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Phgdh Gene Detail
Summary
  • Symbol
    Phgdh
  • Name
    3-phosphoglycerate dehydrogenase
  • Synonyms
    3-PGDH, 3PGDH, A10, PGAD, PGD, PGDH, SERA
  • Feature Type
    protein coding gene
  • IDs
    MGI:1355330
    NCBI Gene: 236539
  • Alliance
    genome feature page
  • Transcription Start Sites
    4 TSS
Location &
Maps
more
  • Sequence Map
    Chr3:98220487-98247285 bp, - strand
    From NCBI annotation of GRCm39
  • View this region in JBrowse
  • Genome Browsers
    Ensembl | UCSC | NCBI
  • Genetic Map
    Chromosome 3, 42.74 cM, cytoband E1
  • Mapping Data
    2 experiments
Strain
Comparison
more
  • SNPs within 2kb
    1027 from dbSNP Build 142
  • Strain Annotations
    19
For selected strains:
Strain Gene Model ID Feature Type Coordinates Select Strains
C57BL/6J MGI_C57BL6J_1355330
 protein coding gene Chr3:98220486-98247306 (-)
129S1/SvImJ ENSMUSG00200043752
 protein coding gene Chr3:94852084-94878898 (-)
A/J ENSMUSG00195040652
 protein coding gene Chr3:95250920-95277741 (-)
AKR/J ENSMUSG00220038277
 protein coding gene Chr3:93603021-93629844 (-)
BALB/cJ ENSMUSG00180033285
 protein coding gene Chr3:95193400-95219693 (-)
C3H/HeJ ENSMUSG00175022185
 protein coding gene Chr3:94809211-94836029 (-)
C57BL/6NJ ENSMUSG00215033338
 protein coding gene Chr3:95579217-95606042 (-)
CAROLI/EiJ MGP_CAROLIEiJ_G0025411
 protein coding gene Chr3:92361329-92387777 (-)
CAST/EiJ ENSTCUG00005017998
 protein coding gene Chr3:95509624-95536535 (-)
CBA/J ENSMUSG00210050670
 protein coding gene Chr3:95362179-95389000 (-)
DBA/2J ENSMUSG00185041380
 protein coding gene Chr3:95815389-95841679 (-)
FVB/NJ ENSMUSG00205020665
 protein coding gene Chr3:94478342-94505153 (-)
JF1/MsJ ENSUMUG00000037521
 protein coding gene Chr3:94723158-94749708 (-)
LP/J ENSMUSG00230040384
 protein coding gene Chr3:97780620-97807432 (-)
NOD/ShiLtJ ENSMUSG00190046422
 protein coding gene Chr3:95990644-96016978 (-)
NZO/HlLtJ ENSMUSG00225008885
 protein coding gene Chr3:100248766-100275475 (-)
PWK/PhJ ENSLUMG00010025394
 protein coding gene Chr3:94720627-94747116 (-)
SPRET/EiJ ENSMSPG00010036705
 protein coding gene Chr3:95000614-95026749 (-)
WSB/EiJ ENSIUOG00005025607
 protein coding gene Chr3:95384068-95410973 (-)



Homology
more
  • Human Ortholog
    PHGDH, phosphoglycerate dehydrogenase
  • Vertebrate Orthologs
    3
Vertebrate Orthology Source
Alliance of Genome Resources
  • Human Ortholog
    PHGDH, phosphoglycerate dehydrogenase
  • Synonyms
    3-PGDH, 3PGDH, HEL-S-113, NLS, NLS1, PDG, PGAD, PGD, PGDH, PHGDHD, SERA
  • Links
    NCBI Gene ID: 26227
    UniProt: O43175

  • Chr Location
    1p12; chr1:119648411-119744227 (+)  GRCh38
Human Diseases
more
  • Diseases
    3 with human PHGDH associations

Human Disease Mouse Models
      
IDs
IDs
IDs
Click on a disease name to see all genes associated with that disease.

