PHGDH (phosphoglycerate dehydrogenase)

Gene
Gene SNPs miRNA Transcription factors Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.
26227
Gene name Gene Name - the full gene name approved by the HGNC.
Phosphoglycerate dehydrogenase
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.
PHGDH
Synonyms (NCBI Gene) Gene synonyms aliases
3-PGDH, 3PGDH, HEL-S-113, NLS, NLS1, PDG, PGAD, PGD, PGDH, PHGDHD, SERA
Chromosome Chromosome number
1
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.
1p12
Summary Summary of gene provided in NCBI Entrez Gene.
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.
Gene SNPs miRNA Transcription factors Gene ontology Other IDs Protein Pathways Associated diseases
Show/Hide all(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.
Gene SNPs miRNA Transcription factors Gene ontology Other IDs Protein Pathways Associated diseases
Show/Hide all(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
Gene SNPs miRNA Transcription factors Gene ontology Other IDs Protein Pathways Associated diseases
Show/Hide all(2)
Transcription factor Regulation Reference
HOXA10 Repression 19778996
SP1 Activation 18378410
Gene ontology (GO) Gene ontology information of associated ontologies with gene provided by GO database.
Gene SNPs miRNA Transcription factors Gene ontology Other IDs Protein Pathways Associated diseases
Show/Hide all(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 ids of gene in databases such as OMIM, HGNC, ENSEMBLE.
Gene SNPs miRNA Transcription factors Gene ontology Other IDs Protein Pathways Associated diseases
MIM HGNC e!Ensembl
606879 8923 ENSG00000092621
Protein
Gene SNPs miRNA Transcription factors Gene ontology Other IDs Protein Pathways Associated diseases
UniProt ID 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
ADVINAAEKLQVVGRAGTGVDNVDLEAATRKGILVMNTPNGNSLSAAELTCGMIMCLARQ
IPQATASMKDGKWERKKFMGTELNGKTLGILGLGRIGREVATRMQSFGMKTIGYDPIISP
EVSASFGVQQLPLEEIWPLCDFITVHTPLLPSTTGLLNDNTFAQCKKGVRVVNCARGGIV
DEGALLRALQSGQCAGAALDVFTEEPPRDRALVDHENVISCPHLGASTKEAQSRCGEEIA
VQFVDMVKGKSLTGVVNAQALTSAFSPHTKPWIGLAEALGTLMRAWAGSPKGTIQVITQG
TSLKNAGNCLSPAVIVGLLKEASKQADVNLVNAKLLVKEAGLNVTTSHSPAAPGEQGFGE
CLLAVALAGAPYQAVGLVQGTTPVLQGLNGAVFRPEVPLRRDLPLLLFRTQTSDPAMLPT
MIGLLAEAGVRLLSYQTSLVSDGETWHVMGISSLLPSLEAWKQHVTEAFQFHF
Sequence length 533
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
Gene SNPs miRNA Transcription factors Gene ontology Other IDs Protein Pathways Associated diseases
  KEGG   Reactome
  Glycine, serine and threonine metabolism
Cysteine and methionine metabolism
Metabolic pathways
Carbon metabolism
Biosynthesis of amino acids 		  Serine biosynthesis
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Associated diseases Disease associations categorized as Causal (pathogenic variants), Unknown (uncertain genetic evidence), or Text Mining (literature-based associations)
Gene SNPs miRNA Transcription factors Gene ontology Other IDs Protein Pathways Associated diseases
Show/Hide Causal Diseases (1)
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
Disease merge term Disease name dbSNP ID References
Neu-Laxova Syndrome neu-laxova syndrome 1 rs769256568, rs1571013274, rs1224279673, rs121907987, rs267606948, rs587777774, rs886041874 N/A
Show/Hide Unknown Diseases (4)
Unknown Includes: (1) ClinVar NON-pathogenic variants (Uncertain, Benign, Conflicting, VUS), (2) GenCC associations, (3) GWAS associations, (4) CBGDA evidence-based associations. NOTE: Diseases with pathogenic evidence are excluded to avoid conflicts.
Disease merge term Disease name Evidence References Source
Breast Cancer Breast cancer N/A N/A GWAS
Gout Gout N/A N/A GWAS
Hepatocellular Carcinoma Hepatocellular carcinoma Inhibition of PHGDH sensitized HCC cells to Sorafenib treatment 31615983 CBGDA
Multiple Sclerosis Multiple sclerosis N/A N/A GWAS
Show/Hide Text Mining Associations (85)
Associations from Text Mining Disease associations identified through Pubtator
Disease Name Relationship Type References
AA amyloidosis Associate 30662332
Acidosis Associate 39900217
Adenocarcinoma Follicular Associate 27277113
Altitude Sickness Associate 35668171
Alzheimer Disease Stimulate 32220323
Alzheimer Disease Associate 35508106
Amyotrophic lateral sclerosis 1 Associate 33311513
Aneurysm Ruptured Stimulate 32589050
Brain Neoplasms Associate 30250195
Breast Neoplasms Associate 18703606, 21437235, 24979213, 25406093, 25496516, 30250195, 33112838, 36782224, 36925195, 8955125