Atlas of Genetics and Cytogenetics in Oncology and Haematology


Home   Genes   Leukemias   Solid Tumors   Cancer-Prone   Deep Insight   Case Reports   Journals  Portal   Teaching   

X Y 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 NA

PHGDH (phosphoglycerate dehydrogenase)

Identity

Alias_symbol (synonym)SERA
PGDH
PDG
Other alias3-PGDH
3PGDH
HEL-S-113
NLS
NLS1
PGAD
PGD
PHGDHD
HGNC (Hugo) PHGDH
LocusID (NCBI) 26227
Atlas_Id 52399
Location 1p12  [Link to chromosome band 1p12]
Location_base_pair Starts at 119711796 and ends at 119744226 bp from pter ( according to hg38-Dec_2013)
Fusion genes
(updated 2016)
ACSL3 (2q36.1) / PHGDH (1p12)HLA-DRA (6p21.32) / PHGDH (1p12)PHGDH (1p12) / EPHX1 (1q42.12)
PHGDH (1p12) / PHGDH (1p12)PHGDH (1p12) / UBAC2 (13q32.3)TTC39A (1p32.3) / PHGDH (1p12)
WARS2 (1p12) / PHGDH (1p12)ACSL3 2q36.1 / PHGDH 1p12TTC39A 1p32.3 / PHGDH 1p12
WARS2 1p12 / PHGDH 1p12

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) [ 1 ]
  Lung: Translocations in Squamous Cell Carcinoma


