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Aliases for PHGDH Gene

Aliases for PHGDH Gene

  • Phosphoglycerate Dehydrogenase 2 3 5
  • EC 4 61
  • 3-PGDH 3 4
  • Epididymis Secretory Protein Li 113 3
  • D-3-Phosphoglycerate Dehydrogenase 3
  • 3-Phosphoglycerate Dehydrogenase 3
  • HEL-S-113 3
  • EC 1.1.1 61
  • PHGDHD 3
  • 3PGDH 3
  • PGDH3 4
  • PGDH 3
  • NLS1 3
  • PGAD 3
  • SERA 3
  • NLS 3
  • PDG 3
  • PGD 3

External Ids for PHGDH Gene

Previous GeneCards Identifiers for PHGDH Gene

  • GC01P120701
  • GC01P119092
  • GC01P119401
  • GC01P119600
  • GC01P119966
  • GC01P120056
  • GC01P120202
  • GC01P118112

Summaries for PHGDH Gene

Entrez Gene Summary for PHGDH Gene

  • 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]

GeneCards Summary for PHGDH Gene

PHGDH (Phosphoglycerate Dehydrogenase) is a Protein Coding gene. Diseases associated with PHGDH include Phosphoglycerate Dehydrogenase Deficiency and Neu-Laxova Syndrome1. Among its related pathways are Glycine, serine and threonine metabolism and Metabolism. GO annotations related to this gene include electron carrier activity and oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor.

Tocris Summary for PHGDH Gene

Gene Wiki entry for PHGDH Gene

No data available for UniProtKB/Swiss-Prot , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PHGDH Gene

Genomics for PHGDH Gene

Regulatory Elements for PHGDH Gene

Enhancers for PHGDH Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH01F119711 1.4 FANTOM5 ENCODE 27.2 +53.3 53312 3.6 PKNOX1 SIN3A FEZF1 DMAP1 ZNF2 PAF1 ZNF263 SP3 SP5 NFYC PHGDH ADAM30 ZNF697 LOC105378937 LOC105378936
GH01F119723 0.9 ENCODE 26.9 +65.3 65254 2.3 ELF3 TBP MLX ARID4B ZSCAN9 RAD21 RARA CREM MIXL1 THAP11 PHGDH ZNF697 HMGCS2 LINC00622 LOC105378936 LOC105378937
GH01F119782 1.1 Ensembl ENCODE 18.1 +125.9 125873 6.9 PKNOX1 RARA YY1 ZNF366 FOS CEBPB REST NR2F2 KAT8 ZNF341 PHGDH REG4 HMGCS2 ADAM30 LOC101929147 WARS2
GH01F119686 0.8 Ensembl ENCODE 18.3 +27.5 27457 1.9 CTBP1 ATF3 CEBPB POU5F1 DPF2 ZNF697 PHGDH LOC105378937
GH01F119630 1.1 Ensembl ENCODE 12 -27.9 -27911 2.8 ELF3 ARID4B SIN3A DMAP1 THRB ZNF48 ZSCAN9 RAD21 RARA SCRT2 PHGDH ZNF697 GC01M119620
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around PHGDH on UCSC Golden Path with GeneCards custom track

Genomic Location for PHGDH Gene

119,659,798 bp from pter
119,744,226 bp from pter
84,429 bases
Plus strand

Genomic View for PHGDH Gene

Genes around PHGDH on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PHGDH Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PHGDH Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PHGDH Gene

Proteins for PHGDH Gene

  • Protein details for PHGDH Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    D-3-phosphoglycerate dehydrogenase
    Protein Accession:
    Secondary Accessions:
    • B2RD08
    • Q5SZU3
    • Q9BQ01

    Protein attributes for PHGDH Gene

    533 amino acids
    Molecular mass:
    56651 Da
    Quaternary structure:
    • Homotetramer.

