ENSG00000111424


Homo sapiens

Features
Gene ID: ENSG00000111424
  
Biological name :VDR
  
Synonyms : P11473 / VDR / vitamin D receptor
  
Possible biological names infered from orthology :
  
Species: Homo sapiens
  
Chr. number: 12
Strand: -1
Band: q13.11
Gene start: 47841537
Gene end: 47943048
  
Corresponding Affymetrix probe sets: 204253_s_at (Human Genome U133 Plus 2.0 Array)   204254_s_at (Human Genome U133 Plus 2.0 Array)   204255_s_at (Human Genome U133 Plus 2.0 Array)   213692_s_at (Human Genome U133 Plus 2.0 Array)   
  
Cross references: Ensembl peptide - ENSP00000450105
Ensembl peptide - ENSP00000449561
Ensembl peptide - ENSP00000449573
Ensembl peptide - ENSP00000229022
Ensembl peptide - ENSP00000378734
Ensembl peptide - ENSP00000447173
Ensembl peptide - ENSP00000448659
Ensembl peptide - ENSP00000449074
NCBI entrez gene - 7421     See in Manteia.
OMIM - 601769
RefSeq - XM_011538720
RefSeq - NM_000376
RefSeq - NM_001017535
RefSeq - NM_001017536
RefSeq - XM_006719587
RefSeq Peptide - NP_001017536
RefSeq Peptide - NP_000367
RefSeq Peptide - NP_001017535
swissprot - F8VVY8
swissprot - F8VXQ9
swissprot - F8VPF8
swissprot - F8VRJ4
swissprot - P11473
swissprot - F1D8P8
Ensembl - ENSG00000111424
  
Related genetic diseases (OMIM): 166710 - ?Osteoporosis, involutional, 166710
  277440 - Rickets, vitamin D-resistant, type IIA, 277440

This gene has been taged as a transcription factor by TFT
See expression report in BioGPS
See gene description in Wikigenes
See gene description in GeneCards
See co-cited genes in PubMed


Ortholog prediction (from Ensembl)
Ortholog nameID Species
 CABZ01088036.1ENSDARG00000112923Danio rerio
 vdraENSDARG00000099483Danio rerio
 vdrbENSDARG00000070721Danio rerio
 VdrENSMUSG00000022479Mus musculus


Paralog prediction (from Ensembl)
Paralog nameIDSimilarity(%)
NR1I2 / O75469 / nuclear receptor subfamily 1 group I member 2ENSG0000014485237
NR1I3 / Q14994 / nuclear receptor subfamily 1 group I member 3ENSG0000014325729
NR1H3 / Q13133 / nuclear receptor subfamily 1 group H member 3ENSG0000002543426
NR1H4 / Q96RI1 / nuclear receptor subfamily 1 group H member 4ENSG0000001250426
NR1H2 / P55055 / nuclear receptor subfamily 1 group H member 2ENSG0000013140825
THRB / P10828 / thyroid hormone receptor betaENSG0000015109024
THRA / P10827 / thyroid hormone receptor, alphaENSG0000012635123
RARG / P13631 / retinoic acid receptor gammaENSG0000017281922
RARB / P10826 / retinoic acid receptor betaENSG0000007709221
RARA / P10276 / retinoic acid receptor alphaENSG0000013175921


Protein motifs (from Interpro)
Interpro ID Name
 IPR000324  Vitamin D receptor
 IPR000536  Nuclear hormone receptor, ligand-binding domain
 IPR001628  Zinc finger, nuclear hormone receptor-type
 IPR001723  Nuclear hormone receptor
 IPR013088  Zinc finger, NHR/GATA-type
 IPR035500  Nuclear hormone receptor-like domain superfamily


