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    PHGDH phosphoglycerate dehydrogenase [ Homo sapiens (human) ]

    Gene ID: 26227, updated on 5-May-2024

    Summary

    Official Symbol
    PHGDHprovided by HGNC
    Official Full Name
    phosphoglycerate dehydrogenaseprovided by HGNC
    Primary source
    HGNC:HGNC:8923
    See related
    Ensembl:ENSG00000092621 MIM:606879; AllianceGenome:HGNC:8923
    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See PHGDH in Genome Data Viewer
    Location:
    1p12
    Exon count:
    18
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (119711934..119744215)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (119725174..119757460)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (120254557..120286838)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 8207 Neighboring gene uncharacterized LOC124904390 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1595 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:120218249-120218750 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr1:120221858-120222433 Neighboring gene uncharacterized LOC105378937 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:120230232-120230835 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:120254349-120254878 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1598 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1248 Neighboring gene 3-hydroxy-3-methylglutaryl-CoA synthase 2 Neighboring gene Sharpr-MPRA regulatory region 1341 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:120323715-120323913 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
    Neu-Laxova syndrome 1
    MedGen: C4551478 OMIM: 256520 GeneReviews: Serine Deficiency Disorders
    Compare labs
    PHGDH deficiency
    MedGen: C1866174 OMIM: 601815 GeneReviews: Serine Deficiency Disorders
    Compare labs

    EBI GWAS Catalog

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

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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
     
    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 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_047273636.1
    XP_047273638.1
    XP_047273639.1
    XP_054191923.1
    XP_054191924.1
    XP_054191925.1
    XP_054191926.1
    XP_054191927.1
    XP_054191928.1

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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
      B2RD08, O43175, Q5SZU3, Q9BQ01
      UniProtKB/TrEMBL
      V9HW79
      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: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      119711934..119744215
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011541226.3XP_011539528.1  D-3-phosphoglycerate dehydrogenase isoform X1

      UniProtKB/TrEMBL
      V9HW79
      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
    2. XM_011541227.3XP_011539529.1  D-3-phosphoglycerate dehydrogenase isoform X2

      UniProtKB/TrEMBL
      B3KSC3
      Conserved Domains (1) summary
      cd12173
      Location:20358
      PGDH_4; Phosphoglycerate dehydrogenases, NAD-binding and catalytic domains
    3. XM_047417680.1XP_047273636.1  D-3-phosphoglycerate dehydrogenase isoform X4

    4. XM_047417682.1XP_047273638.1  D-3-phosphoglycerate dehydrogenase isoform X5

    5. XM_011541228.3XP_011539530.1  D-3-phosphoglycerate dehydrogenase isoform X3

      UniProtKB/TrEMBL
      B3KSC3
      Conserved Domains (1) summary
      cl28378
      Location:7451
      SerA; Phosphoglycerate dehydrogenase or related dehydrogenase [Coenzyme transport and metabolism, General function prediction only]
    6. XM_047417683.1XP_047273639.1  D-3-phosphoglycerate dehydrogenase isoform X6

    RNA

    1. XR_007058634.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      119725174..119757460
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054335948.1XP_054191923.1  D-3-phosphoglycerate dehydrogenase isoform X1

    2. XM_054335949.1XP_054191924.1  D-3-phosphoglycerate dehydrogenase isoform X2

    3. XM_054335951.1XP_054191926.1  D-3-phosphoglycerate dehydrogenase isoform X4

    4. XM_054335952.1XP_054191927.1  D-3-phosphoglycerate dehydrogenase isoform X5

    5. XM_054335950.1XP_054191925.1  D-3-phosphoglycerate dehydrogenase isoform X3

    6. XM_054335953.1XP_054191928.1  D-3-phosphoglycerate dehydrogenase isoform X6

    RNA

    1. XR_008485990.1 RNA Sequence

    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.