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GeneE
26 sources retrieved Β· Most recent: April 2026 Β· Index updated 14 days ago
β“˜GeneE is for informational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.
PHGDH
phosphoglycerate dehydrogenase
Chromosome 1 Β· 1p12
NCBI Gene: 26227Ensembl: ENSG00000092621.14HGNC: HGNC:8923UniProt: O43175
324PubMed Papers
22Diseases
0Drugs
97Pathogenic Variants
RESEARCH IMPACT
TrendingVariant-Rich
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
extracellular exosomeL-serine biosynthetic processprotein bindingphosphoglycerate dehydrogenase activityPHGDH deficiencyNeu-Laxova syndrome 13-phosphoglycerate dehydrogenase deficiency, infantile/juvenile formNeu-Laxova syndrome
✦AI Summary

PHGDH (phosphoglycerate dehydrogenase) catalyzes the first rate-limiting step in de novo serine biosynthesis, converting 3-phosphoglycerate to 3-phosphohydroxypyruvate 1. Beyond its metabolic function, PHGDH exhibits diverse regulatory roles in cancer and neurological disorders. In hepatocellular carcinoma, PHGDH activity is enhanced through PRMT1-mediated arginine methylation at residue 236, promoting serine synthesis and tumor growth 2. This methylation is regulated by FBXO7-mediated ubiquitination of PRMT1 3. Paradoxically, heterogeneous or low PHGDH expression in breast cancer promotes metastasis through non-catalytic mechanisms involving aberrant protein glycosylation and integrin sialylation 4. PHGDH also drives immunosuppression by promoting M2 macrophage polarization via Ξ±-ketoglutarate production and mTORC1 signaling 5. In glioblastoma, PHGDH-mediated endothelial metabolism creates hypoxic, immune-hostile microenvironments that reduce CAR-T cell therapy efficacy 6. Additionally, PHGDH has a transcriptional regulatory function in Alzheimer's disease, promoting IKKΞ± and HMGB1 expression in astrocytes, which accelerates amyloid pathology independent of its enzymatic activity 7. These findings establish PHGDH as a multifunctional protein with both metabolic and non-metabolic roles in disease pathogenesis.

Sources cited
1
PHGDH catalyzes the first rate-limiting step in serine biosynthesis
PMID: 38945960
2
PRMT1-mediated arginine methylation at residue 236 enhances PHGDH activity in hepatocellular carcinoma
PMID: 36823188
3
FBXO7 regulates PHGDH activity through PRMT1 ubiquitination
PMID: 38839752
4
Low PHGDH expression promotes breast cancer metastasis through non-catalytic mechanisms
PMID: 35585241
5
PHGDH promotes M2 macrophage polarization via Ξ±-ketoglutarate and mTORC1 signaling
PMID: 38409249
6
PHGDH-mediated endothelial metabolism creates immune-hostile microenvironments in glioblastoma
PMID: 36804058
7
PHGDH has transcriptional regulatory function in Alzheimer's disease, promoting IKKΞ± and HMGB1 expression
PMID: 40273909
Disease Associationsβ“˜22
PHGDH deficiencyOpen Targets
0.81Strong
Neu-Laxova syndrome 1Open Targets
0.80Strong
3-phosphoglycerate dehydrogenase deficiency, infantile/juvenile formOpen Targets
0.70Moderate
Neu-Laxova syndromeOpen Targets
0.57Moderate
peripheral neuropathyOpen Targets
0.49Moderate
osteomyelitisOpen Targets
0.48Moderate
macular telangiectasia type 2Open Targets
0.47Moderate
neurometabolic disorder due to serine deficiencyOpen Targets
0.44Moderate
multiple sclerosisOpen Targets
0.42Moderate
genetic disorderOpen Targets
0.41Moderate
goutOpen Targets
0.41Moderate
autonomic nervous system diseaseOpen Targets
0.40Moderate
bone diseaseOpen Targets
0.38Weak
chronic ulcer of skinOpen Targets
0.38Weak
ulcer of lower limbOpen Targets
0.38Weak
neuropathyOpen Targets
0.36Weak
diabetic neuropathyOpen Targets
0.33Weak
osteoarthritis, hipOpen Targets
0.33Weak
Epileptic encephalopathyOpen Targets
0.33Weak
SeizureOpen Targets
0.33Weak
Neu-Laxova syndrome 1UniProt
Phosphoglycerate dehydrogenase deficiencyUniProt
Pathogenic Variants97
NM_006623.4(PHGDH):c.171del (p.Lys58fs)Pathogenic
PHGDH deficiency
β˜…β˜…β˜†β˜†2026β†’ Residue 58
NM_006623.4(PHGDH):c.1063C>T (p.Gln355Ter)Pathogenic
PHGDH deficiency|Inborn genetic diseases
