PHGDH phosphoglycerate dehydrogenase [Homo sapiens (human)] - Gene

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: mouse all
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Genomic context

Location:: 1p12

Exon count:: 18

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (119711934..119744215)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (119725174..119757460)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (120254557..120286838)

Chromosome 1 - NC_000001.11 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: HPA RNA-seq normal tissues 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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

On the quaternary structure of human D-3-phosphoglycerate dehydrogenase.
Title: On the quaternary structure of human D-3-phosphoglycerate dehydrogenase.
CircPHGDH downregulation decreases papillary thyroid cancer progression through miR-122-5p/PKM2 axis.
Title: CircPHGDH downregulation decreases papillary thyroid cancer progression through miR-122-5p/PKM2 axis.
KDM4B down-regulation facilitated breast cancer cell stemness via PHGDH upregulation in H3K36me3-dependent manner.
Title: KDM4B down-regulation facilitated breast cancer cell stemness via PHGDH upregulation in H3K36me3-dependent manner.
PRMT1 Sustains De Novo Fatty Acid Synthesis by Methylating PHGDH to Drive Chemoresistance in Triple-Negative Breast Cancer.
Title: PRMT1 Sustains De Novo Fatty Acid Synthesis by Methylating PHGDH to Drive Chemoresistance in Triple-Negative Breast Cancer.
Biochemical and cellular studies of three human 3-phosphoglycerate dehydrogenase variants responsible for pathological reduced L-serine levels.
Title: Biochemical and cellular studies of three human 3-phosphoglycerate dehydrogenase variants responsible for pathological reduced L-serine levels.
Serine synthesis pathway enzyme PHGDH is critical for muscle cell biomass, anabolic metabolism, and mTORC1 signaling.
Title: Serine synthesis pathway enzyme PHGDH is critical for muscle cell biomass, anabolic metabolism, and mTORC1 signaling.
PHGDH preserves one-carbon cycle to confer metabolic plasticity in chemoresistant gastric cancer during nutrient stress.
Title: PHGDH preserves one-carbon cycle to confer metabolic plasticity in chemoresistant gastric cancer during nutrient stress.
The Role of ESRP1 in the Regulation of PHGDH in Estrogen Receptor-Positive Breast Cancer.
Title: The Role of ESRP1 in the Regulation of PHGDH in Estrogen Receptor-Positive Breast Cancer.
PHGDH arginine methylation by PRMT1 promotes serine synthesis and represents a therapeutic vulnerability in hepatocellular carcinoma.
Title: PHGDH arginine methylation by PRMT1 promotes serine synthesis and represents a therapeutic vulnerability in hepatocellular carcinoma.
Comprehensive analysis of PHGDH for predicting prognosis and immunotherapy response in patients with endometrial carcinoma.
Title: Comprehensive analysis of PHGDH for predicting prognosis and immunotherapy response in patients with endometrial carcinoma.

Submit: New GeneRIF Correction See all GeneRIFs (60)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

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 EBI GWAS CatalogPubMed
Genetic variants associated with glycine metabolism and their role in insulin sensitivity and type 2 diabetes. EBI GWAS Catalog EBI GWAS CatalogPubMed
Human metabolic individuality in biomedical and pharmaceutical research. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

T16008 (e-PCR)
- UniSTS:55098

WI-15319 (e-PCR)
- UniSTS:53313

SHGC-83467 (e-PCR)
- UniSTS:101955

D1S514 (e-PCR), detects polymorphism
- UniSTS:29045

SHGC-83620 (e-PCR)
- UniSTS:95899

IB441 (e-PCR)
- UniSTS:58551

A002P44 (e-PCR)
- UniSTS:63475

D1S514 (e-PCR), detects polymorphism
- UniSTS:6140

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables L-malate dehydrogenase (NAD+) 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
enables protein binding	IPI Inferred from Physical Interaction 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 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 more info	PubMed

General protein information

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Preferred Names: D-3-phosphoglycerate dehydrogenase

Names: 2-oxoglutarate reductase; 3-phosphoglycerate dehydrogenase; epididymis secretory protein Li 113; malate dehydrogenase