External links

Nomenclature
HGNC (Hugo)PHGDH   8923
Cards
Entrez_Gene (NCBI)PHGDH  26227  phosphoglycerate dehydrogenase
Aliases3-PGDH; 3PGDH; HEL-S-113; NLS; 
NLS1; PDG; PGAD; PGD; PGDH; PHGDHD; SERA
GeneCards (Weizmann)PHGDH
Ensembl hg19 (Hinxton)ENSG00000092621 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000092621 [Gene_View]  chr1:119711796-119744226 [Contig_View]  PHGDH [Vega]
ICGC DataPortalENSG00000092621
TCGA cBioPortalPHGDH
AceView (NCBI)PHGDH
Genatlas (Paris)PHGDH
WikiGenes26227
SOURCE (Princeton)PHGDH
Genetics Home Reference (NIH)PHGDH
Genomic and cartography
GoldenPath hg38 (UCSC)PHGDH  -     chr1:119711796-119744226 +  1p12   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)PHGDH  -     1p12   [Description]    (hg19-Feb_2009)
EnsemblPHGDH - 1p12 [CytoView hg19]  PHGDH - 1p12 [CytoView hg38]
Mapping of homologs : NCBIPHGDH [Mapview hg19]  PHGDH [Mapview hg38]
OMIM256520   601815   606879   
Gene and transcription
Genbank (Entrez)AF171235 AF171236 AF171237 AI685723 AK093306
RefSeq transcript (Entrez)NM_006623
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)PHGDH
Cluster EST : UnigeneHs.487296 [ NCBI ]
CGAP (NCI)Hs.487296
Alternative Splicing GalleryENSG00000092621
Gene ExpressionPHGDH [ NCBI-GEO ]   PHGDH [ EBI - ARRAY_EXPRESS ]   PHGDH [ SEEK ]   PHGDH [ MEM ]
Gene Expression Viewer (FireBrowse)PHGDH [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)26227
GTEX Portal (Tissue expression)PHGDH
Protein : pattern, domain, 3D structure
UniProt/SwissProtO43175   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtO43175  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProO43175
Splice isoforms : SwissVarO43175
PhosPhoSitePlusO43175
Domaine pattern : Prosite (Expaxy)D_2_HYDROXYACID_DH_1 (PS00065)    D_2_HYDROXYACID_DH_2 (PS00670)    D_2_HYDROXYACID_DH_3 (PS00671)   
Domains : Interpro (EBI)ASB_dom    D-isomer_2_OHA_DH_cat_dom    D-isomer_DH_CS    D-isomer_DH_CS1    D-isomer_DH_NAD-bd    NAD(P)-bd_dom    PGDH   
Domain families : Pfam (Sanger)2-Hacid_dh (PF00389)    2-Hacid_dh_C (PF02826)   
Domain families : Pfam (NCBI)pfam00389    pfam02826   
Conserved Domain (NCBI)PHGDH
DMDM Disease mutations26227
Blocks (Seattle)PHGDH
PDB (SRS)2G76   
PDB (PDBSum)2G76   
PDB (IMB)2G76   
PDB (RSDB)2G76   
Structural Biology KnowledgeBase2G76   
SCOP (Structural Classification of Proteins)2G76   
CATH (Classification of proteins structures)2G76   
SuperfamilyO43175
Human Protein AtlasENSG00000092621
Peptide AtlasO43175
HPRD06047
IPIIPI00011200   IPI01010953   IPI01010638   IPI00642548   
Protein Interaction databases
DIP (DOE-UCLA)O43175
IntAct (EBI)O43175
FunCoupENSG00000092621
BioGRIDPHGDH
STRING (EMBL)PHGDH
ZODIACPHGDH
Ontologies - Pathways
QuickGOO43175
Ontology : AmiGOphosphoglycerate dehydrogenase activity  cytosol  glutamine metabolic process  glycine metabolic process  L-serine biosynthetic process  threonine metabolic process  brain development  electron carrier activity  gamma-aminobutyric acid metabolic process  regulation of gene expression  taurine metabolic process  spinal cord development  glial cell development  neural tube development  L-malate dehydrogenase activity  neuron projection development  myelin sheath  NAD binding  oxidation-reduction process  extracellular exosome  G1 to G0 transition  
Ontology : EGO-EBIphosphoglycerate dehydrogenase activity  cytosol  glutamine metabolic process  glycine metabolic process  L-serine biosynthetic process  threonine metabolic process  brain development  electron carrier activity  gamma-aminobutyric acid metabolic process  regulation of gene expression  taurine metabolic process  spinal cord development  glial cell development  neural tube development  L-malate dehydrogenase activity  neuron projection development  myelin sheath  NAD binding  oxidation-reduction process  extracellular exosome  G1 to G0 transition  
Pathways : KEGGGlycine, serine and threonine metabolism   
NDEx NetworkPHGDH
Atlas of Cancer Signalling NetworkPHGDH
Wikipedia pathwaysPHGDH
Orthology - Evolution
OrthoDB26227
GeneTree (enSembl)ENSG00000092621
Phylogenetic Trees/Animal Genes : TreeFamPHGDH
HOVERGENO43175
HOGENOMO43175
Homologs : HomoloGenePHGDH
Homology/Alignments : Family Browser (UCSC)PHGDH
Gene fusions - Rearrangements
Fusion : MitelmanACSL3/PHGDH [2q36.1/1p12]  [t(1;2)(p12;q36)]  
Fusion : MitelmanTTC39A/PHGDH [1p32.3/1p12]  [t(1;1)(p12;p32)]  
Fusion: TCGAACSL3 2q36.1 PHGDH 1p12 LUAD
Fusion: TCGATTC39A 1p32.3 PHGDH 1p12 LUAD
Fusion: TCGAWARS2 1p12 PHGDH 1p12 LUSC
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerPHGDH [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)PHGDH
dbVarPHGDH
ClinVarPHGDH
1000_GenomesPHGDH 
Exome Variant ServerPHGDH
ExAC (Exome Aggregation Consortium)PHGDH (select the gene name)
Genetic variants : HAPMAP26227
Genomic Variants (DGV)PHGDH [DGVbeta]
DECIPHERPHGDH [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisPHGDH 
Mutations
ICGC Data PortalPHGDH 
TCGA Data PortalPHGDH 
Broad Tumor PortalPHGDH
OASIS PortalPHGDH [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICPHGDH  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDPHGDH
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 PHGDH
DgiDB (Drug Gene Interaction Database)PHGDH
DoCM (Curated mutations)PHGDH (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)PHGDH (select a term)
intoGenPHGDH
Cancer3DPHGDH(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM256520    601815    606879   
Orphanet2439    11377   
MedgenPHGDH
Genetic Testing Registry PHGDH
NextProtO43175 [Medical]
TSGene26227
GENETestsPHGDH
Target ValidationPHGDH
Huge Navigator PHGDH [HugePedia]
snp3D : Map Gene to Disease26227
BioCentury BCIQPHGDH
ClinGenPHGDH
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD26227
Chemical/Pharm GKB GenePA33264
Clinical trialPHGDH
Miscellaneous
canSAR (ICR)PHGDH (select the gene name)
Probes
Litterature
PubMed91 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMinePHGDH
EVEXPHGDH
GoPubMedPHGDH
iHOPPHGDH
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 : Wed Jun 7 12:49:19 CEST 2017

Home   Genes   Leukemias   Solid Tumors   Cancer-Prone   Deep Insight   Case Reports   Journals  Portal   Teaching   

For comments and suggestions or contributions, please contact us

jlhuret@AtlasGeneticsOncology.org.