Free for academic non-profit institutions. Other users need a Commercial license

Aliases for PHGDH Gene

Aliases for PHGDH Gene

  • Phosphoglycerate Dehydrogenase 2 3 5
  • EC 1.1.1.95 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 One carbon pool by folate and Carbon 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
- Elite enhancer/Elite enhancer-gene association

Enhancers around PHGDH on UCSC Golden Path with GeneCards custom track

Genomic Location for PHGDH Gene

Chromosome:
1
Start:
119,659,798 bp from pter
End:
119,744,226 bp from pter
Size:
84,429 bases
Orientation:
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:
    O43175-SERA_HUMAN
    Recommended name:
    D-3-phosphoglycerate dehydrogenase
    Protein Accession:
    O43175
    Secondary Accessions:
    • B2RD08
    • Q5SZU3
    • Q9BQ01

    Protein attributes for PHGDH Gene

    Size:
    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

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:

Domains & Families for PHGDH Gene

Graphical View of Domain Structure for InterPro Entry

O43175

UniProtKB/Swiss-Prot:

SERA_HUMAN :
  • Belongs to the D-isomer specific 2-hydroxyacid dehydrogenase family.
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: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

CRISPR 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

COMPARTMENTS
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

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 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
2-hydroxyglutarate
D-2-Hydroxyglutaric acid
  • (R)-2-hydroxy-Pentanedioate
  • (R)-2-hydroxy-Pentanedioic acid
  • (R)-2-Hydroxyglutarate
  • (R)-2-Hydroxyglutaric acid
  • (R)-a-Hydroxyglutarate
2889-31-8
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
328-50-7
Phosphohydroxypyruvic acid
  • 2-Oxo-3-(phosphonooxy)-Propanoate
  • 2-Oxo-3-(phosphonooxy)-Propanoic acid
  • 3-Phosphohydroxypyruvate
  • 3-Phosphohydroxypyruvic acid
  • 3-Phosphonatooxypyruvate
3913-50-6

(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:

CRISPR Products

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: - - - - - - - - - - - - - - - - - - - - -
SP11:
SP12: - - -
SP13:
SP14:
SP15:

ExUns: 14a · 14b ^ 15 ^ 16a · 16b ^ 17a · 17b · 17c
SP1: - -
SP2: - -
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10: -
SP11: - - - - -
SP12:
SP13: -
SP14:
SP15:

Relevant External Links for PHGDH Gene

GeneLoc Exon Structure for
PHGDH
ECgene alternative splicing isoforms for
PHGDH

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, MaxQB, and MOPED for PHGDH Gene



Protein tissue co-expression partners for PHGDH Gene

NURSA nuclear receptor signaling pathways regulating expression of PHGDH Gene:

PHGDH

SOURCE GeneReport for Unigene cluster for PHGDH Gene:

Hs.487296
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
cow
(Bos Taurus)
Mammalia PHGDH 34
  • 88.12 (n)
  • 89.68 (a)
PHGDH 35
  • 90 (a)
OneToOne
dog
(Canis familiaris)
Mammalia LOC607890 34
  • 89.49 (n)
  • 92.5 (a)
-- 35
  • 92 (a)
OneToMany
-- 35
  • 86 (a)
OneToMany
-- 35
  • 66 (a)
OneToMany
mouse
(Mus musculus)
Mammalia Phgdh 34
  • 88.06 (n)
  • 94.56 (a)
Phgdh 16
Phgdh 35
  • 95 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia PHGDH 34
  • 99.44 (n)
  • 99.44 (a)
PHGDH 35
  • 100 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Phgdh 34
  • 88.24 (n)
  • 94.18 (a)
oppossum
(Monodelphis domestica)
Mammalia PHGDH 35
  • 87 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia PHGDH 35
  • 83 (a)
OneToOne
chicken
(Gallus gallus)
Aves PHGDH 34
  • 68.83 (n)
  • 68.19 (a)
PHGDH 35
  • 68 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia PHGDH 35
  • 68 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia phgdh 34
  • 61.99 (n)
  • 60.98 (a)
Str.20062 34
zebrafish
(Danio rerio)
Actinopterygii phgdh 34
  • 64.88 (n)
  • 61.57 (a)
wufb38f06 34
phgdh 35
  • 61 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta CG6287 36
  • 52 (a)
CG6287 34
  • 57.1 (n)
  • 54.26 (a)
CG6287 35
  • 52 (a)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP008849 34
  • 58.23 (n)
  • 56.25 (a)
worm
(Caenorhabditis elegans)
Secernentea C31C9.2 36
  • 53 (a)
CELE_C31C9.2 34
  • 57.67 (n)
  • 54.29 (a)
C31C9.2 35
  • 53 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SER3 35
  • 27 (a)
ManyToMany
SER33 35
  • 27 (a)
ManyToMany
SER33 37
thale cress
(Arabidopsis thaliana)
eudicotyledons EDA9 34
  • 51.94 (n)
  • 44.44 (a)
rice
(Oryza sativa)
Liliopsida Os04g0650800 34
  • 51.35 (n)
  • 44.7 (a)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.4899 34
sea squirt
(Ciona savignyi)
Ascidiacea CSA.6094 35
  • 61 (a)
OneToOne
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

ENSEMBL:
Gene Tree for PHGDH (if available)
TreeFam:
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
rs121907988 Phosphoglycerate dehydrogenase deficiency (PHGDHD) 119,742,870(+) TGGCC(A/G)TGGCC reference, missense
VAR_059026 Phosphoglycerate dehydrogenase deficiency (PHGDHD)
rs267606947 Phosphoglycerate dehydrogenase deficiency (PHGDHD) 119,735,432(+) TGGAC(A/G)TGTTT reference, missense
VAR_059028 Phosphoglycerate dehydrogenase deficiency (PHGDHD)
rs267606948 Phosphoglycerate dehydrogenase deficiency (PHGDHD) 119,741,817(+) TTGTC(A/G)GCCTC reference, 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)
PHGDH
SNPedia medical, phenotypic, and genealogical associations of SNPs for
PHGDH

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

Disorders for PHGDH Gene

MalaCards: The human disease database

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

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

UniProtKB/Swiss-Prot

SERA_HUMAN
  • 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)
PHGDH
Human Genome Epidemiology (HuGE) Navigator
PHGDH
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
PHGDH
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 65
  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 65
  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 65
  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 65
  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 65

Products for PHGDH Gene

Sources for PHGDH Gene

Content