Atlas of Genetics and Cytogenetics in Oncology and Haematology


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PGD (phosphogluconate dehydrogenase)

Identity

Other alias6PGD
HGNC (Hugo) PGD
LocusID (NCBI) 5226
Atlas_Id 52911
Location 1p36.22  [Link to chromosome band 1p36]
Location_base_pair Starts at 10398992 and ends at 10420511 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)
PER3 (1p36.23) / PGD (1p36.22)PEX14 (1p36.22) / PGD (1p36.22)PGD (1p36.22) / C11orf24 (11q13.2)
PGD (1p36.22) / CAMTA1 (1p36.31)PGD (1p36.22) / ESRP1 (8q22.1)PGD (1p36.22) / PGD (1p36.22)
PGD (1p36.22) / ZNF335 (20q13.12)PER3 1p36.23 / PGD 1p36.22PGD 1p36.22 / CAMTA1 1p36.31

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

 


External links

Nomenclature
HGNC (Hugo)PGD   8891
Cards
Entrez_Gene (NCBI)PGD  5226  phosphogluconate dehydrogenase
Aliases6PGD
GeneCards (Weizmann)PGD
Ensembl hg19 (Hinxton)ENSG00000142657 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000142657 [Gene_View]  chr1:10398992-10420511 [Contig_View]  PGD [Vega]
ICGC DataPortalENSG00000142657
TCGA cBioPortalPGD
AceView (NCBI)PGD
Genatlas (Paris)PGD
WikiGenes5226
SOURCE (Princeton)PGD
Genetics Home Reference (NIH)PGD
Genomic and cartography
GoldenPath hg38 (UCSC)PGD  -     chr1:10398992-10420511 +  1p36.22   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)PGD  -     1p36.22   [Description]    (hg19-Feb_2009)
EnsemblPGD - 1p36.22 [CytoView hg19]  PGD - 1p36.22 [CytoView hg38]
Mapping of homologs : NCBIPGD [Mapview hg19]  PGD [Mapview hg38]
OMIM172200   
Gene and transcription
Genbank (Entrez)AK290404 AK296889 AK298830 AK300952 AK303898
RefSeq transcript (Entrez)NM_001304451 NM_001304452 NM_002631
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)PGD
Cluster EST : UnigeneHs.464071 [ NCBI ]
CGAP (NCI)Hs.464071
Alternative Splicing GalleryENSG00000142657
Gene ExpressionPGD [ NCBI-GEO ]   PGD [ EBI - ARRAY_EXPRESS ]   PGD [ SEEK ]   PGD [ MEM ]
Gene Expression Viewer (FireBrowse)PGD [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)5226
GTEX Portal (Tissue expression)PGD
Human Protein AtlasENSG00000142657-PGD [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtP52209   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtP52209  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP52209
Splice isoforms : SwissVarP52209
PhosPhoSitePlusP52209
Domaine pattern : Prosite (Expaxy)6PGD (PS00461)   
Domains : Interpro (EBI)6-PGluconate_DH_C-like    6PGD_dom_2    6PGD_dom_3    6PGDH_C    6PGDH_Gnd/GntZ    6PGDH_NADP-bd    6PGdom_BS    NAD(P)-bd_dom    Pgluconate_DH   
Domain families : Pfam (Sanger)6PGD (PF00393)    NAD_binding_2 (PF03446)   
Domain families : Pfam (NCBI)pfam00393    pfam03446   
Domain families : Smart (EMBL)6PGD (SM01350)  
Conserved Domain (NCBI)PGD
DMDM Disease mutations5226
Blocks (Seattle)PGD
PDB (SRS)2JKV    4GWG    4GWK   
PDB (PDBSum)2JKV    4GWG    4GWK   
PDB (IMB)2JKV    4GWG    4GWK   
PDB (RSDB)2JKV    4GWG    4GWK   
Structural Biology KnowledgeBase2JKV    4GWG    4GWK   
SCOP (Structural Classification of Proteins)2JKV    4GWG    4GWK   
CATH (Classification of proteins structures)2JKV    4GWG    4GWK   
SuperfamilyP52209
Human Protein Atlas [tissue]ENSG00000142657-PGD [tissue]
Peptide AtlasP52209