Gene Ontology (GO)
TypeGO IDTermEv.Code
 biological_processGO:0000122 negative regulation of transcription by RNA polymerase II IDA
 biological_processGO:0000902 cell morphogenesis IMP
 biological_processGO:0001501 skeletal system development IEA
 biological_processGO:0006351 transcription, DNA-templated IEA
 biological_processGO:0006355 regulation of transcription, DNA-templated IEA
 biological_processGO:0006367 transcription initiation from RNA polymerase II promoter TAS
 biological_processGO:0006816 calcium ion transport IEA
 biological_processGO:0006874 cellular calcium ion homeostasis IEA
 biological_processGO:0007165 signal transduction TAS
 biological_processGO:0007275 multicellular organism development IEA
 biological_processGO:0007595 lactation IEA
 biological_processGO:0008285 negative regulation of cell proliferation IDA
 biological_processGO:0009887 animal organ morphogenesis IEA
 biological_processGO:0010628 positive regulation of gene expression IMP
 biological_processGO:0010839 negative regulation of keratinocyte proliferation IMP
 biological_processGO:0010980 positive regulation of vitamin D 24-hydroxylase activity IDA
 biological_processGO:0038183 bile acid signaling pathway IDA
 biological_processGO:0042359 vitamin D metabolic process TAS
 biological_processGO:0043401 steroid hormone mediated signaling pathway IEA
 biological_processGO:0045618 positive regulation of keratinocyte differentiation IMP
 biological_processGO:0045892 negative regulation of transcription, DNA-templated IDA
 biological_processGO:0045944 positive regulation of transcription by RNA polymerase II IMP
 biological_processGO:0046697 decidualization IEP
 biological_processGO:0050892 intestinal absorption IEA
 biological_processGO:0060058 positive regulation of apoptotic process involved in mammary gland involution IEA
 biological_processGO:0060558 regulation of calcidiol 1-monooxygenase activity ISS
 biological_processGO:0060745 mammary gland branching involved in pregnancy IEA
 biological_processGO:0070561 vitamin D receptor signaling pathway IMP
 cellular_componentGO:0005634 nucleus IDA
 cellular_componentGO:0005654 nucleoplasm TAS
 cellular_componentGO:0005737 cytoplasm IEA
 cellular_componentGO:0043235 receptor complex IDA
 cellular_componentGO:0090575 RNA polymerase II transcription factor complex IDA
 molecular_functionGO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding NAS
 molecular_functionGO:0003677 DNA binding IDA
 molecular_functionGO:0003700 DNA-binding transcription factor activity IDA
 molecular_functionGO:0003707 steroid hormone receptor activity IEA
 molecular_functionGO:0004879 nuclear receptor activity IEA
 molecular_functionGO:0005515 protein binding IPI
 molecular_functionGO:0008270 zinc ion binding IEA
 molecular_functionGO:0008434 calcitriol receptor activity IMP
 molecular_functionGO:0038186 lithocholic acid receptor activity IDA
 molecular_functionGO:0043565 sequence-specific DNA binding IEA
 molecular_functionGO:0046872 metal ion binding IEA
 molecular_functionGO:0046965 retinoid X receptor binding IDA
 molecular_functionGO:0070644 vitamin D response element binding IDA
 molecular_functionGO:1902098 calcitriol binding IMP
 molecular_functionGO:1902121 lithocholic acid binding IDA


Pathways (from Reactome)
Pathway description
Vitamin D (calciferol) metabolism
Nuclear Receptor transcription pathway
SUMOylation of intracellular receptors


