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Aliases for PHGDH Gene

Aliases for PHGDH Gene

  • Phosphoglycerate Dehydrogenase 2 3 5
  • EC 4 63
  • 3-PGDH 3 4
  • Epididymis Secretory Protein Li 113 3
  • 3-Phosphoglycerate Dehydrogenase 3
  • HEL-S-113 3
  • EC 1.1.1 63
  • 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 Neu-Laxova Syndrome1 and Phosphoglycerate Dehydrogenase Deficiency. Among its related pathways are Glucose / Energy Metabolism and Amino acid synthesis and interconversion (transamination). 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 Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

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

Proteomics data for PHGDH Gene at MOPED

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

ENSEMBL proteins:
REFSEQ proteins:

Antibody Products

  • Cell Signaling Technology (CST) Antibodies for PHGDH (PHGDH)

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

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

No data available for Gene Ontology (GO) - Molecular Function , Transcription Factor Targets and HOMER Transcription for PHGDH Gene

Localization for PHGDH Gene

Subcellular locations from

Jensen Localization Image for PHGDH Gene COMPARTMENTS Subcellular localization image for PHGDH gene
Compartment Confidence
cytosol 5
extracellular 5
nucleus 3
mitochondrion 2
plasma membrane 2
cytoskeleton 1
endoplasmic reticulum 1

No data available for Subcellular locations from UniProtKB/Swiss-Prot and Gene Ontology (GO) - Cellular Components 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:0006563 L-serine metabolic process IEA --
GO:0006566 threonine metabolic process IEA --
GO:0008152 metabolic process IEA --
GO:0009070 serine family amino acid biosynthetic process IBA --
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, HMDB, and Novoseek

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

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

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

Transcripts for PHGDH Gene

Unigene Clusters for PHGDH Gene

Phosphoglycerate dehydrogenase:
Representative Sequences:

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 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, MOPED, and MaxQB for PHGDH Gene

SOURCE GeneReport for Unigene cluster for PHGDH Gene Hs.487296

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

Protein tissue co-expression partners for PHGDH Gene

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
(Bos Taurus)
Mammalia PHGDH 35
  • 88.12 (n)
  • 89.68 (a)
  • 90 (a)
(Canis familiaris)
Mammalia LOC607890 35
  • 89.49 (n)
  • 92.5 (a)
-- 36
  • 92 (a)
-- 36
  • 86 (a)
-- 36
  • 66 (a)
(Mus musculus)
Mammalia Phgdh 35
  • 88.06 (n)
  • 94.56 (a)
Phgdh 16
Phgdh 36
  • 95 (a)
(Pan troglodytes)
Mammalia PHGDH 35
  • 99.44 (n)
  • 99.44 (a)
  • 100 (a)
(Rattus norvegicus)
Mammalia Phgdh 35
  • 88.24 (n)
  • 94.18 (a)
(Monodelphis domestica)
Mammalia PHGDH 36
  • 87 (a)
(Ornithorhynchus anatinus)
Mammalia PHGDH 36
  • 83 (a)
(Gallus gallus)
Aves PHGDH 35
  • 68.83 (n)
  • 68.19 (a)
  • 68 (a)
(Anolis carolinensis)
Reptilia PHGDH 36
  • 68 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia phgdh 35
  • 61.99 (n)
  • 60.98 (a)
Str.20062 35
(Danio rerio)
Actinopterygii phgdh 35
  • 64.88 (n)
  • 61.57 (a)
wufb38f06 35
phgdh 36
  • 61 (a)
fruit fly
(Drosophila melanogaster)
Insecta CG6287 37
  • 52 (a)
CG6287 35
  • 57.1 (n)
  • 54.26 (a)
CG6287 36
  • 52 (a)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP008849 35
  • 58.23 (n)
  • 56.25 (a)
(Caenorhabditis elegans)
Secernentea C31C9.2 37
  • 53 (a)
CELE_C31C9.2 35
  • 57.67 (n)
  • 54.29 (a)
C31C9.2 36
  • 53 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SER3 36
  • 27 (a)
SER33 36
  • 27 (a)
SER33 38
thale cress
(Arabidopsis thaliana)
eudicotyledons EDA9 35
  • 51.94 (n)
  • 44.44 (a)
(Oryza sativa)
Liliopsida Os04g0650800 35
  • 51.35 (n)
  • 44.7 (a)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.4899 35
sea squirt
(Ciona savignyi)
Ascidiacea CSA.6094 36
  • 61 (a)
Species with no ortholog for PHGDH:
  • 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
VAR_013461 Phosphoglycerate dehydrogenase deficiency (PHGDHD)
VAR_059026 Phosphoglycerate dehydrogenase deficiency (PHGDHD)
VAR_059027 Phosphoglycerate dehydrogenase deficiency (PHGDHD)
VAR_059028 Phosphoglycerate dehydrogenase deficiency (PHGDHD)
VAR_059029 Phosphoglycerate dehydrogenase deficiency (PHGDHD)

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

Variant ID Type Subtype PubMed ID
nsv524681 CNV Gain 19592680
nsv831204 CNV Gain+Loss 17160897
nsv831215 CNV Gain 17160897
dgv93e1 CNV Complex 17122850
nsv428201 CNV Gain 18775914
dgv94e1 CNV Complex 17122850

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)

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

Disorders for PHGDH Gene

MalaCards: The human disease database

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

- 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 23 67
  2. 3-Phosphoglycerate dehydrogenase expression is regulated by HOXA10 in murine endometrium and human endometrial cells. (PMID: 19778996) Du H. … Taylor H.S. (Reproduction 2010) 3 23
  3. Role of the anion-binding site in catalysis and regulation of Mycobacterium tuberculosis D-3-phosphoglycerate dehydrogenase. (PMID: 19388702) Burton R.L. … Grant G.A. (Biochemistry 2009) 3 23
  4. [Cloning and expression of 3-phosphoglycerate dehydrogenase gene and its correlative antibodies in diagnosis of autoimmune hepatitis]. (PMID: 19497206) XIANG D.J. … YANG J.X. (Zhonghua Gan Zang Bing Za Zhi 2009) 3 23
  5. Structural analysis of substrate and effector binding in Mycobacterium tuberculosis D-3-phosphoglycerate dehydrogenase. (PMID: 18627175) Dey S. … Sacchettini J.C. (Biochemistry 2008) 3 23

Products for PHGDH Gene

Sources for PHGDH Gene