    Three dimensional structures from OCA and Proteopedia for PHGDH Gene

neXtProt entry for PHGDH Gene

Selected DME Specific Peptides for PHGDH Gene


Post-translational modifications for PHGDH Gene

  • Ubiquitination at Lys 21, Lys 38, Lys 146, Lys 289, Lys 351, Lys 364, Lys 380, and Lys 384
  • Modification sites at PhosphoSitePlus

Other Protein References for PHGDH Gene

Domains & Families for PHGDH Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the D-isomer specific 2-hydroxyacid dehydrogenase family.
  • Belongs to the D-isomer specific 2-hydroxyacid dehydrogenase family.
genes like me logo Genes that share domains with PHGDH: view

No data available for Gene Families for PHGDH Gene

Function for PHGDH Gene

Molecular function for PHGDH Gene

UniProtKB/Swiss-Prot BiophysicochemicalProperties:
Kinetic parameters: KM=21.6 uM for 3-phosphohydroxypyruvate {ECO:0000269 PubMed:19235232}; Vmax=35 nmol/min/mg enzyme with 3-phosphohydroxypyruvate as substrate (in patient-derived fibroblasts) {ECO:0000269 PubMed:19235232}; Vmax=168 nmol/min/mg enzyme with 3-phosphohydroxypyruvate as substrate (in 3-PGDH overexpressed cells) {ECO:0000269 PubMed:19235232};
UniProtKB/Swiss-Prot CatalyticActivity:
3-phospho-D-glycerate + NAD(+) = 3-phosphonooxypyruvate + NADH.
UniProtKB/Swiss-Prot CatalyticActivity:
2-hydroxyglutarate + NAD(+) = 2-oxoglutarate + NADH.
UniProtKB/Swiss-Prot Induction:
Induced by 17-beta-estradiol (estrogenic ligand) and 4-hydroxytamoxifen (agonist/antagonist ligand). Positively regulated by the transcription factors SP1 and NF-Y.

Enzyme Numbers (IUBMB) for PHGDH Gene

Gene Ontology (GO) - Molecular Function for PHGDH Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004617 phosphoglycerate dehydrogenase activity TAS --
GO:0009055 electron carrier activity TAS 8758134
GO:0016491 oxidoreductase activity IEA --
GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor IEA --
GO:0051287 NAD binding IEA --
genes like me logo Genes that share ontologies with PHGDH: view
genes like me logo Genes that share phenotypes with PHGDH: view

Human Phenotype Ontology for PHGDH Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for PHGDH Gene

MGI Knock Outs for PHGDH:

Animal Model Products

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for PHGDH

Flow Cytometry Products

No data available for Transcription Factor Targets and HOMER Transcription for PHGDH Gene

Localization for PHGDH Gene

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for PHGDH gene
Compartment Confidence
extracellular 5
cytosol 5
nucleus 4
plasma membrane 3
mitochondrion 2
cytoskeleton 1
endoplasmic reticulum 1

Gene Ontology (GO) - Cellular Components for PHGDH Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005829 cytosol TAS --
GO:0043209 myelin sheath IEA --
GO:0070062 extracellular exosome IDA 19056867
genes like me logo Genes that share ontologies with PHGDH: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for PHGDH Gene

Pathways & Interactions for PHGDH Gene

genes like me logo Genes that share pathways with PHGDH: view

UniProtKB/Swiss-Prot O43175-SERA_HUMAN

  • Pathway: Amino-acid biosynthesis; L-serine biosynthesis; L-serine from 3-phospho-D-glycerate: step 1/3.

Gene Ontology (GO) - Biological Process for PHGDH Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006541 glutamine metabolic process IEA --
GO:0006544 glycine metabolic process IEA --
GO:0006563 L-serine metabolic process IEA --
GO:0006564 L-serine biosynthetic process IEA,TAS --
GO:0006566 threonine metabolic process IEA --
genes like me logo Genes that share ontologies with PHGDH: view

No data available for SIGNOR curated interactions for PHGDH Gene

Drugs & Compounds for PHGDH Gene

(5) Drugs for PHGDH Gene - From: DrugBank, ApexBio, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
3-Phosphoglyceric acid Experimental Pharma 0
NADH Nutra Target 0
CBR-5884 Pharma selective inhibitor of PHGDH 0
NAD Pharma Full agonist, Agonist 0

(11) Additional Compounds for PHGDH Gene - From: HMDB and Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
D-2-Hydroxyglutaric acid
  • (R)-2-hydroxy-Pentanedioate
  • (R)-2-hydroxy-Pentanedioic acid
  • (R)-2-Hydroxyglutarate
  • (R)-2-Hydroxyglutaric acid
  • (R)-a-Hydroxyglutarate
Hydrogen Ion
  • Hydrogen cation
  • Hydron
  • Proton
Oxoglutaric acid
  • 2-Ketoglutarate
  • 2-Ketoglutaric acid
  • 2-Oxo-1,5-pentanedioate
  • 2-Oxo-1,5-pentanedioic acid
  • 2-Oxoglutarate
Phosphohydroxypyruvic acid
  • 2-Oxo-3-(phosphonooxy)-Propanoate
  • 2-Oxo-3-(phosphonooxy)-Propanoic acid
  • 3-Phosphohydroxypyruvate
  • 3-Phosphohydroxypyruvic acid
  • 3-Phosphonatooxypyruvate

