U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

PHGDH phosphoglycerate dehydrogenase [ Homo sapiens (human) ]

Gene ID: 26227, updated on 11-Apr-2024

Summary

Go to the top of the page Help
Official Symbol
PHGDHprovided by HGNC
Official Full Name
phosphoglycerate dehydrogenaseprovided by HGNC
Primary source
HGNC:HGNC:8923
See related
Ensembl:ENSG00000092621 MIM:606879; AllianceGenome:HGNC:8923
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
NLS; PDG; PGD; NLS1; PGAD; PGDH; SERA; 3PGDH; 3-PGDH; PHGDHD; HEL-S-113
Summary
This gene encodes the enzyme which is involved in the early steps of L-serine synthesis in animal cells. L-serine is required for D-serine and other amino acid synthesis. The enzyme requires NAD/NADH as a cofactor and forms homotetramers for activity. Mutations in this gene have been found in a family with congenital microcephaly, psychomotor retardation and other symptoms. Multiple alternatively spliced transcript variants have been found, however the full-length nature of most are not known. [provided by RefSeq, Aug 2011]
Expression
Broad expression in fat (RPKM 36.0), skin (RPKM 33.6) and 23 other tissues See more
Orthologs
mouse all
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
See PHGDH in Genome Data Viewer
Location:
1p12
Exon count:
18
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (119711934..119744215)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (119725174..119757460)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (120254557..120286838)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 8207 Neighboring gene uncharacterized LOC124904390 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1595 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:120218249-120218750 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr1:120221858-120222433 Neighboring gene uncharacterized LOC105378937 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:120230232-120230835 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:120254349-120254878 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1598 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1248 Neighboring gene 3-hydroxy-3-methylglutaryl-CoA synthase 2 Neighboring gene Sharpr-MPRA regulatory region 1341 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:120323715-120323913 Neighboring gene regenerating family member 4

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help
  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

Go to the top of the pageHelp

Related articles in PubMed

  1. PHGDH preserves one-carbon cycle to confer metabolic plasticity in chemoresistant gastric cancer during nutrient stress. Yoon BK, et al. Proc Natl Acad Sci U S A, 2023 May 23. PMID 37192160, Free PMC Article
  2. Comprehensive analysis of PHGDH for predicting prognosis and immunotherapy response in patients with endometrial carcinoma. Zhang H, et al. BMC Med Genomics, 2023 Feb 20. PMID 36803157, Free PMC Article
  3. PHGDH expression increases with progression of Alzheimer's disease pathology and symptoms. Chen X, et al. Cell Metab, 2022 May 3. PMID 35508105, Free PMC Article
  4. Biophysical and biochemical properties of PHGDH revealed by studies on PHGDH inhibitors. Tan Y, et al. Cell Mol Life Sci, 2021 Dec 31. PMID 34971423
  5. Serine biosynthesis defect due to haploinsufficiency of PHGDH causes retinal disease. Eade K, et al. Nat Metab, 2021 Mar. PMID 33758422, Free PMC Article

