Gene Gene information from NCBI Gene database.
Entrez ID 26227
Gene name Phosphoglycerate dehydrogenase
Gene symbol PHGDH
Synonyms (NCBI Gene)
3-PGDH3PGDHHEL-S-113NLSNLS1PDGPGADPGDPGDHPHGDHDSERA
Chromosome 1
Chromosome location 1p12
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. Mut
SNPs SNP information provided by dbSNP.
12
SNP ID Visualize variation Clinical significance Consequence
rs121907987 G>A Pathogenic Missense variant, coding sequence variant
rs121907988 G>A Pathogenic Missense variant, coding sequence variant
rs267606947 G>A Likely-pathogenic Missense variant, coding sequence variant
rs267606948 G>A,C Pathogenic Missense variant, coding sequence variant
rs587777774 G>A Pathogenic Coding sequence variant, missense variant
miRNA miRNA information provided by mirtarbase database.
45
miRTarBase ID miRNA Experiments Reference
MIRT020945 hsa-miR-155-5p Proteomics 18668040
MIRT030040 hsa-miR-26b-5p Microarray 19088304
MIRT048300 hsa-miR-107 CLASH 23622248
MIRT043507 hsa-miR-331-3p CLASH 23622248
MIRT039728 hsa-miR-615-3p CLASH 23622248
Transcription factors Transcription factors information provided by TRRUST V2 database.
2
Transcription factor Regulation Reference
HOXA10 Repression 19778996
SP1 Activation 18378410
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
27
GO ID Ontology Definition Evidence Reference
GO:0004617 Function Phosphoglycerate dehydrogenase activity IBA
GO:0004617 Function Phosphoglycerate dehydrogenase activity IEA
GO:0004617 Function Phosphoglycerate dehydrogenase activity TAS 8758134
GO:0005515 Function Protein binding IPI 25036637, 33961781, 35271311
GO:0005829 Component Cytosol TAS
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
606879 8923 ENSG00000092621
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
O43175
Protein name D-3-phosphoglycerate dehydrogenase (3-PGDH) (EC 1.1.1.95) (2-oxoglutarate reductase) (EC 1.1.1.399) (Malate dehydrogenase) (EC 1.1.1.37)
Protein function Catalyzes the reversible oxidation of 3-phospho-D-glycerate to 3-phosphonooxypyruvate, the first step of the phosphorylated L-serine biosynthesis pathway. Also catalyzes the reversible oxidation of 2-hydroxyglutarate to 2-oxoglutarate and the re
PDB 2G76 , 5N53 , 5N6C , 5NZO , 5NZP , 5NZQ , 5OFM , 5OFV , 5OFW , 6CWA , 6PLF , 6PLG , 6RIH , 6RJ2 , 6RJ3 , 6RJ5 , 6RJ6 , 7CVP , 7DKM , 7EWH , 7VA1
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF00389 2-Hacid_dh 9 317 D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain Domain
PF02826 2-Hacid_dh_C 111 285 D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain Domain
Sequence
MAFANLRKVLISDSLDPCCRKILQDGGLQVVEKQNLSKEELIAELQDCEGLIVRSATKVT
ADVINAAEKLQVVGRAGTGVDNVDLEAATRKGILVMNTPNGNSLSAAELT
CGMIMCLARQ
IPQATASMKDGKWERKKFMGTELNGKTLGILGLGRIGREVATRMQSFGMKTIGYDPIISP
EVSASFGVQQLPLEEIWPLCDFITVHTPLLPSTTGLLNDNTFAQCKKGVRVVNCARGGIV
DEGALLRALQSGQCAGAALDVFTEEPPRDRALVDHENVISCPHLG
ASTKEAQSRCGEEIA
VQFVDMVKGKSLTGVVN
AQALTSAFSPHTKPWIGLAEALGTLMRAWAGSPKGTIQVITQG
TSLKNAGNCLSPAVIVGLLKEASKQADVNLVNAKLLVKEAGLNVTTSHSPAAPGEQGFGE
CLLAVALAGAPYQAVGLVQGTTPVLQGLNGAVFRPEVPLRRDLPLLLFRTQTSDPAMLPT
MIGLLAEAGVRLLSYQTSLVSDGETWHVMGISSLLPSLEAWKQHVTEAFQFHF
Sequence length 533
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
  KEGG  Reactome
  Glycine, serine and threonine metabolism
Cysteine and methionine metabolism
Metabolic pathways
Carbon metabolism
Biosynthesis of amino acids
  Serine biosynthesis
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
44
Evidence Score: ★☆☆☆☆  Gene-disease association found in Text Mining only ★★☆☆☆  Found in Text Mining and Unknown/Other Associations ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession Evidence Score
Epileptic encephalopathy Likely pathogenic; Pathogenic rs886041874 RCV000415201
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Neu-Laxova syndrome 1 Likely pathogenic; Pathogenic rs2101221217, rs766427173, rs951372478, rs1331155296, rs749134845, rs587777774, rs121907987, rs267606949, rs267606948, rs149128100, rs2464204681, rs886041874, rs2464160831, rs2464159619, rs2464187735
View all (5 more)
RCV005014544
RCV001420191
RCV003339747
RCV005006219
RCV005016804
View all (16 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
PHGDH deficiency Likely pathogenic; Pathogenic rs2101195348, rs2101225889, rs979237677, rs1652150288, rs2101221217, rs1652224758, rs766427173, rs951372478, rs781273456, rs1418800829, rs1331155296, rs758517215, rs2101205361, rs1302054606, rs1651264976
View all (61 more)
RCV001377803
RCV001379151
RCV001383227
RCV001382946
RCV001388882
View all (74 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
PHGDH-related disorder Likely pathogenic; Pathogenic rs121907987 RCV004757095
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Phenotype Name Clinical Significance Source Evidence Score
Acute myeloid leukemia Benign; Likely benign ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
AMINO ACID METABOLISM, INBORN ERRORS Disgenet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
BREAST CANCER GWAS catalog
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
BREAST CARCINOMA GWAS catalog
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Associations from Text Mining Disease associations identified through text mining
Disease Name Disease (Merged) Source PMID Relationship Type Evidence Score
3-Phosphoglycerate dehydrogenase deficiency 3-phosphoglycerate dehydrogenase deficiency ORPHANET_DG 11055895
★☆☆☆☆
Found in Text Mining only
3-phosphoglycerate dehydrogenase deficiency, infantile/juvenile form 3-phosphoglycerate dehydrogenase deficiency Orphanet
★☆☆☆☆
Found in Text Mining only
Ablepharon Ablepharon HPO_DG
★☆☆☆☆
Found in Text Mining only
Absence of septum pellucidum Absence Of Septum Pellucidum HPO_DG
★☆☆☆☆
Found in Text Mining only
Acute Promyelocytic Leukemia Promyelocytic Leukemia BEFREE 27499693
★☆☆☆☆
Found in Text Mining only
Adenocarcinoma Adenocarcinoma BEFREE 25735395, 28614715, 30744688
★☆☆☆☆
Found in Text Mining only
Adenocarcinoma of lung (disorder) Lung adenocarcinoma BEFREE 28614715, 29556358
★☆☆☆☆
Found in Text Mining only
Adenomatous Polyposis Coli Multiple polyposis syndrome BEFREE 12955080, 26186212
★☆☆☆☆
Found in Text Mining only
Adult Diffuse Large B-Cell Lymphoma B-cell Lymphoma BEFREE 28031410
★☆☆☆☆
Found in Text Mining only
Adult Rickets Rickets HPO_DG
★☆☆☆☆
Found in Text Mining only