Phenotype (from MGI, Zfin or HPO)
IDPhenotypeDefinition Genetic BG
 HP:0000006 Autosomal dominant inheritance "A mode of inheritance that is observed for traits related to a gene encoded on one of the autosomes (i.e., the human chromosomes 1-22) in which a trait manifests in heterozygotes. In the context of medical genetics, an autosomal dominant disorder is caused when a single copy of the mutant allele is present. Males and females are affected equally, and can both transmit the disorder with a risk of 50% for each child of inheriting the mutant allele." [HPO:curators]
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 HP:0000007 Autosomal recessive inheritance "A mode of inheritance that is observed for traits related to a gene encoded on one of the autosomes (i.e., the human chromosomes 1-22) in which a trait manifests in homozygotes. In the context of medical genetics, autosomal recessive disorders manifest in homozygotes (with two copies of the mutant allele) or compound heterozygotes (whereby each copy of a gene has a distinct mutant allele)." [HPO:curators]
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 HP:0000268 Dolichocephaly 
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 HP:0000670 Carious teeth 
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 HP:0000684 Delayed dentition "Delayed eruption of teeth." [HPO:curators]
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 HP:0000737 Irritability 
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 HP:0000765 Abnormality of the thorax "Any abnormality of the thorax (the region of the body formed by the sternum, the thoracic vertebrae and the ribs)." [HPO:curators]
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 HP:0000787 Kidney stones 
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 HP:0000843 Hyperparathyroidism 
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 HP:0000867 Secondary hyperparathyroidism 
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 HP:0000886 Deformed rib cage 
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 HP:0000893 Bulging of the costochondral junction 
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 HP:0000939 Osteoporosis "Osteoporosis is a systemic skeletal disease characterized by low bone density and microarchitectural deterioration of bone tissue with a consequent increase in bone fragility. According to the WHO, osteoporosis is characterized by a value of BMD 2.5 standard deviations or more below the young adult mean." [HPO:curators]
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 HP:0000944 Abnormality of the metaphyses 
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 HP:0000951 Abnormality of the skin "An abnormality of the `skin` (FMA:7163)." [HPO:probinson]
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 HP:0001252 Muscular hypotonia "Muscular hypotonia is an abnormally low muscle tone (the amount of tension or resistance to movement in a muscle), often involving reduced muscle strength. Hypotonia is characterized by a diminished resistance to passive stretching." [HPO:curators]
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 HP:0001270 Motor retardation 
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 HP:0001288 Gait disturbance "The term gait disturbance can refer to any disruption of the ability to walk. In general, this can refer to neurological diseases but also fractures or other sources of pain that is triggered upon walking. However, in the current context gait disturbance refers to difficulty walking on the basis of a neurological or muscular disease." [HPO:curators]
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 HP:0001290 Generalized hypotonia "Generalized muscular hypotonia (abnormally low muscle tone)." [HPO:curators]
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 HP:0001373 Joint dislocation "Displacement or malalignment of joints." [HPO:curators]
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 HP:0001508 Failure to thrive 
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 HP:0001510 Growth retardation 
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 HP:0001538 Protuberant abdomen "A thrusting or bulging out of the abdomen." [HPO:curators]
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 HP:0001596 Alopecia "Loss of hair from the head or body." [HPO:curators]
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 HP:0002007 Frontal bossing "The presence of an unusually prominent forehead." [HPO:curators]
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 HP:0002148 Hypophosphatemia "A lower than normal level of blood phosphate." [HPO:curators]
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 HP:0002199 Seizures due to hypocalcemia 
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 HP:0002289 Alopecia, complete 
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 HP:0002355 Difficulty walking 
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 HP:0002650 Scoliosis "The presence of an abnormal lateral curvature of the spine." [HPO:curators]
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 HP:0002653 Bone pain 
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 HP:0002663 Late ossifying epiphyses 
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 HP:0002748 Rickets 
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 HP:0002749 Osteomalacia "Osteomalacia is a general term for bone weakness owing to a defect in mineralization of the protein framework known as osteoid. This defective mineralization is mainly caused by lack in vitamin D. Osteomalacia in children is known as rickets." [HPO:curators]
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 HP:0002752 Sparse bone trabeculae 
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 HP:0002753 Thin bony cortex "Abnormal thinning of the cortical region of bones." [HPO:curators]
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 HP:0002757 Recurrent fractures "The repeated occurence of bone fractures (implying an abnormally increased tendency for fracture)." [HPO:curators]
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 HP:0002797 Osteolysis 
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 HP:0002857 Genu valgum 
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 HP:0002901 Hypocalcemia "A level of blood calcium that is lower than normal." [HPO:curators]
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 HP:0002970 Genu varum 
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 HP:0002979 Bowing of the legs 
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 HP:0002980 Femoral bowing "Bowing (abnormal curvature) of the femur." [HPO:curators]
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 HP:0002982 Tibial bowing "A developmental defect with posteromedial tibial angulation." [HPO:curators]
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 HP:0003013 Bulging epiphyses 
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 HP:0003020 Enlargement of the wrists 
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 HP:0003025 Irregular metaphyses 
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 HP:0003029 Enlargement of the ankles 
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 HP:0003106 Subperiosteal erosions due to secondary hyperparathyroidism 
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 HP:0003152 Increased serum 1,25-dihydroxyvitamin D3 
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 HP:0003155 Elevated alkaline phosphatase "Abnormally increased serum levels of `alkaline phosphatase activity` (GO:0004035)." [HPO:probinson]
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 HP:0003165 Elevated serum parathyroid hormone (PTH) level 
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 HP:0003272 Abnormality of the hip "An abnormality of the hip joint or the surrounding anatomic region." [HPO:curators]
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 HP:0003312 Abnormal form of the vertebral bodies 
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 HP:0003593 Early onset 
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 HP:0003698 Difficulty standing 
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 HP:0004322 Decreased body height "A height below that which is expected according to age and gender norms. Although there is no universally accepted definition of short stature, many refer to "short stature" as height more than 2 standard deviations below the mean for age and gender (or below the 3rd percentile for age and gender dependent norms)." [HPO:curators]
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 HP:0004492 Widely patent fontanels and sutures "An abnormally increased width of the cranial sutures of striking degree." [HPO:curators]
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 HP:0005469 Occipital plagiocephaly "Occipital plagiocephaly can result from fusion or sclerosis of the lambdoid suture. If unilateral, this is accompanied by unilateral occipital flattening and bulging of the ispilateral frontal bone." [HPO:curators]
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 HP:0006297 Hypoplastic dental enamel 
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 HP:0006323 Premature deciduous tooth loss 
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 HP:0009023 Abdominal wall muscle weakness 
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 HP:0009124 Abnormality of adipose tissue "An abnormality of adipose (or fat) tissue, which is loose connective tissue composed of adipocytes." [HPO:curators]
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 HP:0010502 Fibular bowing "A developmental defect with posteromedial fibular angulation." [HPO:curators]
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 HP:0012062 Bone cyst "A fluid filled cavity that develops with a bone." [HPO:probinson]
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 HP:0100670 Rough bone trabeculation 
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Interacting proteins (from Reactome)
Interactor ID Name Interaction type
 ENSG00000103275 UBE2I / P63279 / ubiquitin conjugating enzyme E2 I  / reaction
 ENSG00000188612 SUMO2 / P61956 / small ubiquitin-like modifier 2  / reaction






 

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