NP_006614.2

EC 1.1.1.37

EC 1.1.1.399

EC 1.1.1.95

XP_011539528.1

EC 1.1.1.37

EC 1.1.1.399

EC 1.1.1.95

XP_011539529.1

EC 1.1.1.37

EC 1.1.1.399

EC 1.1.1.95

XP_011539530.1

EC 1.1.1.37

EC 1.1.1.399

EC 1.1.1.95

XP_047273636.1

EC 1.1.1.37

EC 1.1.1.399

EC 1.1.1.95

XP_047273638.1

EC 1.1.1.37

EC 1.1.1.399

EC 1.1.1.95

XP_047273639.1

EC 1.1.1.37

EC 1.1.1.399

EC 1.1.1.95

XP_054191923.1

EC 1.1.1.37

EC 1.1.1.399

EC 1.1.1.95

XP_054191924.1

EC 1.1.1.37

EC 1.1.1.399

EC 1.1.1.95

XP_054191925.1

EC 1.1.1.37

EC 1.1.1.399

EC 1.1.1.95

XP_054191926.1

EC 1.1.1.37

EC 1.1.1.399

EC 1.1.1.95

XP_054191927.1

EC 1.1.1.37

EC 1.1.1.399

EC 1.1.1.95

XP_054191928.1

EC 1.1.1.37

EC 1.1.1.399

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.

Genomic

NG_009188.1 RefSeqGene

Range

5139..37420

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_006623.4 → NP_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:7 → 318

SerA; Phosphoglycerate dehydrogenase or related dehydrogenase [Coenzyme transport and metabolism, General function prediction only]

cd12173
Location:8 → 310

PGDH_4; Phosphoglycerate dehydrogenases, NAD-binding and catalytic domains

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000001.11 Reference GRCh38.p14 Primary Assembly

Range

119711934..119744215

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/TrEMBL

V9HW79

Conserved Domains (2) summary

COG0111
Location:7 → 392

SerA; Phosphoglycerate dehydrogenase or related dehydrogenase [Coenzyme transport and metabolism, General function prediction only]

cd12173
Location:8 → 384

PGDH_4; Phosphoglycerate dehydrogenases, NAD-binding and catalytic domains
XM_011541227.3 → XP_011539529.1 D-3-phosphoglycerate dehydrogenase isoform X2

UniProtKB/TrEMBL

B3KSC3

Conserved Domains (1) summary

cd12173
Location:20 → 358

PGDH_4; Phosphoglycerate dehydrogenases, NAD-binding and catalytic domains
XM_047417680.1 → XP_047273636.1 D-3-phosphoglycerate dehydrogenase isoform X4
XM_047417682.1 → XP_047273638.1 D-3-phosphoglycerate dehydrogenase isoform X5
XM_011541228.3 → XP_011539530.1 D-3-phosphoglycerate dehydrogenase isoform X3

UniProtKB/TrEMBL

B3KSC3

Conserved Domains (1) summary

cl28378
Location:7 → 451

SerA; Phosphoglycerate dehydrogenase or related dehydrogenase [Coenzyme transport and metabolism, General function prediction only]
XM_047417683.1 → XP_047273639.1 D-3-phosphoglycerate dehydrogenase isoform X6

RNA

XR_007058634.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

NC_060925.1 Alternate T2T-CHM13v2.0

Range

119725174..119757460

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054335948.1 → XP_054191923.1 D-3-phosphoglycerate dehydrogenase isoform X1
XM_054335949.1 → XP_054191924.1 D-3-phosphoglycerate dehydrogenase isoform X2
XM_054335951.1 → XP_054191926.1 D-3-phosphoglycerate dehydrogenase isoform X4
XM_054335952.1 → XP_054191927.1 D-3-phosphoglycerate dehydrogenase isoform X5
XM_054335950.1 → XP_054191925.1 D-3-phosphoglycerate dehydrogenase isoform X3
XM_054335953.1 → XP_054191928.1 D-3-phosphoglycerate dehydrogenase isoform X6

RNA

XR_008485990.1 RNA Sequence

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

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.