006816	calcium ion transport	IEA	biological_process
GO:0006874	cellular calcium ion home ostasis	IEA	biological_process
GO:0007165	signal transduction	TAS	biological_process
GO:0007595	lactation	IEA	biological_process
GO:0008270	zinc ion binding	IEA	molecular_function
GO:0008285	negative regulation of ce ll proliferation	IDA	biological_process
GO:0008434	calcitriol receptor activ ity	IDA	molecular_function
GO:0008434	calcitriol receptor activ ity	IDA	molecular_function
GO:0008434	calcitriol receptor activ ity	IDA	molecular_function
GO:0010628	positive regulation of ge ne expression	IMP	biological_process
GO:0010839	negative regulation of ke ratinocyte proliferation	IMP	biological_process
GO:0010980	positive regulation of vi tamin D 24-hydroxylase ac tivity	IDA	biological_process
GO:0038183	bile acid signaling pathw ay	IDA	biological_process
GO:0038186	lithocholic acid receptor activity	IDA	molecular_function
GO:0043235	receptor complex	IDA	cellular_component
GO:0043401	steroid hormone mediated signaling pathway	IEA	biological_process
GO:0043565	sequence-specific DNA bin ding	IEA	molecular_function
GO:0045618	positive regulation of ke ratinocyte differentiatio n	IMP	biological_process
GO:0045892	negative regulation of tr anscription, DNA-template d	IDA	biological_process
GO:0045944	positive regulation of tr anscription from RNA poly merase II promoter	IMP	biological_process
GO:0045944	positive regulation of tr anscription from RNA poly merase II promoter	IMP	biological_process
GO:0046697	decidualization	IEP	biological_process
GO:0046965	retinoid X receptor bindi ng	IPI	molecular_function
GO:0050892	intestinal absorption	IEA	biological_process
GO:0060058	positive regulation of ap optotic process involved in mammary gland involuti on	IEA	biological_process
GO:0060558	regulation of calcidiol 1 -monooxygenase activity	ISS	biological_process
GO:0060745	mammary gland branching i nvolved in pregnancy	IEA	biological_process
GO:0070561	vitamin D receptor signal ing pathway	IDA	biological_process
GO:0090575	RNA polymerase II transcr iption factor complex	IDA	cellular_component
GO:1902098	calcitriol binding	IDA	molecular_function
GO:1902098	calcitriol binding	IDA	molecular_function
GO:1902121	lithocholic acid binding	IDA	molecular_function
GO:0003700	transcription factor acti vity, sequence-specific D NA binding	IDA	molecular_function
GO:0070644	vitamin D response elemen t binding	IDA	molecular_function
GO:0000122	negative regulation of tr anscription from RNA poly merase II promoter	IDA	biological_process
GO:0000902	cell morphogenesis	IMP	biological_process
GO:0001501	skeletal system developme nt	IEA	biological_process
GO:0003677	DNA binding	IEA	molecular_function
GO:0003677	DNA binding	IEA	molecular_function
GO:0003677	DNA binding	IEA	molecular_function
GO:0003677	DNA binding	IDA	molecular_function
GO:0003677	DNA binding	TAS	molecular_function
GO:0003700	transcription factor acti vity, sequence-specific D NA binding	IEA	molecular_function
GO:0003707	steroid hormone receptor activity	IEA	molecular_function
GO:0004879	RNA polymerase II transcr iption factor activity, l igand-activated sequence- specific DNA binding	IEA	molecular_function
GO:0005515	protein binding	IPI	molecular_function
GO:0005515	protein binding	IPI	molecular_function
GO:0005515	protein binding	IPI	molecular_function
GO:0005515	protein binding	IPI	molecular_function
GO:0005515	protein binding	IPI	molecular_function
GO:0005515	protein binding	IPI	molecular_function
GO:0005515	protein binding	IPI	molecular_function
GO:0005515	protein binding	IPI	molecular_function
GO:0005515	protein binding	IPI	molecular_function
GO:0005515	protein binding	IPI	molecular_function
GO:0005515	protein binding	IPI	molecular_function
GO:0005515	protein binding	IPI	molecular_function
GO:0005515	protein binding	IPI	molecular_function
GO:0005515	protein binding	IPI	molecular_function
GO:0005634	nucleus	IEA	cellular_component
GO:0005634	nucleus	IEA	cellular_component
GO:0005634	nucleus	IEA	cellular_component
GO:0005634	nucleus	IDA	cellular_component
GO:0005634	nucleus	IDA	cellular_component
GO:0005654	nucleoplasm	IDA	cellular_component
GO:0005654	nucleoplasm	TAS	cellular_component
GO:0006351	transcription, DNA-templa ted	IEA	biological_process
GO:0006355	regulation of transcripti on, DNA-templated	IEA	biological_process
GO:0006355	regulation of transcripti on, DNA-templated	IEA	biological_process
GO:0006355	regulation of transcripti on, DNA-templated	IEA	biological_process
GO:0006367	transcription initiation from RNA polymerase II pr omoter	TAS	biological_process
GO:0006816	calcium ion transport	IEA	biological_process
GO:0006874	cellular calcium ion home ostasis	IEA	biological_process
GO:0007165	signal transduction	TAS	biological_process
GO:0007275	multicellular organism de velopment	IEA	biological_process
GO:0007595	lactation	IEA	biological_process
GO:0008270	zinc ion binding	IEA	molecular_function
GO:0008285	negative regulation of ce ll proliferation	IDA	biological_process
GO:0008434	calcitriol receptor activ ity	IEA	molecular_function
GO:0008434	calcitriol receptor activ ity	IDA	molecular_function
GO:0008434	calcitriol receptor activ ity	IDA	molecular_function
