Selected-GenAtlas references	SOURCE	GeneCards	NCBI Gene	Swiss-Prot	Orphanet	Ensembl
	HGNC	UniGene	Nucleotide	OMIM		UCSC

Home Page

FLASH GENE

Symbol

PHGDH

contributors: mct - updated : 18-06-2016

HGNC name	phosphoglycerate dehydrogenase
HGNC id	8923

FLASH GENE DNA RNA EXPRESSION PROTEIN DISORDER ANIMAL & CELL MODELS

DNA

TYPE	functioning gene
STRUCTURE	32.43 kb     12 Exon(s)

Genomic sequence alignment details
10 Kb 5' upstream gene genomic sequence study

regulatory sequence	Promoter (CAAT box)
	cytosine-phosphate-guanine/HTF
	Binding site   transcription factor
text structure	positively regulated by the action of transcription factors Sp1 and NF-Y
	promoter region exhibited several putative transcription factor binding sites for NF-Y, Sp1, GATA-1, TP53, AP2, and AP1, with no TATA-box motif
	core positive promoter activity resided in the -276 to +1, which contains two GC-motifs for binding Sp1 and one CCAAT-motif for NF-Y.(both the proximal GC-motif and CCAAT-motif were crucial for full induction of the promoter activity)

MAPPING

cloned

Y

linked

N

status

provisional

RNA

TRANSCRIPTS	type	messenger

identification nb exons type bp product Protein kDa AA specific expression Year Pubmed NM_006623 12 splicing 2021 NP_006614 - 533 - 2000 10713460

EXPRESSION

Type

widely

expressed in	(based on citations)
organ(s)	System Organ level 1 Organ level 2 Organ level 3 Organ level 4 Level Pubmed Species Stage Rna symbol Digestive liver       highly Homo sapiens Lymphoid/Immune spleen       highly Homo sapiens Nervous brain       highly Homo sapiens Reproductive male system testis     highly Homo sapiens Urinary kidney       highly Homo sapiens

cells

System Cell Pubmed Species Stage Rna symbol Nervous neuron Homo sapiens

cell lineage
cell lines
fluid/secretion	predominantly in lymph

at STAGE

physiological period

fetal

Text	highly expressed in all fetal tissues, including brain tissue

PROTEIN

PHYSICAL PROPERTIES

STRUCTURE

motifs/domains	each monomer comprises three distinct domains
	a nucleotide-binding domain (residues 108–294)
	a substrate-binding domain (residues 7–107 and 295–336)
	a regulatory domain that binds serine (residues 337–533)

mono polymer

homomer , tetramer

HOMOLOGY

interspecies	homolog to rattus Phgdh (94.2 pc)
	homolog to murine Phdgh (94.6 pc)

Homologene

FAMILY

D-isomer specific 2-hydroxyacid dehydrogenase family

CATEGORY

enzyme , transport carrier

SUBCELLULAR LOCALIZATION	intracellular
	intracellular,cytoplasm,cytosolic,vesicle

basic FUNCTION	involved in transition of phosphoglycerate to 3- phosphohydroxyglycerate, initiating and rate limiting step in the phosphorylated pathway of serine biosynthesis pathway
	necessary for serine biosynthesis, which serves as a substrate for protein synthesis
	catalyzes the first step in L-serine synthesis via the phosphorylated pathway

CELLULAR PROCESS

PHYSIOLOGICAL PROCESS

development , electron transport

text	electron carrier
	brain development

PATHWAY

metabolism

aminoacid

signaling

amino-acid biosynthesis (L-serine from 3-phospho-D-glyceric acid)

a component

tetramer consisting of four identical subunits

INTERACTION

DNA

RNA

small molecule	cofactor, nucleotide,
	NAD+

protein	target of HOXA10 regulation in endometrial cells
	PRKCZ represses the expression of PHGDH and PSAT1, and phosphorylates PHGDH at key residues to inhibit its enzymatic activity
	PRKCZ acts as a metabolic tumor suppressor by inhibiting PHGDH expression and activity
	PHGDH promotes pancreatic cancer development through enhancing the translation initiations by interacting with EIF4A1 and EIF4E

cell & other

REGULATION

ASSOCIATED DISORDERS

corresponding disease(s)

PHGDH , NELAS

Other morbid association(s)

Type Gene Modification Chromosome rearrangement Protein expression Protein Function tumoral     --over   in leukemia, lymphoma and carcinoma constitutional     --other   in cycling endometrial tissue, is relatively high in the proliferative phase in glandular cells and lower in the secretory phase constitutional   deletion     L-serine deficiency caused by its deletion leads to robust induction of EIF4EBP1 and subsequent repression of translation initiation in the developing central nervous system

Susceptibility

Variant & Polymorphism

Candidate gene

Marker

Therapy target

ANIMAL & CELL MODELS

	impaired neurogenesis in embryonic spinal cord of Phgdh knockout mice, a serine deficiency disorder model
	severe impairment in neurogenesis of the central nervous system of Phgdh knockout (KO) embryos and a reduction in the protein content of their brains