See all (259) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. PRMT1 Sustains De Novo Fatty Acid Synthesis by Methylating PHGDH to Drive Chemoresistance in Triple-Negative Breast Cancer.
    Title: PRMT1 Sustains De Novo Fatty Acid Synthesis by Methylating PHGDH to Drive Chemoresistance in Triple-Negative Breast Cancer.
  2. Biochemical and cellular studies of three human 3-phosphoglycerate dehydrogenase variants responsible for pathological reduced L-serine levels.
    Title: Biochemical and cellular studies of three human 3-phosphoglycerate dehydrogenase variants responsible for pathological reduced L-serine levels.
  3. Serine synthesis pathway enzyme PHGDH is critical for muscle cell biomass, anabolic metabolism, and mTORC1 signaling.
    Title: Serine synthesis pathway enzyme PHGDH is critical for muscle cell biomass, anabolic metabolism, and mTORC1 signaling.
  4. PHGDH preserves one-carbon cycle to confer metabolic plasticity in chemoresistant gastric cancer during nutrient stress.
    Title: PHGDH preserves one-carbon cycle to confer metabolic plasticity in chemoresistant gastric cancer during nutrient stress.
  5. The Role of ESRP1 in the Regulation of PHGDH in Estrogen Receptor-Positive Breast Cancer.
    Title: The Role of ESRP1 in the Regulation of PHGDH in Estrogen Receptor-Positive Breast Cancer.
  6. PHGDH arginine methylation by PRMT1 promotes serine synthesis and represents a therapeutic vulnerability in hepatocellular carcinoma.
    Title: PHGDH arginine methylation by PRMT1 promotes serine synthesis and represents a therapeutic vulnerability in hepatocellular carcinoma.
  7. Comprehensive analysis of PHGDH for predicting prognosis and immunotherapy response in patients with endometrial carcinoma.
    Title: Comprehensive analysis of PHGDH for predicting prognosis and immunotherapy response in patients with endometrial carcinoma.
  8. PHGDH Inhibits Ferroptosis and Promotes Malignant Progression by Upregulating SLC7A11 in Bladder Cancer.
    Title: PHGDH Inhibits Ferroptosis and Promotes Malignant Progression by Upregulating SLC7A11 in Bladder Cancer.
  9. PHGDH expression increases with progression of Alzheimer's disease pathology and symptoms.
    Title: PHGDH expression increases with progression of Alzheimer's disease pathology and symptoms.
  10. Biophysical and biochemical properties of PHGDH revealed by studies on PHGDH inhibitors.
    Title: Biophysical and biochemical properties of PHGDH revealed by studies on PHGDH inhibitors.
Submit: New GeneRIF Correction See all GeneRIFs (57)

Phenotypes

Go to the top of the page Help

Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Neu-Laxova syndrome 1
MedGen: C4551478 OMIM: 256520 GeneReviews: Serine Deficiency Disorders
Compare labs
PHGDH deficiency
MedGen: C1866174 OMIM: 601815 GeneReviews: Serine Deficiency Disorders
Compare labs

EBI GWAS Catalog

Description
An atlas of genetic influences on human blood metabolites.
EBI GWAS Catalog
Genetic variants associated with glycine metabolism and their role in insulin sensitivity and type 2 diabetes.
EBI GWAS Catalog
Human metabolic individuality in biomedical and pharmaceutical research.
EBI GWAS Catalog

Variation

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

HIV-1 interactions

Go to the top of the page Help

Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp120 env HIV-1 gp120 upregulates the expression of PHGDH in umbilical cord blood mononuclear cells and T-cell lines PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

Go to the top of the page

Interactions

Go to the top of the page Help
Products Interactant Other Gene Complex Source Pubs Description

General gene information

Go to the top of the page Help

Markers

Homology

Clone Names

  • MGC3017

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables L-malate dehydrogenase activity IEA
Inferred from Electronic Annotation
more info
  
enables NAD binding IEA
Inferred from Electronic Annotation
more info
  
enables electron transfer activity TAS
Traceable Author Statement
more info
 PubMed 
enables phosphoglycerate dehydrogenase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in G1 to G0 transition IEA
Inferred from Electronic Annotation
more info
  
involved_in L-serine biosynthetic process IEA
Inferred from Electronic Annotation
more info
  
involved_in brain development TAS
Traceable Author Statement
more info
 PubMed 
involved_in gamma-aminobutyric acid metabolic process IEA
Inferred from Electronic Annotation
more info
  
involved_in glial cell development IEA
Inferred from Electronic Annotation
more info
  
involved_in glutamine metabolic process IEA
Inferred from Electronic Annotation
more info
  
involved_in glycine metabolic process IEA
Inferred from Electronic Annotation
more info
  
involved_in neural tube development IEA
Inferred from Electronic Annotation
more info
  
involved_in neuron projection development IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of gene expression IEA
Inferred from Electronic Annotation
more info
  
involved_in spinal cord development IEA
Inferred from Electronic Annotation
more info
  
involved_in taurine metabolic process IEA
Inferred from Electronic Annotation
more info
  
involved_in threonine metabolic process IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in cytosol TAS
Traceable Author Statement
more info
  
located_in extracellular exosome HDA PubMed 

General protein information

Go to the top of the page Help
Preferred Names
D-3-phosphoglycerate dehydrogenase
Names
2-oxoglutarate reductase
3-phosphoglycerate dehydrogenase
epididymis secretory protein Li 113
malate dehydrogenase
NP_006614.2
XP_011539528.1
XP_011539529.1
XP_011539530.1
XP_047273636.1
XP_047273638.1
XP_047273639.1
XP_054191923.1
XP_054191924.1
XP_054191925.1
XP_054191926.1
XP_054191927.1
XP_054191928.1