β˜…β˜…β˜†β˜†2026β†’ Residue 355
NM_006623.4(PHGDH):c.1030C>T (p.Arg344Ter)Pathogenic
Neu-Laxova syndrome 1|PHGDH deficiency|not provided
β˜…β˜…β˜†β˜†2026β†’ Residue 344
NM_006623.4(PHGDH):c.2T>C (p.Met1Thr)Pathogenic
PHGDH deficiency|Neu-Laxova syndrome 1
β˜…β˜…β˜†β˜†2025β†’ Residue 1
NM_006623.4(PHGDH):c.357-1G>APathogenic
Neu-Laxova syndrome 1|PHGDH deficiency|not provided|PHGDH deficiency;Neu-Laxova syndrome 1
β˜…β˜…β˜†β˜†2025
NM_006623.4(PHGDH):c.1129G>A (p.Gly377Ser)Pathogenic
PHGDH deficiency|PHGDH deficiency;Neu-Laxova syndrome 1|not provided|Neu-Laxova syndrome 1|Autosomal recessive PHGDH-related disorders
β˜…β˜…β˜†β˜†2025β†’ Residue 377
NM_006623.4(PHGDH):c.1468G>A (p.Val490Met)Pathogenic
PHGDH deficiency|See cases|Neu-Laxova syndrome 1|PHGDH deficiency;Neu-Laxova syndrome 1|PHGDH-related disorder|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 490
NM_006623.4(PHGDH):c.1078+1G>ALikely pathogenic
PHGDH deficiency|PHGDH deficiency;Neu-Laxova syndrome 1|Neu-Laxova syndrome 1
β˜…β˜…β˜†β˜†2025
NM_006623.4(PHGDH):c.1394del (p.Leu465fs)Pathogenic
PHGDH deficiency|Neu-Laxova syndrome 1
β˜…β˜…β˜†β˜†2025β†’ Residue 465
NM_006623.4(PHGDH):c.348C>A (p.Cys116Ter)Pathogenic
PHGDH deficiency|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 116
NM_006623.4(PHGDH):c.874C>T (p.Gln292Ter)Pathogenic
PHGDH deficiency|PHGDH deficiency;Neu-Laxova syndrome 1
β˜…β˜…β˜†β˜†2025β†’ Residue 292
NM_006623.4(PHGDH):c.418G>A (p.Gly140Arg)Pathogenic
Neu-Laxova syndrome 1|not provided|PHGDH deficiency
β˜…β˜…β˜†β˜†2025β†’ Residue 140
NM_006623.4(PHGDH):c.367C>T (p.Gln123Ter)Pathogenic
PHGDH deficiency
β˜…β˜…β˜†β˜†2025β†’ Residue 123
NM_006623.4(PHGDH):c.22A>T (p.Lys8Ter)Pathogenic
PHGDH deficiency|Autosomal recessive PHGDH-related disorders
β˜…β˜…β˜†β˜†2025β†’ Residue 8
NM_006623.4(PHGDH):c.211C>T (p.Gln71Ter)Pathogenic
PHGDH deficiency
β˜…β˜…β˜†β˜†2025β†’ Residue 71
NM_006623.4(PHGDH):c.403C>T (p.Arg135Trp)Pathogenic
PHGDH deficiency|PHGDH deficiency;Neu-Laxova syndrome 1|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 135
NM_006623.4(PHGDH):c.1153C>T (p.Gln385Ter)Pathogenic
PHGDH deficiency|PHGDH deficiency;Neu-Laxova syndrome 1
β˜…β˜…β˜†β˜†2025β†’ Residue 385
NM_006623.4(PHGDH):c.901del (p.Val301fs)Pathogenic
not provided|PHGDH deficiency|Neu-Laxova syndrome 1
β˜…β˜…β˜†β˜†2025β†’ Residue 301
NM_006623.4(PHGDH):c.139-2A>GLikely pathogenic
PHGDH deficiency
β˜…β˜…β˜†β˜†2024
NM_006623.4(PHGDH):c.399G>A (p.Trp133Ter)Pathogenic
PHGDH deficiency
β˜…β˜…β˜†β˜†2024β†’ Residue 133
View on ClinVar β†—
Related Genes
FOXG1Shared pathway100%VCYShared pathway100%MATCAP1Shared pathway100%VCX3BShared pathway100%FOXR1Shared pathway100%DNAJC30Shared pathway100%
Tissue Expression6 tissues
Liver
100%
Brain
89%
Bone Marrow
42%
Ovary
37%
Heart
10%
Lung
8%
Gene Interaction Network
Click a node to explore
PHGDHFOXG1VCYMATCAP1VCX3BFOXR1DNAJC30
PROTEIN STRUCTURE
Preparing viewer…
PDB5NZO Β· 1.29 Γ… Β· X-ray
View on RCSB β†—
Constraintβ“˜
LOEUFβ“˜
1.16LoF Tolerant
pLIβ“˜
0.00Tolerant
Observed/Expected LoF0.90 [0.70–1.16]
RankingsWhere PHGDH stands among ~20K protein-coding genes
  • #1,019of 20,598
    Most Researched324 Β· top 5%
  • #796of 5,498
    Most Pathogenic Variants97 Β· top quartile
  • #12,043of 17,882
    Most Constrained (LOEUF)1.16
Genes detectedPHGDH
Sources retrieved26 papers
Response timeβ€”
πŸ“„ Sources
26β–Ό
1
PHGDH Inhibits Ferroptosis and Promotes Malignant Progression by Upregulating SLC7A11 in Bladder Cancer.
PMID: 36147463
Int J Biol Sci Β· 2022
1.00
2
PHGDH heterogeneity potentiates cancerΒ cell dissemination and metastasis.
PMID: 35585241
Nature Β· 2022
0.90
3
FBXO7 ubiquitinates PRMT1 to suppress serine synthesis and tumor growth in hepatocellular carcinoma.
PMID: 38839752
Nat Commun Β· 2024
0.80
4
Serine metabolism antagonizes antiviral innate immunity by preventing ATP6V0d2-mediated YAP lysosomal degradation.
PMID: 33798471
Cell Metab Β· 2021
0.76
5
PHGDH-mediated endothelial metabolism drives glioblastoma resistance to chimeric antigen receptor TΒ cell immunotherapy.
PMID: 36804058
Cell Metab Β· 2023
0.70