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PHGDH (phosphoglycerate dehydrogenase)

Identity

Alias (NCBI)3-PGDH
3PGDH
HEL-S-113
NLS
NLS1
PDG
PGAD
PGD
PGDH
PHGDHD
SERA
HGNC (Hugo) PHGDH
HGNC Alias symbSERA
PGDH
PDG
HGNC Alias nameD-3-phosphoglycerate dehydrogenase
LocusID (NCBI) 26227
Atlas_Id 52399
Location 1p12  [Link to chromosome band 1p12]
Location_base_pair Starts at 119711934 and ends at 119744215 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)
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

 



External links

 

Nomenclature
HGNC (Hugo)PHGDH   8923
Cards
Entrez_Gene (NCBI)PHGDH    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]  ENSG00000092621 [Sequence]  chr1:119711934-119744215 [Contig_View]  PHGDH [Vega]
ICGC DataPortalENSG00000092621
TCGA cBioPortalPHGDH
AceView (NCBI)PHGDH
Genatlas (Paris)PHGDH
SOURCE (Princeton)PHGDH
Genetics Home Reference (NIH)PHGDH
Genomic and cartography
GoldenPath hg38 (UCSC)PHGDH  -     chr1:119711934-119744215 +  1p12   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)PHGDH  -     1p12   [Description]    (hg19-Feb_2009)
GoldenPathPHGDH - 1p12 [CytoView hg19]  PHGDH - 1p12 [CytoView hg38]
ImmunoBaseENSG00000092621
Genome Data Viewer NCBIPHGDH [Mapview hg19]  
OMIM256520   601815   606879   
Gene and transcription
Genbank (Entrez)AF171235 AF171236 AF171237 AI685723 AK093306
RefSeq transcript (Entrez)NM_006623
Consensus coding sequences : CCDS (NCBI)PHGDH
Gene ExpressionPHGDH [ NCBI-GEO ]   PHGDH [ EBI - ARRAY_EXPRESS ]   PHGDH [ SEEK ]   PHGDH [ MEM ]
Gene Expression Viewer (FireBrowse)PHGDH [ Firebrowse - Broad ]
GenevisibleExpression of PHGDH in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)26227
GTEX Portal (Tissue expression)PHGDH
Human Protein AtlasENSG00000092621-PHGDH [pathology]   [cell]   [tissue]
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
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_sf    D-isomer_2_OHA_DH_cat_dom    D-isomer_DH_CS    D-isomer_DH_CS1    D-isomer_DH_NAD-bd    NAD(P)-bd_dom_sf    PGDH   
Domain families : Pfam (Sanger)2-Hacid_dh (PF00389)    2-Hacid_dh_C (PF02826)   
Domain families : Pfam (NCBI)pfam00389    pfam02826   
Conserved Domain (NCBI)PHGDH
PDB (RSDB)2G76    5N53    5N6C    5NZO    5NZP    5NZQ    5OFM    5OFV    5OFW    6CWA    6PLF    6PLG    6RIH    6RJ2    6RJ3    6RJ5    6RJ6    7CVP   
PDB Europe2G76    5N53    5N6C    5NZO    5NZP    5NZQ    5OFM    5OFV    5OFW    6CWA    6PLF    6PLG    6RIH    6RJ2    6RJ3    6RJ5    6RJ6    7CVP   
PDB (PDBSum)2G76    5N53    5N6C    5NZO    5NZP    5NZQ    5OFM    5OFV    5OFW    6CWA    6PLF    6PLG    6RIH    6RJ2    6RJ3    6RJ5    6RJ6    7CVP   
PDB (IMB)2G76    5N53    5N6C    5NZO    5NZP    5NZQ    5OFM    5OFV    5OFW    6CWA    6PLF    6PLG    6RIH    6RJ2    6RJ3    6RJ5    6RJ6    7CVP   
Structural Biology KnowledgeBase2G76    5N53    5N6C    5NZO    5NZP    5NZQ    5OFM    5OFV    5OFW    6CWA    6PLF    6PLG    6RIH    6RJ2    6RJ3    6RJ5    6RJ6    7CVP   
SCOP (Structural Classification of Proteins)2G76    5N53    5N6C    5NZO    5NZP    5NZQ    5OFM    5OFV    5OFW    6CWA    6PLF    6PLG    6RIH    6RJ2    6RJ3    6RJ5    6RJ6    7CVP   
CATH (Classification of proteins structures)2G76    5N53    5N6C    5NZO    5NZP    5NZQ    5OFM    5OFV    5OFW    6CWA    6PLF    6PLG    6RIH    6RJ2    6RJ3    6RJ5    6RJ6    7CVP   
SuperfamilyO43175
AlphaFold pdb e-kbO43175   
Human Protein Atlas [tissue]ENSG00000092621-PHGDH [tissue]
HPRD06047
Protein Interaction databases
DIP (DOE-UCLA)O43175
IntAct (EBI)O43175
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 transfer activity  gamma-aminobutyric acid metabolic process  regulation of gene expression  taurine metabolic process  spinal cord development  glial cell development  neural tube development  electron transport chain  L-malate dehydrogenase activity  neuron projection development  NAD binding  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 transfer activity  gamma-aminobutyric acid metabolic process  regulation of gene expression  taurine metabolic process  spinal cord development  glial cell development  neural tube development  electron transport chain  L-malate dehydrogenase activity  neuron projection development  NAD binding  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
Homologs : HomoloGenePHGDH
Homology/Alignments : Family Browser (UCSC)PHGDH
Gene fusions - Rearrangements
Fusion : MitelmanACSL3/PHGDH [2q36.1/1p12]  
Fusion : MitelmanTTC39A/PHGDH [1p32.3/1p12]  
Fusion : QuiverPHGDH
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerPHGDH [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)PHGDH
dbVarPHGDH
ClinVarPHGDH
MonarchPHGDH
1000_GenomesPHGDH 
Exome Variant ServerPHGDH
GNOMAD BrowserENSG00000092621
Varsome BrowserPHGDH
ACMGPHGDH variants
VarityO43175
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]  
Somatic Mutations in Cancer : COSMIC3DPHGDH
Mutations and Diseases : HGMDPHGDH
LOVD (Leiden Open Variation Database)[gene] [transcripts] [variants]
BioMutaPHGDH
DgiDB (Drug Gene Interaction Database)PHGDH
DoCM (Curated mutations)PHGDH
CIViC (Clinical Interpretations of Variants in Cancer)PHGDH
Cancer3DPHGDH
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM256520    601815    606879   
Orphanet2439    11377   
DisGeNETPHGDH
MedgenPHGDH
Genetic Testing Registry PHGDH
NextProtO43175 [Medical]
GENETestsPHGDH
Target ValidationPHGDH
Huge Navigator PHGDH [HugePedia]
ClinGenPHGDH
Clinical trials, drugs, therapy
MyCancerGenomePHGDH
Protein Interactions : CTDPHGDH
Pharm GKB GenePA33264
PharosO43175
Clinical trialPHGDH
Miscellaneous
canSAR (ICR)PHGDH
HarmonizomePHGDH
DataMed IndexPHGDH
Probes
Litterature
PubMed183 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
EVEXPHGDH
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Mon Oct 4 15:25:10 CEST 2021

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