(1) ApexBio Compounds for PHGDH Gene

Compound Action Cas Number
CBR-5884 selective inhibitor of PHGDH
genes like me logo Genes that share compounds with PHGDH: view

Transcripts for PHGDH Gene

Unigene Clusters for PHGDH Gene

Phosphoglycerate dehydrogenase:
Representative Sequences:

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for PHGDH

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for PHGDH Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3a · 3b ^ 4a · 4b · 4c ^ 5a · 5b ^ 6 ^ 7 ^ 8a · 8b ^ 9a · 9b · 9c ^ 10 ^ 11a · 11b · 11c ^ 12a · 12b ^ 13a · 13b ^
SP1: - - - - - - -
SP2: - - - - -
SP3: - - - - - - - -
SP4: - - - - - - - - -
SP5: - - - - - -
SP6: - - - - - - - - -
SP7: - - - -
SP8: - -
SP9: - - - -
SP10: - - - - - - - - - - - - - - - - - - - - -
SP12: - - -

ExUns: 14a · 14b ^ 15 ^ 16a · 16b ^ 17a · 17b · 17c
SP1: - -
SP2: - -
SP10: -
SP11: - - - - -
SP13: -

Relevant External Links for PHGDH Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for PHGDH Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for PHGDH Gene

Protein differential expression in normal tissues from HIPED for PHGDH Gene

This gene is overexpressed in Bone (14.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for PHGDH Gene

Protein tissue co-expression partners for PHGDH Gene

NURSA nuclear receptor signaling pathways regulating expression of PHGDH Gene:


SOURCE GeneReport for Unigene cluster for PHGDH Gene:

genes like me logo Genes that share expression patterns with PHGDH: view

Primer Products

No data available for mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for PHGDH Gene

Orthologs for PHGDH Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for PHGDH Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia PHGDH 34 35
  • 99.44 (n)
(Canis familiaris)
Mammalia -- 35
  • 92 (a)
LOC607890 34
  • 89.49 (n)
-- 35
  • 86 (a)
-- 35
  • 66 (a)
(Rattus norvegicus)
Mammalia Phgdh 34
  • 88.24 (n)
(Bos Taurus)
Mammalia PHGDH 34 35
  • 88.12 (n)
(Mus musculus)
Mammalia Phgdh 34 16 35
  • 88.06 (n)
(Monodelphis domestica)
Mammalia PHGDH 35
  • 87 (a)
(Ornithorhynchus anatinus)
Mammalia PHGDH 35
  • 83 (a)
(Gallus gallus)
Aves PHGDH 34 35
  • 68.83 (n)
(Anolis carolinensis)
Reptilia PHGDH 35
  • 68 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia phgdh 34
  • 61.99 (n)
Str.20062 34
(Danio rerio)
Actinopterygii phgdh 34 35
  • 64.88 (n)
wufb38f06 34
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP008849 34
  • 58.23 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG6287 36 34 35
  • 57.1 (n)
(Caenorhabditis elegans)
Secernentea CELE_C31C9.2 34
  • 57.67 (n)
C31C9.2 36 35
  • 53 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SER3 35
  • 27 (a)
SER33 35 37
  • 27 (a)
thale cress
(Arabidopsis thaliana)
eudicotyledons EDA9 34
  • 51.94 (n)
(Oryza sativa)
Liliopsida Os04g0650800 34
  • 51.35 (n)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.6094 35
  • 61 (a)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.4899 34
Species where no ortholog for PHGDH was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for PHGDH Gene

Gene Tree for PHGDH (if available)
Gene Tree for PHGDH (if available)