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_009188.1 RefSeqGene

    Range
    5139..37420
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_006623.4 → NP_006614.2  D-3-phosphoglycerate dehydrogenase

    See identical proteins and their annotated locations for NP_006614.2

    Status: REVIEWED

    Source sequence(s)
    AL589734, BC011262
    Consensus CDS
    CCDS904.1
    UniProtKB/Swiss-Prot
    B2RD08, O43175, Q5SZU3, Q9BQ01
    UniProtKB/TrEMBL
    V9HW79
    Related
    ENSP00000493175.1, ENST00000641023.2
    Conserved Domains (2) summary
    COG0111
    Location:7 → 318
    SerA; Phosphoglycerate dehydrogenase or related dehydrogenase [Coenzyme transport and metabolism, General function prediction only]
    cd12173
    Location:8 → 310
    PGDH_4; Phosphoglycerate dehydrogenases, NAD-binding and catalytic domains

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    119711934..119744215
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011541226.3 → XP_011539528.1  D-3-phosphoglycerate dehydrogenase isoform X1

    UniProtKB/TrEMBL
    V9HW79
    Conserved Domains (2) summary
    COG0111
    Location:7 → 392
    SerA; Phosphoglycerate dehydrogenase or related dehydrogenase [Coenzyme transport and metabolism, General function prediction only]
    cd12173
    Location:8 → 384
    PGDH_4; Phosphoglycerate dehydrogenases, NAD-binding and catalytic domains

  2. XM_011541227.3 → XP_011539529.1  D-3-phosphoglycerate dehydrogenase isoform X2

    UniProtKB/TrEMBL
    B3KSC3
    Conserved Domains (1) summary
    cd12173
    Location:20 → 358
    PGDH_4; Phosphoglycerate dehydrogenases, NAD-binding and catalytic domains

  3. XM_047417680.1 → XP_047273636.1  D-3-phosphoglycerate dehydrogenase isoform X4

  4. XM_047417682.1 → XP_047273638.1  D-3-phosphoglycerate dehydrogenase isoform X5

  5. XM_011541228.3 → XP_011539530.1  D-3-phosphoglycerate dehydrogenase isoform X3

    UniProtKB/TrEMBL
    B3KSC3
    Conserved Domains (1) summary
    cl28378
    Location:7 → 451
    SerA; Phosphoglycerate dehydrogenase or related dehydrogenase [Coenzyme transport and metabolism, General function prediction only]

  6. XM_047417683.1 → XP_047273639.1  D-3-phosphoglycerate dehydrogenase isoform X6

RNA

  1. XR_007058634.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    119725174..119757460
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054335948.1 → XP_054191923.1  D-3-phosphoglycerate dehydrogenase isoform X1

  2. XM_054335949.1 → XP_054191924.1  D-3-phosphoglycerate dehydrogenase isoform X2

  3. XM_054335951.1 → XP_054191926.1  D-3-phosphoglycerate dehydrogenase isoform X4

  4. XM_054335952.1 → XP_054191927.1  D-3-phosphoglycerate dehydrogenase isoform X5

  5. XM_054335950.1 → XP_054191925.1  D-3-phosphoglycerate dehydrogenase isoform X3

  6. XM_054335953.1 → XP_054191928.1  D-3-phosphoglycerate dehydrogenase isoform X6

RNA

  1. XR_008485990.1 RNA Sequence

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_032692.1: Suppressed sequence

    Description
    NM_032692.1: This RefSeq record was removed by NCBI staff. Contact info@ncbi.nlm.nih.gov for further information.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O43175.4 GenPept UniProtKB/Swiss-Prot:O43175

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Chemical Information
Medical
Molecular Biology Databases
Research Materials
Tools
Miscellaneous