  • References
    1 with disease annotations
Mutations,
Alleles, and
Phenotypes
less
  • Phenotype Summary
    48 phenotypes from 3 alleles in 3 genetic backgrounds
    1 phenotype from multigenic genotypes
    2 images
    33 phenotype references
Phenotype Overview

adipose tissue
behavior/neurological
cardiovascular system
cellular
craniofacial
digestive/alimentary system
embryo
endocrine/exocrine glands
growth/size/body
hearing/vestibular/ear
hematopoietic system
homeostasis/metabolism
integument
immune system
limbs/digits/tail
liver/biliary system
mortality/aging
muscle
nervous system
pigmentation
renal/urinary system
reproductive system
respiratory system
skeleton
taste/olfaction
neoplasm
vision/eye

Click cells to view annotations.
Mice homozygous for a null allele die by E13.5 and exhibit abnormal neural development.
Gene Ontology
(GO)
Classifications
less
  • All GO Annotations
    35
  • GO References
    15
Molecular Function

carbohydrate derivative binding
cytoskeletal protein binding
DNA binding
enzyme regulator
hydrolase
ligase
lipid binding
oxidoreductase
RNA binding
signaling receptor activity
signaling receptor binding
transcription
transferase
transporter
Biological Process

carbohydrate derivative metabolism
cell differentiation
cell population proliferation
cellular component organization
DNA-templated transcription
establishment of localization
homeostatic process
immune system process
lipid metabolic process
programmed cell death
protein metabolic process
response to stimulus
signaling
system development
Cellular Component

cell projection
cytoplasmic vesicle
cytoskeleton
cytosol
endoplasmic reticulum
endosome
extracellular region
Golgi apparatus
mitochondrion
membraneless organelle
nucleus
organelle envelope
organelle lumen
plasma membrane
protein-containing complex
synapse
vacuole
Click cells to view annotations.
Expression
less
Expression Overview

early conceptus
embryo ectoderm
embryo endoderm
embryo mesoderm
embryo mesenchyme
extraembryonic component
alimentary system
auditory system
branchial arches
cardiovascular system
connective tissue
endocrine system
exocrine system
hemolymphoid system
integumental system
limbs
liver and biliary system
musculoskeletal system
nervous system
olfactory system
reproductive system
respiratory system
urinary system
visual system
Click cells to view annotations.


  • Assay Results
    728
  • Tissues
    118
  • cDNA Data
    9
  • Literature Summary
    15
  • Comparison Matrix
    Gene Expression + Phenotype
    • Sequences &
    Gene Models
    less
    Representative SequencesLengthStrain/SpeciesFlank
    genomic 236539 NCBI Gene Model | MGI Sequence Detail 26799 C57BL/6J ±  kb
    transcript NM_016966 RefSeq | MGI Sequence Detail 1871 C57BL/6  
    polypeptide Q61753 UniProt | EBI | MGI Sequence Detail 533 Not Applicable  
    For the selected sequence
    Protein
    Information
    less
    • UniProt
      2 Sequences
    • Protein Ontology
      PR:000012656 D-3-phosphoglycerate dehydrogenase
      (term hierarchy)
    • EC
      1.1.1.95
    • InterPro Domains
      IPR029009 Allosteric substrate binding domain superfamily
      IPR006236 D-3-phosphoglycerate dehydrogenase
      IPR045626 D-3-phosphoglycerate dehydrogenase, ASB domain
      IPR006139 D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain
      IPR006140 D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain
      IPR029753 D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site
      IPR029752 D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1
      IPR036291 NAD(P)-binding domain superfamily
    • GlyGen
      Q61753 1 site, 1 O-linked glycan (1 site)
    Molecular
    Reagents
    less
    • All nucleic 14
      cDNA 11
      Primer pair 3
      Antibodies 3

      Microarray probesets 5
    References
    more
    • Summaries
      All 93
      Developmental Gene Expression 15
      Diseases 1
      Gene Ontology 15
      Phenotypes 33
    • Earliest
      J:382894 Bridgers WF, The biosynthesis of serine in mouse brain extracts. J Biol Chem. 1965 Dec;240(12):4591-7
    • Latest
      J:375868 Hu P, et al., Macrophage-specific PHGDH protects against MAFLD by suppressing TAK1. Cell Rep. 2025 Mar 25;44(3):115426
    Contributing Projects:
    Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB)), Gene Ontology (GO)
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    Funding Information
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    Send questions and comments to User Support.     		last database update
    09/08/2026
    MGI 6.24     		The Jackson Laboratory