Paralogs for PHGDH Gene

(2) SIMAP similar genes for PHGDH Gene using alignment to 3 proteins:

genes like me logo Genes that share paralogs with PHGDH: view

No data available for Paralogs for PHGDH Gene

Variants for PHGDH Gene

Sequence variations from dbSNP and Humsavar for PHGDH Gene

SNP ID Clin Chr 01 pos Sequence Context AA Info Type
rs121907987 Phosphoglycerate dehydrogenase deficiency (PHGDHD) [MIM:601815], Pathogenic 119,743,906(+) CAGGC(A/G)TGCGG reference, missense
rs121907988 Phosphoglycerate dehydrogenase deficiency (PHGDHD) [MIM:601815], Pathogenic 119,742,870(+) TGGCC(A/G)TGGCC reference, missense
rs267606947 Phosphoglycerate dehydrogenase deficiency (PHGDHD) [MIM:601815], Pathogenic 119,735,432(+) TGGAC(A/G)TGTTT reference, missense
rs267606948 Phosphoglycerate dehydrogenase deficiency (PHGDHD) [MIM:601815], Pathogenic 119,741,817(+) TTGTC(A/G)GCCTC reference, missense
rs267606949 Phosphoglycerate dehydrogenase deficiency (PHGDHD) [MIM:601815], Pathogenic 119,726,897(+) GGGAG(A/C/G/T)GGAAG upstream-variant-2KB, reference, synonymous-codon, missense

Structural Variations from Database of Genomic Variants (DGV) for PHGDH Gene

Variant ID Type Subtype PubMed ID
nsv428201 CNV gain 18775914
nsv524681 CNV gain 19592680
nsv831204 CNV gain+loss 17160897
nsv831215 CNV gain 17160897

Variation tolerance for PHGDH Gene

Residual Variation Intolerance Score: 17.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.98; 36.63% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for PHGDH Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PHGDH Gene

Disorders for PHGDH Gene

MalaCards: The human disease database

(10) MalaCards diseases for PHGDH Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
phosphoglycerate dehydrogenase deficiency
  • phgdh deficiency
neu-laxova syndrome1
  • neu-laxova syndrome 1
serine deficiency
phosphoserine phosphatase deficiency
  • psph deficiency
cerebral folate deficiency
  • neurodegeneration due to cerebral folate transport deficiency
- elite association - COSMIC cancer census association via MalaCards
Search PHGDH in MalaCards View complete list of genes associated with diseases


  • Neu-Laxova syndrome 1 (NLS1) [MIM:256520]: A lethal, autosomal recessive multiple malformation syndrome characterized by ichthyosis, marked intrauterine growth restriction, microcephaly, short neck, limb deformities, hypoplastic lungs, edema, and central nervous system anomalies including lissencephaly, cerebellar hypoplasia and/or abnormal/agenesis of the corpus callosum. Abnormal facial features include severe proptosis with ectropion, hypertelorism, micrognathia, flattened nose, and malformed ears. {ECO:0000269 PubMed:24836451}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Phosphoglycerate dehydrogenase deficiency (PHGDHD) [MIM:601815]: An autosomal recessive inborn error of L-serine biosynthesis, clinically characterized by congenital microcephaly, psychomotor retardation, and seizures. {ECO:0000269 PubMed:11055895, ECO:0000269 PubMed:19235232}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for PHGDH

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
genes like me logo Genes that share disorders with PHGDH: view

No data available for Genatlas for PHGDH Gene

Publications for PHGDH Gene

  1. Novel mutations in 3-phosphoglycerate dehydrogenase (PHGDH) are distributed throughout the protein and result in altered enzyme kinetics. (PMID: 19235232) Tabatabaie L. … Klomp L.W.J. (Hum. Mutat. 2009) 3 4 22 64
  2. V490M, a common mutation in 3-phosphoglycerate dehydrogenase deficiency, causes enzyme deficiency by decreasing the yield of mature enzyme. (PMID: 11751922) Pind S. … Natowicz M.R. (J. Biol. Chem. 2002) 3 4 22 64
  3. Nucleotide sequence and differential expression of the human 3- phosphoglycerate dehydrogenase gene. (PMID: 10713460) Cho H.M. … Kim Y.H. (Gene 2000) 3 4 22 64
  4. Molecular characterization of 3-phosphoglycerate dehydrogenase deficiency -- a neurometabolic disorder associated with reduced L- serine biosynthesis. (PMID: 11055895) Klomp L.W.J. … Berger R. (Am. J. Hum. Genet. 2000) 3 4 22 64
  5. Neu-Laxova syndrome, an inborn error of serine metabolism, is caused by mutations in PHGDH. (PMID: 24836451) Shaheen R. … Alkuraya F.S. (Am. J. Hum. Genet. 2014) 3 4 64

Products for PHGDH Gene

Sources for PHGDH Gene

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