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Aliases for PHGDH Gene

Aliases for PHGDH Gene

  • Phosphoglycerate Dehydrogenase 2 3
  • EC 1.1.1.95 4 63
  • 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 63
  • PHGDHD 3
  • 3PGDH 3
  • PGDH3 4
  • NLS1 3
  • PGAD 3
  • PGDH 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 Metabolism and Carbon metabolism. GO annotations related to this gene include electron carrier activity and phosphoglycerate dehydrogenase activity. An important paralog of this gene is CTBP2.

Gene Wiki entry for PHGDH Gene

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

Genomics for PHGDH Gene

Regulatory Elements for PHGDH Gene

Genomic Location for PHGDH Gene

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

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
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

Proteomics data for PHGDH Gene at MOPED

Post-translational modifications for PHGDH Gene

  • Ubiquitination at Lys21, Lys33, Lys38, Lys58, Lys146, Lys289, Lys351, Lys364, Lys380, Lys384, and Lys394
  • Modification sites at PhosphoSitePlus

Other Protein References for PHGDH Gene

ENSEMBL proteins:
Reactome Protein details:
REFSEQ proteins:

Domains for PHGDH Gene

Suggested Antigen Peptide Sequences for PHGDH Gene

Graphical View of Domain Structure for InterPro Entry

O43175

UniProtKB/Swiss-Prot:

SERA_HUMAN :
  • O43175
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:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor --
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

Animal Models for PHGDH Gene

MGI Knock Outs for PHGDH:

No data available for Transcription Factor Targeting 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 4
plasma membrane 3
mitochondrion 2
cytoskeleton 1
endoplasmic reticulum 1
extracellular 1
nucleus 1

Gene Ontology (GO) - Cellular Components for PHGDH Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005829 cytosol TAS --
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 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 --
GO:0006564 L-serine biosynthetic process TAS --
GO:0006566 threonine metabolic process IEA --
genes like me logo Genes that share ontologies with PHGDH: view

Compounds for PHGDH Gene

(5) HMDB Compounds for PHGDH Gene

Compound Synonyms Cas Number PubMed IDs
3-Phosphoglyceric acid
  • 3-(dihydrogen phosphate)Glycerate
820-11-1
NAD
  • 3-Carbamoyl-1-D-ribofuranosylpyridinium hydroxide 5'-ester with adenosine 5'-pyrophosphate
53-84-9
NADH
  • 1,4-Dihydronicotinamide adenine dinucleotide
58-68-4
Oxoglutaric acid
  • 2-Ketoglutarate
328-50-7
Phosphohydroxypyruvic acid
  • 2-oxo-3-(phosphonooxy)-Propanoate
3913-50-6

(1) Drugbank Compounds for PHGDH Gene

Compound Synonyms Cas Number Type Actions PubMed IDs
NADH
  • beta-DPNH
606-68-8 target

(8) Novoseek inferred chemical compound relationships for PHGDH Gene

Compound -log(P) Hits PubMed IDs
3-phosphoglycerate 96.6 50
3-phosphohydroxypyruvate 94.7 1
serine 74 42
phosphoserine 56.8 3
5-methyltetrahydrofolate 53.1 1
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: - - - - - - - - - - - - - - - - - - - - -
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

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Integrated Proteomics: protein expression 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 expressions with PHGDH: view

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
chimpanzee
(Pan troglodytes)
Mammalia PHGDH 35
  • 99.44 (n)
  • 99.44 (a)
PHGDH 36
  • 100 (a)
OneToOne
cow
(Bos Taurus)
Mammalia PHGDH 35
  • 88.12 (n)
  • 89.68 (a)
PHGDH 36
  • 90 (a)
OneToOne
dog
(Canis familiaris)
Mammalia -- 36
  • 92 (a)
OneToMany
-- 36
  • 86 (a)
OneToMany
-- 36
  • 66 (a)
OneToMany
LOC607890 35
  • 89.49 (n)
  • 92.5 (a)
mouse
(Mus musculus)
Mammalia Phgdh 35
  • 88.06 (n)
  • 94.56 (a)
Phgdh 16
Phgdh 36
  • 95 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia PHGDH 36
  • 87 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia PHGDH 36
  • 83 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Phgdh 35
  • 88.24 (n)
  • 94.18 (a)
chicken
(Gallus gallus)
Aves PHGDH 35
  • 68.83 (n)
  • 68.19 (a)
PHGDH 36
  • 68 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia PHGDH 36
  • 68 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia phgdh 35
  • 61.99 (n)
  • 60.98 (a)
Str.20062 35
zebrafish
(Danio rerio)
Actinopterygii phgdh 35
  • 64.88 (n)
  • 61.57 (a)
phgdh 36
  • 61 (a)
OneToOne
wufb38f06 35
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP008849 35
  • 58.23 (n)
  • 56.25 (a)
fruit fly
(Drosophila melanogaster)
Insecta CG6287 35
  • 57.1 (n)
  • 54.26 (a)
CG6287 36
  • 52 (a)
OneToOne
CG6287 37
  • 52 (a)
worm
(Caenorhabditis elegans)
Secernentea C31C9.2 36
  • 53 (a)
OneToOne
CELE_C31C9.2 35
  • 57.67 (n)
  • 54.29 (a)
C31C9.2 37
  • 53 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SER3 36
  • 27 (a)
ManyToMany
SER33 36
  • 27 (a)
ManyToMany
SER33 38
thale cress
(Arabidopsis thaliana)
eudicotyledons EDA9 35
  • 51.94 (n)
  • 44.44 (a)
rice
(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)
OneToOne
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

ENSEMBL:
Gene Tree for PHGDH (if available)
TreeFam:
Gene Tree for PHGDH (if available)

Paralogs for PHGDH Gene

Paralogs for PHGDH Gene

Selected SIMAP similar genes for PHGDH Gene using alignment to 3 proteins:

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

Variants for PHGDH Gene

Sequence variations from dbSNP and Humsavar for PHGDH Gene

SNP ID Clin Chr 01 pos Sequence Context AA Info Type MAF
rs10230 -- 119,743,036(+) GCCTA(A/C)CATGA missense, reference
rs14855 -- 119,744,072(+) TGGGG(C/T)TTTTC utr-variant-3-prime
rs477992 -- 119,714,953(+) AATGA(A/G)CCTCA intron-variant
rs478093 -- 119,712,503(+) GCGCA(A/G)TTGTT intron-variant
rs483180 -- 119,724,882(-) GTTTT(C/G)ATGCA intron-variant

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

Relevant External Links for PHGDH Gene

HapMap Linkage Disequilibrium report
PHGDH
Human Gene Mutation Database (HGMD)
PHGDH

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

Disorders for PHGDH Gene

(1) OMIM Diseases for PHGDH Gene (606879)

UniProtKB/Swiss-Prot

SERA_HUMAN
  • Phosphoglycerate dehydrogenase deficiency (PHGDH deficiency) [MIM:601815]: 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.
  • 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.

(3) University of Copenhagen DISEASES for PHGDH Gene

(3) Novoseek inferred disease relationships for PHGDH Gene

Disease -log(P) Hits PubMed IDs
microcephaly 83.8 9
tuberculosis 19.9 10
shock 11.1 4

Relevant External Links for PHGDH

Genetic Association Database (GAD)
PHGDH
Human Genome Epidemiology (HuGE) Navigator
PHGDH
genes like me logo Genes that share disorders with PHGDH: view

Publications for PHGDH Gene

  1. 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 23
  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 23
  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 23
  4. 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
  5. 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

Products for PHGDH Gene

  • Addgene plasmids for PHGDH

Sources for PHGDH Gene

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