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PHGDH phosphoglycerate dehydrogenase [ Homo sapiens (human) ]

Gene ID: 26227, updated on 4-Nov-2018

Summary

Official Symbol
PHGDHprovided by HGNC
Official Full Name
phosphoglycerate dehydrogenaseprovided by HGNC
Primary source
HGNC:HGNC:8923
See related
Ensembl:ENSG00000092621 MIM:606879; Vega:OTTHUMG00000012100
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
NLS; PDG; PGD; NLS1; PGAD; PGDH; SERA; 3PGDH; 3-PGDH; PHGDHD; HEL-S-113
Summary
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]
Expression
Broad expression in fat (RPKM 36.0), skin (RPKM 33.6) and 23 other tissues See more
Orthologs

Genomic context

See PHGDH in Genome Data Viewer
Location:
1p12
Exon count:
16
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 1 NC_000001.11 (119711796..119744226)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (120254419..120286849)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene hydroxy-delta-5-steroid dehydrogenase, 3 beta, pseudogene 5 Neighboring gene zinc finger protein 697 Neighboring gene uncharacterized LOC105378937 Neighboring gene uncharacterized LOC105378936 Neighboring gene 3-hydroxy-3-methylglutaryl-CoA synthase 2 Neighboring gene regenerating family member 4

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Neu-Laxova syndrome 1
MedGen: CN032230 OMIM: 256520 GeneReviews: Not available
Compare labs
Phosphoglycerate dehydrogenase deficiency
MedGen: C1866174 OMIM: 601815 GeneReviews: Not available
Compare labs

NHGRI GWAS Catalog

Description
An atlas of genetic influences on human blood metabolites.
NHGRI GWA Catalog
Genetic variants associated with glycine metabolism and their role in insulin sensitivity and type 2 diabetes.
NHGRI GWA Catalog
Human metabolic individuality in biomedical and pharmaceutical research.
NHGRI GWA Catalog

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp120 env HIV-1 gp120 upregulates the expression of PHGDH in umbilical cord blood mononuclear cells and T-cell lines PubMed

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

  • Amino acid synthesis and interconversion (transamination), organism-specific biosystem (from REACTOME)
    Amino acid synthesis and interconversion (transamination), organism-specific biosystemThese reactions mediate the synthesis of aspartate, asparagine, glutamate, and glutamine from ammonia and intermediates of glycolysis, and allow the utilization of the carbon atoms from these four am...
  • Biosynthesis of amino acids, organism-specific biosystem (from KEGG)
    Biosynthesis of amino acids, organism-specific biosystemThis map presents a modular architecture of the biosynthesis pathways of twenty amino acids, which may be viewed as consisting of the core part and its extensions. The core part is the KEGG module fo...
  • Biosynthesis of amino acids, conserved biosystem (from KEGG)
    Biosynthesis of amino acids, conserved biosystemThis map presents a modular architecture of the biosynthesis pathways of twenty amino acids, which may be viewed as consisting of the core part and its extensions. The core part is the KEGG module fo...
  • Carbon metabolism, organism-specific biosystem (from KEGG)
    Carbon metabolism, organism-specific biosystemCarbon metabolism is the most basic aspect of life. This map presents an overall view of central carbon metabolism, where the number of carbons is shown for each compound denoted by a circle, excludi...
  • Carbon metabolism, conserved biosystem (from KEGG)
    Carbon metabolism, conserved biosystemCarbon metabolism is the most basic aspect of life. This map presents an overall view of central carbon metabolism, where the number of carbons is shown for each compound denoted by a circle, excludi...
  • Glycine, serine and threonine metabolism, organism-specific biosystem (from KEGG)
    Glycine, serine and threonine metabolism, organism-specific biosystemSerine is derived from 3-phospho-D-glycerate, an intermediate of glycolysis [MD:M00020], and glycine is derived from serine. Threonine is an essential amino acid, which animals cannot synthesize. In ...
  • Glycine, serine and threonine metabolism, conserved biosystem (from KEGG)
    Glycine, serine and threonine metabolism, conserved biosystemSerine is derived from 3-phospho-D-glycerate, an intermediate of glycolysis [MD:M00020], and glycine is derived from serine. Threonine is an essential amino acid, which animals cannot synthesize. In ...
  • Metabolic pathways, organism-specific biosystem (from KEGG)
    Metabolic pathways, organism-specific biosystem
    Metabolic pathways
  • Metabolism, organism-specific biosystem (from REACTOME)
    Metabolism, organism-specific biosystemMetabolic processes in human cells generate energy through the oxidation of molecules consumed in the diet and mediate the synthesis of diverse essential molecules not taken in the diet as well as th...
  • Metabolism of amino acids and derivatives, organism-specific biosystem (from REACTOME)
    Metabolism of amino acids and derivatives, organism-specific biosystemThis group of reactions is responsible for: 1) the breakdown of amino acids; 2) the synthesis of urea from ammonia and amino groups generated by amino acid breakdown; 3) the synthesis of the ten amin...
  • Serine biosynthesis, organism-specific biosystem (from REACTOME)
    Serine biosynthesis, organism-specific biosystemL-Serine is needed in human brain in large amounts as precursor to important biomolecules such as nucleotides, phospholipids and the neurotransmitters glycine and D-serine. The pathway for its synthe...
  • Serine biosynthesis, glycerate-3P => serine, organism-specific biosystem (from KEGG)
    Serine biosynthesis, glycerate-3P => serine, organism-specific biosystemPathway module; Nucleotide and amino acid metabolism; Serine and threonine metabolism
  • Serine biosynthesis, glycerate-3P => serine, conserved biosystem (from KEGG)
    Serine biosynthesis, glycerate-3P => serine, conserved biosystemPathway module; Nucleotide and amino acid metabolism; Serine and threonine metabolism
  • Trans-sulfuration and one carbon metabolism, organism-specific biosystem (from WikiPathways)
    Trans-sulfuration and one carbon metabolism, organism-specific biosystem
    Trans-sulfuration and one carbon metabolism

