Atlas of Genetics and Cytogenetics in Oncology and Haematology


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VDR (vitamin D receptor)

Identity

Alias_namesregulatory subunit 163
Alias_symbol (synonym)NR1I1
PPP1R163
Other alias
HGNC (Hugo) VDR
LocusID (NCBI) 7421
Atlas_Id 45741
Location 12q13.11  [Link to chromosome band 12q13]
Location_base_pair Starts at 47841537 and ends at 47905031 bp from pter ( according to hg38-Dec_2013)
Fusion genes
(updated 2017)
Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)
LMBR1L (12q13.12) / VDR (12q13.11)VDR (12q13.11) / SLC1A5 (19q13.32)VDR (12q13.11) / VDR (12q13.11)
LMBR1L 12q13.12 / VDR 12q13.11

Note

Non-annotated gene. Preliminary data : if you are an author
who wish to write a full paper/card on this gene, go to  How to contribute

DNA/RNA

 


Other Solid tumors implicated (Data extracted from papers in the Atlas) [ 2 ]
  HDAC7/VDR (12q13)
LMBR1L/VDR (12q13)


External links

Nomenclature
HGNC (Hugo)VDR   12679
Cards
Entrez_Gene (NCBI)VDR  7421  vitamin D receptor
AliasesNR1I1; PPP1R163
GeneCards (Weizmann)VDR
Ensembl hg19 (Hinxton)ENSG00000111424 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000111424 [Gene_View]  ENSG00000111424 [Sequence]  chr12:47841537-47905031 [Contig_View]  VDR [Vega]
ICGC DataPortalENSG00000111424
TCGA cBioPortalVDR
AceView (NCBI)VDR
Genatlas (Paris)VDR
WikiGenes7421
SOURCE (Princeton)VDR
Genetics Home Reference (NIH)VDR
Genomic and cartography
GoldenPath hg38 (UCSC)VDR  -     chr12:47841537-47905031 -  12q13.11   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)VDR  -     12q13.11   [Description]    (hg19-Feb_2009)
EnsemblVDR - 12q13.11 [CytoView hg19]  VDR - 12q13.11 [CytoView hg38]
Mapping of homologs : NCBIVDR [Mapview hg19]  VDR [Mapview hg38]
OMIM166710   277440   601769   
Gene and transcription
Genbank (Entrez)AB307700 AF026260 AK024830 AK225844 AK299446
RefSeq transcript (Entrez)NM_000376 NM_001017535 NM_001017536 NM_001364085
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)VDR
Cluster EST : UnigeneHs.524368 [ NCBI ]
CGAP (NCI)Hs.524368
Alternative Splicing GalleryENSG00000111424
Gene ExpressionVDR [ NCBI-GEO ]   VDR [ EBI - ARRAY_EXPRESS ]   VDR [ SEEK ]   VDR [ MEM ]
Gene Expression Viewer (FireBrowse)VDR [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)7421
GTEX Portal (Tissue expression)VDR
Human Protein AtlasENSG00000111424-VDR [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtP11473   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtP11473  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP11473
Splice isoforms : SwissVarP11473
PhosPhoSitePlusP11473
Domaine pattern : Prosite (Expaxy)NR_LBD (PS51843)    NUCLEAR_REC_DBD_1 (PS00031)    NUCLEAR_REC_DBD_2 (PS51030)   
Domains : Interpro (EBI)NHR_like_dom_sf    Nucl_hrmn_rcpt_lig-bd    Nuclear_hrmn_rcpt    VitD_rcpt    Znf_hrmn_rcpt    Znf_NHR/GATA   
Domain families : Pfam (Sanger)Hormone_recep (PF00104)    zf-C4 (PF00105)   
Domain families : Pfam (NCBI)pfam00104    pfam00105   
Domain families : Smart (EMBL)HOLI (SM00430)  ZnF_C4 (SM00399)  
Conserved Domain (NCBI)VDR
DMDM Disease mutations7421
Blocks (Seattle)VDR
PDB (SRS)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    5V39   
PDB (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    5V39   
PDB (IMB)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    5V39   
PDB (RSDB)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    5V39   
Structural Biology KnowledgeBase1DB1    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    5V39   
SCOP (Structural Classification of Proteins)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    5V39   
CATH (Classification of proteins structures)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    5V39   
SuperfamilyP11473
Human Protein Atlas [tissue]ENSG00000111424-VDR [tissue]
