PHGDH - phosphoglycerate dehydrogenase Gene

Also Known as NLS; PDG; PGD; NLS1; PGAD; PGDH; SERA; 3PGDH; 3-PGDH; PHGDHD; HEL-S-113

Species: Homo sapiens

Gene Type: protein coding

Gene ID: 26227

About PHGDH

Cytogenetic location: 1p12 Genomic coordinates (GRCh38): 1:119,711,934-119,744,215 (from NCBI)

This gene has 34 transcripts (splice variants), 217 orthologues, 3 paralogues and is associated with 5 phenotypes. Broad expression in fat (RPKM 36.0), skin (RPKM 33.6) and 23 other tissues.

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]

PHGDH Products (9)

mRNA	Protein	Name
XM_047417680.1	XP_047273636.1	D-3-phosphoglycerate dehydrogenase isoform X4
XM_011541228.3	XP_011539530.1	D-3-phosphoglycerate dehydrogenase isoform X3
XM_011541227.3	XP_011539529.1	D-3-phosphoglycerate dehydrogenase isoform X2
XM_047417682.1	XP_047273638.1	D-3-phosphoglycerate dehydrogenase isoform X5
NM_032692.1
XM_011541226.3	XP_011539528.1	D-3-phosphoglycerate dehydrogenase isoform X1
XM_047417683.1	XP_047273639.1	D-3-phosphoglycerate dehydrogenase isoform X6
NM_006623.4	NP_006614.2	D-3-phosphoglycerate dehydrogenase
XR_007058634.1

Gene Ontology

Molecular Function

Molecular Function GO Annotation	Evidence	References	Source
enables protein binding	IPI IPI: Inferred from physical interaction	25036637	GOA

EXP: Inferred from Experiment IDA: Inferred from direct assay IPI: Inferred from physical interaction IMP: Inferred from mutant phenotype IGI: Inferred from genetic interaction IEP: Inferred from expression pattern

PHGDH Protein Structure

2-Hacid_dh

2-Hacid_dh_C

0
100
200
300
400
500
533 a.a.

Protein Preferred Names	Protein Names
D-3-phosphoglycerate dehydrogenase	2-oxoglutarate reductase 3-phosphoglycerate dehydrogenase epididymis secretory protein Li 113 malate dehydrogenase

PHGDH Protein-protein interaction Information

Type	Protein Name	Protein ID	Interactor	Interactor Species	Interactor ID	Detection Method	References
Intra	PHGDH	O43175	EPN1	Homo sapiens	Q9Y6I3	Anti Tag CoIP	25036637
Intra	PHGDH	O43175	EPN1	Homo sapiens	Q9Y6I3	Anti Tag CoIP	33961781
Intra	PHGDH	O43175	EPN1	Homo sapiens	Q9Y6I3	Anti Tag CoIP	35271311