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC3017

Gene Ontology Provided by GOA

Function Evidence Code Pubs
L-malate dehydrogenase activity IEA
Inferred from Electronic Annotation
more info
 
NAD binding IEA
Inferred from Electronic Annotation
more info
 
electron transfer activity TAS
Traceable Author Statement
more info
PubMed 
phosphoglycerate dehydrogenase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
phosphoglycerate dehydrogenase activity TAS
Traceable Author Statement
more info
 
Process Evidence Code Pubs
G1 to G0 transition IEA
Inferred from Electronic Annotation
more info
 
L-serine biosynthetic process TAS
Traceable Author Statement
more info
 
brain development TAS
Traceable Author Statement
more info
PubMed 
electron transport chain IEA
Inferred from Electronic Annotation
more info
 
gamma-aminobutyric acid metabolic process IEA
Inferred from Electronic Annotation
more info
 
glial cell development IEA
Inferred from Electronic Annotation
more info
 
glutamine metabolic process IEA
Inferred from Electronic Annotation
more info
 
glycine metabolic process IEA
Inferred from Electronic Annotation
more info
 
neural tube development IEA
Inferred from Electronic Annotation
more info
 
neuron projection development IEA
Inferred from Electronic Annotation
more info
 
regulation of gene expression IEA
Inferred from Electronic Annotation
more info
 
spinal cord development IEA
Inferred from Electronic Annotation
more info
 
taurine metabolic process IEA
Inferred from Electronic Annotation
more info
 
threonine metabolic process IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
cytosol TAS
Traceable Author Statement
more info
 
extracellular exosome HDA PubMed 
myelin sheath IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
D-3-phosphoglycerate dehydrogenase
Names
2-oxoglutarate reductase
3-phosphoglycerate dehydrogenase
epididymis secretory protein Li 113
malate dehydrogenase
NP_006614.2
XP_011539528.1
XP_011539529.1
XP_011539530.1
XP_011539533.1
XP_024302106.1

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_009188.1 RefSeqGene

    Range
    5001..37431
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_006623.3NP_006614.2  D-3-phosphoglycerate dehydrogenase

    See identical proteins and their annotated locations for NP_006614.2

    Status: REVIEWED

    Source sequence(s)
    AI685723, AL139251, AL589734, BC011262, DA731339
    Consensus CDS
    CCDS904.1
    UniProtKB/Swiss-Prot
    O43175
    Related
    ENSP00000493175.1, OTTHUMP00000013926, ENST00000641023.1, OTTHUMT00000033464
    Conserved Domains (2) summary
    COG0111
    Location:7318
    SerA; Phosphoglycerate dehydrogenase or related dehydrogenase [Coenzyme transport and metabolism, General function prediction only]
    cd12173
    Location:8310
    PGDH_4; Phosphoglycerate dehydrogenases, NAD-binding and catalytic domains

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p12 Primary Assembly

    Range
    119711796..119744226
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011541231.2XP_011539533.1  D-3-phosphoglycerate dehydrogenase isoform X4

    Conserved Domains (1) summary
    cd12173
    Location:10212
    PGDH_4; Phosphoglycerate dehydrogenases, NAD-binding and catalytic domains
  2. XM_011541226.2XP_011539528.1  D-3-phosphoglycerate dehydrogenase isoform X1

    Conserved Domains (2) summary
    COG0111
    Location:7392
    SerA; Phosphoglycerate dehydrogenase or related dehydrogenase [Coenzyme transport and metabolism, General function prediction only]
    cd12173
    Location:8384
    PGDH_4; Phosphoglycerate dehydrogenases, NAD-binding and catalytic domains
  3. XM_011541227.2XP_011539529.1  D-3-phosphoglycerate dehydrogenase isoform X2

    Conserved Domains (1) summary
    cd12173
    Location:20358
    PGDH_4; Phosphoglycerate dehydrogenases, NAD-binding and catalytic domains
  4. XM_011541228.2XP_011539530.1  D-3-phosphoglycerate dehydrogenase isoform X3

    Conserved Domains (1) summary
    cl28378
    Location:7451
    SerA; Phosphoglycerate dehydrogenase or related dehydrogenase [Coenzyme transport and metabolism, General function prediction only]
  5. XM_024446338.1XP_024302106.1  D-3-phosphoglycerate dehydrogenase isoform X3

    Conserved Domains (1) summary
    cl28378
    Location:7451
    SerA; Phosphoglycerate dehydrogenase or related dehydrogenase [Coenzyme transport and metabolism, General function prediction only]
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