Peptide AtlasP11473
HPRD03463
IPIIPI00005716   IPI01012259   IPI00443026   IPI00976483   IPI01021765   IPI01021623   IPI01021431   IPI01022572   
Protein Interaction databases
DIP (DOE-UCLA)P11473
IntAct (EBI)P11473
FunCoupENSG00000111424
BioGRIDVDR
STRING (EMBL)VDR
ZODIACVDR
Ontologies - Pathways
QuickGOP11473
Ontology : AmiGOnegative regulation of transcription by RNA polymerase II  cell morphogenesis  transcription regulatory region sequence-specific DNA binding  RNA polymerase II regulatory region sequence-specific DNA binding  RNA polymerase II transcription factor activity, sequence-specific DNA binding  RNA polymerase II transcription factor activity, sequence-specific DNA binding  RNA polymerase II transcription factor activity, sequence-specific DNA binding  transcription factor activity, RNA polymerase II transcription factor binding  skeletal system development  DNA binding  DNA-binding transcription factor activity  DNA-binding transcription factor activity  steroid hormone receptor activity  nuclear receptor activity  vitamin D binding  protein binding  nucleus  nucleus  nucleoplasm  nucleoplasm  cytoplasm  transcription initiation from RNA polymerase II promoter  calcium ion transport  cellular calcium ion homeostasis  signal transduction  multicellular organism development  lactation  transcription factor binding  zinc ion binding  negative regulation of cell proliferation  calcitriol receptor activity  calcitriol receptor activity  calcitriol receptor activity  animal organ morphogenesis  positive regulation of gene expression  negative regulation of keratinocyte proliferation  positive regulation of vitamin D 24-hydroxylase activity  cell differentiation  nuclear receptor transcription coactivator activity  bile acid signaling pathway  lithocholic acid receptor activity  vitamin D metabolic process  receptor complex  steroid hormone mediated signaling pathway  positive regulation of keratinocyte differentiation  negative regulation of transcription, DNA-templated  positive regulation of transcription by RNA polymerase II  positive regulation of transcription by RNA polymerase II  decidualization  retinoid X receptor binding  retinoid X receptor binding  intestinal absorption  positive regulation of apoptotic process involved in mammary gland involution  epithelium development  regulation of calcidiol 1-monooxygenase activity  mammary gland branching involved in pregnancy  vitamin D receptor signaling pathway  vitamin D receptor signaling pathway  vitamin D response element binding  vitamin D response element binding  RNA polymerase II transcription factor complex  RNA polymerase II transcription factor complex  transcription factor activity, direct ligand regulated sequence-specific DNA binding  calcitriol binding  calcitriol binding  calcitriol binding  lithocholic acid binding  
Ontology : EGO-EBInegative regulation of transcription by RNA polymerase II  cell morphogenesis  transcription regulatory region sequence-specific DNA binding  RNA polymerase II regulatory region sequence-specific DNA binding  RNA polymerase II transcription factor activity, sequence-specific DNA binding  RNA polymerase II transcription factor activity, sequence-specific DNA binding  RNA polymerase II transcription factor activity, sequence-specific DNA binding  transcription factor activity, RNA polymerase II transcription factor binding  skeletal system development  DNA binding  DNA-binding transcription factor activity  DNA-binding transcription factor activity  steroid hormone receptor activity  nuclear receptor activity  vitamin D binding  protein binding  nucleus  nucleus  nucleoplasm  nucleoplasm  cytoplasm  transcription initiation from RNA polymerase II promoter  calcium ion transport  cellular calcium ion homeostasis  signal