GO:0008434	calcitriol receptor activ ity	IDA	molecular_function
GO:0009887	animal organ morphogenesi s	IEA	biological_process
GO:0010628	positive regulation of ge ne expression	IMP	biological_process
GO:0010839	negative regulation of ke ratinocyte proliferation	IMP	biological_process
GO:0010980	positive regulation of vi tamin D 24-hydroxylase ac tivity	IDA	biological_process
GO:0038183	bile acid signaling pathw ay	IDA	biological_process
GO:0038186	lithocholic acid receptor activity	IDA	molecular_function
GO:0043235	receptor complex	IDA	cellular_component
GO:0043401	steroid hormone mediated signaling pathway	IEA	biological_process
GO:0043565	sequence-specific DNA bin ding	IEA	molecular_function
GO:0045618	positive regulation of ke ratinocyte differentiatio n	IMP	biological_process
GO:0045892	negative regulation of tr anscription, DNA-template d	IDA	biological_process
GO:0045944	positive regulation of tr anscription from RNA poly merase II promoter	IMP	biological_process
GO:0045944	positive regulation of tr anscription from RNA poly merase II promoter	IMP	biological_process
GO:0046697	decidualization	IEP	biological_process
GO:0046872	metal ion binding	IEA	molecular_function
GO:0046965	retinoid X receptor bindi ng	IPI	molecular_function
GO:0050892	intestinal absorption	IEA	biological_process
GO:0060058	positive regulation of ap optotic process involved in mammary gland involuti on	IEA	biological_process
GO:0060558	regulation of calcidiol 1 -monooxygenase activity	IEA	biological_process
GO:0060558	regulation of calcidiol 1 -monooxygenase activity	ISS	biological_process
GO:0060745	mammary gland branching i nvolved in pregnancy	IEA	biological_process
GO:0070561	vitamin D receptor signal ing pathway	IDA	biological_process
GO:0090575	RNA polymerase II transcr iption factor complex	IDA	cellular_component
GO:1902098	calcitriol binding	IDA	molecular_function
GO:1902098	calcitriol binding	IDA	molecular_function
GO:1902121	lithocholic acid binding	IDA	molecular_function
GO:0003700	transcription factor acti vity, sequence-specific D NA binding	IDA	molecular_function
GO:0070644	vitamin D response elemen t binding	IDA	molecular_function
GO:0000122	negative regulation of tr anscription from RNA poly merase II promoter	IDA	biological_process
GO:0000902	cell morphogenesis	IMP	biological_process
GO:0003677	DNA binding	IDA	molecular_function
GO:0003677	DNA binding	TAS	molecular_function
GO:0005515	protein binding	IPI	molecular_function
GO:0005515	protein binding	IPI	molecular_function
GO:0005515	protein binding	IPI	molecular_function
GO:0005515	protein binding	IPI	molecular_function
GO:0005515	protein binding	IPI	molecular_function
GO:0005515	protein binding	IPI	molecular_function
GO:0005515	protein binding	IPI	molecular_function
GO:0005515	protein binding	IPI	molecular_function
GO:0005515	protein binding	IPI	molecular_function
GO:0005515	protein binding	IPI	molecular_function
GO:0005515	protein binding	IPI	molecular_function
GO:0005515	protein binding	IPI	molecular_function
GO:0005515	protein binding	IPI	molecular_function
GO:0005515	protein binding	IPI	molecular_function
GO:0005634	nucleus	IDA	cellular_component
GO:0005634	nucleus	IDA	cellular_component
GO:0005654	nucleoplasm	IDA	cellular_component
GO:0005654	nucleoplasm	TAS	cellular_component
GO:0006367	transcription initiation from RNA polymerase II pr omoter	TAS	biological_process
GO:0007165	signal transduction	TAS	biological_process
GO:0008285	negative regulation of ce ll proliferation	IDA	biological_process
GO:0008434	calcitriol receptor activ ity	IDA	molecular_function
GO:0008434	calcitriol receptor activ ity	IDA	molecular_function
GO:0008434	calcitriol receptor activ ity	IDA	molecular_function
GO:0010628	positive regulation of ge ne expression	IMP	biological_process
GO:0010839	negative regulation of ke ratinocyte proliferation	IMP	biological_process
GO:0010980	positive regulation of vi tamin D 24-hydroxylase ac tivity	IDA	biological_process
GO:0038183	bile acid signaling pathw ay	IDA	biological_process
GO:0038186	lithocholic acid receptor activity	IDA	molecular_function
GO:0043235	receptor complex	IDA	cellular_component
GO:0045618	positive regulation of ke ratinocyte differentiatio n	IMP	biological_process
GO:0045892	negative regulation of tr anscription, DNA-template d	IDA	biological_process
GO:0045944	positive regulation of tr anscription from RNA poly merase II promoter	IMP	biological_process
GO:0045944	positive regulation of tr anscription from RNA poly merase II promoter	IMP	biological_process
GO:0046697	decidualization	IEP	biological_process
GO:0046965	retinoid X receptor bindi ng	IPI	molecular_function
GO:0060558	regulation of calcidiol 1 -monooxygenase activity	ISS	biological_process
GO:0070561	vitamin D receptor signal ing pathway	IDA	biological_process
GO:0090575	RNA polymerase II transcr iption factor complex	IDA	cellular_component
GO:1902098	calcitriol binding	IDA	molecular_function
GO:1902098	calcitriol binding	IDA	molecular_function
GO:1902121	lithocholic acid binding	IDA	molecular_function
GO:0003700	transcription factor acti vity, sequence-specific D NA binding	IDA	molecular_function
GO:0070644	vitamin D response elemen t binding	IDA	molecular_function

