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PHGDH phosphoglycerate dehydrogenase [ Homo sapiens (human) ]

Gene ID: 26227, updated on 5-Sep-2021

Summary

Official Symbol
PHGDHprovided by HGNC
Official Full Name
phosphoglycerate dehydrogenaseprovided by HGNC
Primary source
HGNC:HGNC:8923
See related
Ensembl:ENSG00000092621 MIM:606879
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
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Genomic context

See PHGDH in Genome Data Viewer
Location:
1p12
Exon count:
16
Annotation release Status Assembly Chr Location
109.20210514 current GRCh38.p13 (GCF_000001405.39) 1 NC_000001.11 (119711934..119744218)
105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (120254557..120286838)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes 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 Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
An atlas of genetic influences on human blood metabolites.
GeneReviews: Not available
Genetic variants associated with glycine metabolism and their role in insulin sensitivity and type 2 diabetes.
GeneReviews: Not available
Human metabolic individuality in biomedical and pharmaceutical research.
GeneReviews: Not available
Neu-Laxova syndrome 1
MedGen: C4551478 OMIM: 256520 GeneReviews: Not available
Compare labs
Phosphoglycerate dehydrogenase deficiency
MedGen: C1866174 OMIM: 601815 GeneReviews: Not available
Compare labs

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 PubChem

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

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)

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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
    5139..37420
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_006623.4NP_006614.2  D-3-phosphoglycerate dehydrogenase

    See identical proteins and their annotated locations for NP_006614.2

    Status: REVIEWED

    Source sequence(s)
    AL589734, BC011262
    Consensus CDS
    CCDS904.1
    UniProtKB/Swiss-Prot
    O43175
    Related
    ENSP00000493175.1, ENST00000641023.2
    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 Updated Annotation Release 109.20210514

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p13 Primary Assembly

    Range
    119711934..119744218
    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]

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_032692.1: Suppressed sequence

    Description
    NM_032692.1: This RefSeq record was removed by NCBI staff. Contact info@ncbi.nlm.nih.gov for further information.
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