transduction  multicellular organism development  lactation  transcription factor binding  zinc ion binding  negative regulation of cell proliferation  calcitriol receptor activity  calcitriol receptor activity  calcitriol receptor activity  animal organ morphogenesis  positive regulation of gene expression  negative regulation of keratinocyte proliferation  positive regulation of vitamin D 24-hydroxylase activity  cell differentiation  nuclear receptor transcription coactivator activity  bile acid signaling pathway  lithocholic acid receptor activity  vitamin D metabolic process  receptor complex  steroid hormone mediated signaling pathway  positive regulation of keratinocyte differentiation  negative regulation of transcription, DNA-templated  positive regulation of transcription by RNA polymerase II  positive regulation of transcription by RNA polymerase II  decidualization  retinoid X receptor binding  retinoid X receptor binding  intestinal absorption  positive regulation of apoptotic process involved in mammary gland involution  epithelium development  regulation of calcidiol 1-monooxygenase activity  mammary gland branching involved in pregnancy  vitamin D receptor signaling pathway  vitamin D receptor signaling pathway  vitamin D response element binding  vitamin D response element binding  RNA polymerase II transcription factor complex  RNA polymerase II transcription factor complex  transcription factor activity, direct ligand regulated sequence-specific DNA binding  calcitriol binding  calcitriol binding  calcitriol binding  lithocholic acid binding  
Pathways : KEGGEndocrine and other factor-regulated calcium reabsorption    Mineral absorption    Tuberculosis   
NDEx NetworkVDR
Atlas of Cancer Signalling NetworkVDR
Wikipedia pathwaysVDR
Orthology - Evolution
OrthoDB7421
GeneTree (enSembl)ENSG00000111424
Phylogenetic Trees/Animal Genes : TreeFamVDR
HOVERGENP11473
HOGENOMP11473
Homologs : HomoloGeneVDR
Homology/Alignments : Family Browser (UCSC)VDR
Gene fusions - Rearrangements
Fusion : MitelmanLMBR1L/VDR [12q13.12/12q13.11]  [t(12;12)(q13;q13)]  
Fusion PortalLMBR1L 12q13.12 VDR 12q13.11 LUAD
Fusion : QuiverVDR
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerVDR [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)VDR
dbVarVDR
ClinVarVDR
1000_GenomesVDR 
Exome Variant ServerVDR
ExAC (Exome Aggregation Consortium)ENSG00000111424
GNOMAD BrowserENSG00000111424
Varsome BrowserVDR
Genetic variants : HAPMAP7421
Genomic Variants (DGV)VDR [DGVbeta]
DECIPHERVDR [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisVDR 
Mutations
ICGC Data PortalVDR 
TCGA Data PortalVDR 
Broad Tumor PortalVDR
OASIS PortalVDR [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICVDR  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDVDR
LOVD (Leiden Open Variation Database)TBsLVD Tuberculosis susceptibility Locus Variation Database
BioMutasearch VDR
DgiDB (Drug Gene Interaction Database)VDR
DoCM (Curated mutations)VDR (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)VDR (select a term)
intoGenVDR
Cancer3DVDR(select the gene name)
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM166710    277440    601769   
Orphanet12173   
DisGeNETVDR
MedgenVDR
Genetic Testing Registry VDR
NextProtP11473 [Medical]
TSGene7421
GENETestsVDR
Target ValidationVDR
Huge Navigator VDR [HugePedia]
snp3D : Map Gene to Disease7421
BioCentury BCIQVDR
ClinGenVDR
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD7421
Chemical/Pharm GKB GenePA37301
Clinical trialVDR
Miscellaneous
canSAR (ICR)VDR (select the gene name)
Probes
Litterature
PubMed499 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineVDR
EVEXVDR
GoPubMedVDR
iHOPVDR
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Mon Aug 27 12:01:19 CEST 2018

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