KEGG pathways

hsa05152  Tuberculosis
hsa04978  Mineral absorption
hsa04961  Endocrine and other factor-regulated calcium reabsorption
PTHR24082:SF38  Vitamin D metabolism and pathway

Diseases

Associated diseases	References
Addison's disease	PMID: 12444895
Alopecia areata	PMID: 15246940
Alzheimer's disease	PMID: 12555245
Amyotrophic lateral sclerosis (ALS)	PMID: 12896855
Anemia	PMID: 12324918
Asthma	PMID: 15663557
Autoimmune diseases	PMID: 16710576
Benign prostatic hyperplasia	PMID: 11248649
Biliary liver cirrhosis	PMID: 15683428
Calcium Metabolism Disorders	PMID: 15141345
Calcium nephrolithiasis	PMID: 12814692
Cancer	PMID: 18285546
Chronic ulcerative colitis	PMID: 15684874
Crohn's disease	PMID: 10896912
Diabetes	PMID: 11914750
Endometriosis	PMID: 26398313
Fabry disease	PMID: 18278558
Graves disease	PMID: 11134121
Hashimoto's thyroiditis	PMID: 16721822
Hyperandrogenism	PMID: 26747961
Hypercalcemia	PMID: 11033842
Hyperparathyroidism	PMID: 11522087
Hyperthyroidism	PMID: 11028447
Hypogonadotropic hypogonadism	PMID: 16370560
Inflammatory bowel disease	PMID: 18194505
Juvenile arthritis	PMID: 12375338
Kidney disease	PMID: 12018632
Lumbar spondylosis	PMID: 16362385
Endometriosis associated infertility	INFBASE26398313
Endometriosis	INFBASE26398313
Male infertility	PMID: 20172873
Multiple sclerosis	PMID: 10967184
Myocardial infarction	PMID: 11335187
Nephrolithiasis	PMID: 10436404
Obesity	PMID: 11454514
Osteoarthritis	PMID: 11824954
Osteomalacia	PMID: 14691685
Osteonecrosis	PMID: 15459215
Osteoporosis	PMID: 10689545
Parkinson's disease	PMID: 15953876
Periodontitis	PMID: 10505806
Polycystic ovary syndrome (PCOS)	PMID: 21082232
Premature menopause	PMID: 17135034
Primary biliary cirrhosis	PMID: 14642064
Prostatic hyperplasia	PMID: 16461080
Psoriasis	PMID: 12192493
Recurrent miscarriage	PMID: 11383910
Renal failure	PMID: 9335382
Rheumatoid arthritis	PMID: 11251690
Rickets	PMID: 18285415
Scoliosis	PMID: 17785083
Spermatogenetic defects	PMID: 21427118
Spinal ossification	PMID: 12195069
Systemic lupus erythematosus	PMID: 10773761
Turner Syndrome(TS)	PMID: 22117179
Urolithiasis	PMID: 18036039
Vitamin D-dependent rickets	KEGG: H01143

PubMed references

PMID	Condition	Mutation	Ethnicity	Population details	Infertility_type	Associated_genes	Abstract
26398313	Endometrio sis	GC rs1155563, rs2298849 and rs7041; RXRA rs10881578, rs10776909 and rs749759; VDR BsmI rs1544410; and FokI rs2228570		501 (154 women with endometrio sis?associated infertility, 34 7 controls)	Female infertility	GC RXRA VDR BsmI FokI	Show abstract