Phgdh 3-phosphoglycerate dehydrogenase [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Phgdhprovided by MGI
Official Full Name: 3-phosphoglycerate dehydrogenaseprovided by MGI
Primary source: MGI:MGI:1355330
See related: Ensembl:ENSMUSG00000053398 AllianceGenome:MGI:1355330
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: A10; PGD; PGAD; PGDH; SERA; 3PGDH; 3-PGDH; 4930479N23
Summary: Predicted to enable phosphoglycerate dehydrogenase activity. Acts upstream of or within several processes, including G1 to G0 transition; cellular amino acid metabolic process; and nervous system development. Located in myelin sheath. Is expressed in several structures, including alimentary system; brain; genitourinary system; integumental system; and sensory organ. Human ortholog(s) of this gene implicated in Neu-Laxova syndrome 1; PHGDH deficiency; and amino acid metabolic disorder. Orthologous to human PHGDH (phosphoglycerate dehydrogenase). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Broad expression in placenta adult (RPKM 138.0), genital fat pad adult (RPKM 127.9) and 25 other tissues See more
Orthologs: human all
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Genomic context

Location:: 3 F2.2; 3 42.74 cM

Exon count:: 12

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	3	NC_000069.7 (98220487..98247285, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	3	NC_000069.6 (98313171..98339969, complement)

Chromosome 3 - NC_000069.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Yap/Taz activity is associated with increased expression of phosphoglycerate dehydrogenase that supports myoblast proliferation.
Title: Yap/Taz activity is associated with increased expression of phosphoglycerate dehydrogenase that supports myoblast proliferation.
Low glucose metabolite 3-phosphoglycerate switches PHGDH from serine synthesis to p53 activation to control cell fate.
Title: Low glucose metabolite 3-phosphoglycerate switches PHGDH from serine synthesis to p53 activation to control cell fate.
ZEB1 Transcriptionally Activates PHGDH to Facilitate Carcinogenesis and Progression of HCC.
Title: ZEB1 Transcriptionally Activates PHGDH to Facilitate Carcinogenesis and Progression of HCC.
Phosphoglycerate dehydrogenase activates PKM2 to phosphorylate histone H3T11 and attenuate cellular senescence.
Title: Phosphoglycerate dehydrogenase activates PKM2 to phosphorylate histone H3T11 and attenuate cellular senescence.
Chemical Components of the Fruits of Morus nigra Linn.: Methyl Caffeate as a Potential Anticancer Agent by Targeting 3-Phosphoglycerate Dehydrogenase.
Title: Chemical Components of the Fruits of Morus nigra Linn.: Methyl Caffeate as a Potential Anticancer Agent by Targeting 3-Phosphoglycerate Dehydrogenase.
Inverse Data-Driven Modeling and Multiomics Analysis Reveals Phgdh as a Metabolic Checkpoint of Macrophage Polarization and Proliferation.
Title: Inverse Data-Driven Modeling and Multiomics Analysis Reveals Phgdh as a Metabolic Checkpoint of Macrophage Polarization and Proliferation.
Reduced Phgdh expression and serine levels are closely associated with the development of Fatty Liver Disease.
Title: Downregulation of PHGDH expression and hepatic serine level contribute to the development of fatty liver disease.
PHGDH-mediated serine biosynthesis has important roles in adipose tissue glucose metabolism and could be a therapeutic target for diabetes in humans
Title: Deletion of PHGDH in adipocytes improves glucose intolerance in diet-induced obese mice.
These results indicate that the PHGDH gene expression, dictated by IL-2R signaling, is a crucial event for DNA synthesis during S phase of activated T cells.
Title: Requirement of the expression of 3-phosphoglycerate dehydrogenase for traversing S phase in murine T lymphocytes following immobilized anti-CD3 activation.
Using transgenic mice expressing enhanced GFP under the Srr promoter and mice with targeted deletion of Srr or 3-Phosphoglycerate dehydrogenase, we demonstrate predominantly neuronal sources of d-serine dependent on astrocytic supply of l-serine.
Title: D-serine in glia and neurons derives from 3-phosphoglycerate dehydrogenase.

Submit: New GeneRIF Correction See all GeneRIFs (22)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (4)
Targeted (3) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Phgdh (e-PCR), detects polymorphism
- UniSTS:546936

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables NAD binding	IEA Inferred from Electronic Annotation more info
enables oxidoreductase activity	IEA Inferred from Electronic Annotation more info
enables oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor	IEA Inferred from Electronic Annotation more info
enables phosphoglycerate dehydrogenase activity	IBA Inferred from Biological aspect of Ancestor more info
enables phosphoglycerate dehydrogenase activity	ISO Inferred from Sequence Orthology more info
enables phosphoglycerate dehydrogenase activity	TAS Traceable Author Statement more info	PubMed

Process	Evidence Code	Pubs
acts_upstream_of_or_within G1 to G0 transition	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within L-serine biosynthetic process	IEA Inferred from Electronic Annotation more info
involved_in L-serine biosynthetic process	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within L-serine metabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within amino acid biosynthetic process	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within gamma-aminobutyric acid metabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within glial cell development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within glutamine metabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within glycine metabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within neural tube development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within neurogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within neuron projection development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of gene expression	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within spinal cord development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within taurine metabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within threonine metabolic process	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in myelin sheath	HDA more info	PubMed

General protein information

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Preferred Names: D-3-phosphoglycerate dehydrogenase

Names: 3-phosphoglycerate dehyrogenase

NP_058662.2

EC 1.1.1.95

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.

mRNA and Protein(s)

NM_016966.3 → NP_058662.2 D-3-phosphoglycerate dehydrogenase

See identical proteins and their annotated locations for NP_058662.2

Status: VALIDATED

Source sequence(s)

AK076815, AW545294, BY290664

Consensus CDS

CCDS17663.1

UniProtKB/Swiss-Prot

Q3TEE5, Q61753, Q75SV9, Q8C603

Related

ENSMUSP00000064755.6, ENSMUST00000065793.12

Conserved Domains (2) summary

PRK13581
Location:8 → 490

PRK13581; D-3-phosphoglycerate dehydrogenase; Provisional

cd12173
Location:8 → 310

PGDH_4; Phosphoglycerate dehydrogenases, NAD-binding and catalytic domains