Cross: Cross-species interaction Intra: Intraspecies interaction

Related Diseases

Diseases	Alias
Retinitis Pigmentosa 61	RP61 Retinitis Pigmentosa, Type 61
Phosphoglycerate Dehydrogenase Deficiency	Phgdh Deficiency 3-Phosphoglycerate Dehydrogenase Deficiency PHGDHD 3-Pgdh Deficiency 3-Phosphoglycerate Dehydrogenase Deficiency, Infantile/Juvenile Form Phgdh Deficiency, Infantile/Juvenile Form Deficiency, Phosphoglycerate Dehydrogenase
Short-Rib Thoracic Dysplasia 2 With Or Without Polydactyly	Asphyxiating Thoracic Dystrophy 2 SRTD2 Atd2 Jatd Jeune Asphyxiating Thoracic Dystrophy Jeune Syndrome 2
Neu-Laxova Syndrome Due To 3-Phosphoglycerate Dehydrogenase Deficiency	3-Phosphoglycerate Dehydrogenase Deficiency, Prenatal Form
Microcephaly	Microencephaly Microcephalus Microcephalic Nanocephaly Congenital Microcephaly Brain Hypoplasia Brain Nondevelopment Cephalic Hypoplasia Undeveloped Cerebrum Undeveloped Brain Micrencephalon Micrencephaly
Ichthyosis	Ichthyoses Non-Syndromic Ichthyosis Congenital Ichthyosis
Ectropion	Ectropion Of Eyelid Everted Margin Eversion Of The Eyelid Eyelashes Turned Out Eyelid Everted Eyelid Turned Out Unspecified Ectropion Of Unspecified Eye
Retinitis Pigmentosa	RP Rod-Cone Dystrophy Autosomal Recessive Retinitis Pigmentosa Non-Syndromic Retinitis Pigmentosa Pericentral Pigmentary Retinopathy Pigmentary Retinopathy Tapetoretinal Degeneration Rcd Retinitis Pigmentosa Autosomal Recessive ARRP Retinitis Pigmentosa, Autosomal Recessive Retinitis Pigmentosa 1
Amyotrophic Lateral Sclerosis 1	Amyotrophic Lateral Sclerosis ALS Lou Gehrig Disease Amyotrophic Lateral Sclerosis Type 1 Charcot Disease ALS1 Amyotrophic Lateral Sclerosis, Susceptibility To Fals Lou Gehrig'S Disease Mnd Motor Neuron Disease Familial Amyotrophic Lateral Sclerosis Amyotrophic Lateral Sclerosis 1, Familial Amyotrophic Lateral Sclerosis 1, Autosomal Dominant Motor Neuron Disease, Bulbar Motor Neurone Disease Amyotrophic Lateral Sclerosis With Dementia Dementia With Amyotrophic Lateral Sclerosis Motor Neuron Disease, Amyotrophic Lateral Sclerosis Sclerosis, Lateral, Amyotrophic Sclerosis, Lateral, Amyotrophic, Type 1 Amyotrophic Sclerosis Als - [Amyotrophic Lateral Sclerosis] Wasting Palsy Amyotrophic Paralysis Amyotrophy Lateral Sclerosis Wasting Paralysis Spinal Progressive Amyotrophy Progressive Atrophic Paralysis
Phosphoserine Aminotransferase Deficiency	Psat Deficiency PSATD Phosphoserine Aminotransferase Deficiency, Infantile/Juvenile Form Psat Deficiency, Infantile/Juvenile Form Deficiency, Phosphoserine Aminotransferase
Neu-Laxova Syndrome 1	Neu-Laxova Syndrome NLS1 Nls Neu Laxova Syndrome 3-Phosphoglycerate Dehydrogenase Deficiency, Neonatal Form
Lissencephaly	Pachygyria Broad Gyri Of Cerebrum Large Gyri Of Cerebrum Macrogyria
Serine Deficiency
Familial Thyroid Dyshormonogenesis	Thyroid Dyshormonogenesis Familial Dyshormonogenetic Goiter
Split-Hand/Foot Malformation 2	SHFM2 Shfd2 Shsf2 Split Hand/Foot Malformation 2 Split Hand-Foot Malformation 2 Split-Hand/Split-Foot Anomaly, X-Linked Split-Hand/Foot Deformity 2 Split Hand/Foot Malformation X-Linked Split Hand Foot Anomaly - X-Linked Split Hand Foot Deformity 2
Breast Cancer	Breast Carcinoma Breast Cancer, Familial Malignant Neoplasm Of Breast Male Breast Cancer Breast Cancer, Susceptibility To Breast Cancer, Early-Onset Malignant Tumor Of Breast Carcinoma Of Male Breast Breast Cancer, Invasive Ductal Breast Cancer, Protection Against Breast Cancer, Somatic Breast Cancer, Male Breast Cancer, Lobular, Somatic Breast Tumor Mammary Cancer Mammary Tumor Malignant Neoplasm Of Male Breast Mammary Carcinoma Male Breast Carcinoma Familial Cancer Of Breast Invasive Ductal Breast Carcinoma Breast Cancer Susceptibility Breast Cancer, Male, Susceptibility To Breast Cancer, Early-Onset, Susceptibility To Malignant Tumor Of The Breast Mammary Neoplasm Primary Breast Cancer Neoplasm Of Male Breast Carcinoma Of Breast Breast Cancer In Men Familial Breast Cancer Cancer Of Breast BC Breast Cancer Familial Breast Cancer Familial Male Breast Cancer, Familial Male Breast Male Carcinoma Breast Neoplasms Breast Neoplasms, Male Mammary Tumors Mammary Carcinomas Cancer, Breast Cancer, Breast, Susceptibility Invasive Breast Ductal Carcinoma Breast Neoplasm Susceptibility To Breast Cancer Mammary Neoplasms Animal Mammary Neoplasms Primary Malignant Neoplasm Of Breast Infiltrating Ductal Carcinoma Of Breast Infiltrating Duct Carcinoma Of Unspecified Site Infiltrating Ductular Carcinoma Of Unspecified Site Invasive Breast Carcinoma Of No Special Type Microinvasive Carcinoma Of Breast Carcinoma With Apocrine Differentiation
Cerebellar Hypoplasia
Congenital Nervous System Abnormality	Congenital Neurologic Anomaly Congenital Nervous System Disorder

Diseases	Alias
Waldenstroem'S Macroglobulinemia	Waldenstroem'S Macroglobulinemia Waldenstroem'S Macroglobulinemia Macroglobulinemia Of Waldenstrom Lymphoplasmacytic Lymphoma With Igm Gammopathy Lymphoplasmacytic Lymphoma Waldenstroem'S Macroglobulinemia Waldenstroem'S Macroglobulinemia Macroglobulinemia Of Waldenstrom Lymphoplasmacytic Lymphoma With Igm Gammopathy Lymphoplasmacytic Lymphoma

Orthologs Information

Species	Symbol	Source	ID
Macaca mulatta	PHGDH	VGNC	VGNC:75976
Rattus norvegicus	PHGDH	RGD	RGD:61987
Felis catus	PHGDH	VGNC	VGNC:68824
Bos taurus	PHGDH	VGNC	VGNC:55654
Mus musculus	PHGDH	MGD	MGI:1355330
Others	PHGDH	NCBI