HPRD01391
IPIIPI00219525   IPI00910950   IPI01009353   IPI01012504   IPI01011970   
Protein Interaction databases
DIP (DOE-UCLA)P52209
IntAct (EBI)P52209
FunCoupENSG00000142657
BioGRIDPGD
STRING (EMBL)PGD
ZODIACPGD
Ontologies - Pathways
QuickGOP52209
Ontology : AmiGOphosphogluconate dehydrogenase (decarboxylating) activity  phosphogluconate dehydrogenase (decarboxylating) activity  nucleus  cytosol  pentose-phosphate shunt  pentose-phosphate shunt  pentose-phosphate shunt, oxidative branch  pentose biosynthetic process  D-gluconate metabolic process  oxidation-reduction process  extracellular exosome  
Ontology : EGO-EBIphosphogluconate dehydrogenase (decarboxylating) activity  phosphogluconate dehydrogenase (decarboxylating) activity  nucleus  cytosol  pentose-phosphate shunt  pentose-phosphate shunt  pentose-phosphate shunt, oxidative branch  pentose biosynthetic process  D-gluconate metabolic process  oxidation-reduction process  extracellular exosome  
Pathways : KEGGPentose phosphate pathway    Glutathione metabolism   
NDEx NetworkPGD
Atlas of Cancer Signalling NetworkPGD
Wikipedia pathwaysPGD
Orthology - Evolution
OrthoDB5226
GeneTree (enSembl)ENSG00000142657
Phylogenetic Trees/Animal Genes : TreeFamPGD
HOVERGENP52209
HOGENOMP52209
Homologs : HomoloGenePGD
Homology/Alignments : Family Browser (UCSC)PGD
Gene fusions - Rearrangements
Fusion : MitelmanPER3/PGD [1p36.23/1p36.22]  [t(1;1)(p36;p36)]  
Fusion : MitelmanPGD/CAMTA1 [1p36.22/1p36.31]  [t(1;1)(p36;p36)]  
Fusion: TCGA_MDACCPER3 1p36.23 PGD 1p36.22 GBM
Fusion: TCGA_MDACCPGD 1p36.22 CAMTA1 1p36.31 GBM
Tumor Fusion PortalPGD
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerPGD [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)PGD
dbVarPGD
ClinVarPGD
1000_GenomesPGD 
Exome Variant ServerPGD
ExAC (Exome Aggregation Consortium)ENSG00000142657
GNOMAD BrowserENSG00000142657
Genetic variants : HAPMAP5226
Genomic Variants (DGV)PGD [DGVbeta]
DECIPHERPGD [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisPGD 
Mutations
ICGC Data PortalPGD 
TCGA Data PortalPGD 
Broad Tumor PortalPGD
OASIS PortalPGD [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICPGD  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDPGD
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch PGD
DgiDB (Drug Gene Interaction Database)PGD
DoCM (Curated mutations)PGD (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)PGD (select a term)
intoGenPGD
Cancer3DPGD(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM172200   
Orphanet
DisGeNETPGD
MedgenPGD
Genetic Testing Registry PGD
NextProtP52209 [Medical]
TSGene5226
GENETestsPGD
Target ValidationPGD
Huge Navigator PGD [HugePedia]
snp3D : Map Gene to Disease5226
BioCentury BCIQPGD
ClinGenPGD
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD5226
Chemical/Pharm GKB GenePA33229
Clinical trialPGD
Miscellaneous
canSAR (ICR)PGD (select the gene name)
Probes
Litterature
PubMed41 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMinePGD
EVEXPGD
GoPubMedPGD
iHOPPGD
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

Search in all EBI   NCBI

© Atlas of Genetics and Cytogenetics in Oncology and Haematology
indexed on : Tue Nov 21 14:28:30 CET 2017

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