Gene Gene information from NCBI Gene database.
Entrez ID 5230
Gene name Phosphoglycerate kinase 1
Gene symbol PGK1
Synonyms (NCBI Gene)
HEL-S-68pMIG10PGKA
Chromosome X
Chromosome location Xq21.1
Summary The protein encoded by this gene is a glycolytic enzyme that catalyzes the conversion of 1,3-diphosphoglycerate to 3-phosphoglycerate. The encoded protein may also act as a cofactor for polymerase alpha. Additionally, this protein is secreted by tumor cel
SNPs SNP information provided by dbSNP.
19
SNP ID Visualize variation Clinical significance Consequence
rs137852528 G>A Pathogenic Coding sequence variant, missense variant
rs137852529 G>A,C Pathogenic Coding sequence variant, missense variant
rs137852531 T>C Pathogenic Coding sequence variant, missense variant
rs137852532 G>T Pathogenic Coding sequence variant, missense variant
rs137852533 T>C Pathogenic Coding sequence variant, missense variant
miRNA miRNA information provided by mirtarbase database.
603
miRTarBase ID miRNA Experiments Reference
MIRT050550 hsa-miR-20a-5p CLASH 23622248
MIRT043151 hsa-miR-324-5p CLASH 23622248
MIRT040970 hsa-miR-18a-3p CLASH 23622248
MIRT717331 hsa-miR-181a-2-3p HITS-CLIP 19536157
MIRT717330 hsa-miR-1273g-3p HITS-CLIP 19536157
Transcription factors Transcription factors information provided by TRRUST V2 database.
2
Transcription factor Regulation Reference
HIF1A Activation 8089148
MYC Unknown 18809243
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
45
GO ID Ontology Definition Evidence Reference
GO:0000166 Function Nucleotide binding IEA
GO:0004618 Function Phosphoglycerate kinase activity EXP 1278465, 5009693
GO:0004618 Function Phosphoglycerate kinase activity IBA
GO:0004618 Function Phosphoglycerate kinase activity IEA
GO:0004618 Function Phosphoglycerate kinase activity IMP 7391028
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
311800 8896 ENSG00000102144
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
P00558
Protein name Phosphoglycerate kinase 1 (EC 2.7.11.1) (EC 2.7.2.3) (Cell migration-inducing gene 10 protein) (Primer recognition protein 2) (PRP 2)
Protein function Catalyzes one of the two ATP producing reactions in the glycolytic pathway via the reversible conversion of 1,3-diphosphoglycerate to 3-phosphoglycerate (PubMed:30323285, PubMed:7391028). Both L- and D- forms of purine and pyrimidine nucleotides
PDB 2WZB , 2WZC , 2WZD , 2X13 , 2X14 , 2X15 , 2XE6 , 2XE7 , 2XE8 , 2Y3I , 2YBE , 2ZGV , 3C39 , 3C3A , 3C3B , 3C3C , 3ZOZ , 4AXX , 4O33 , 5M1R , 5M3U , 5M6Z , 5MXM , 5NP8 , 5O7D , 8YHP
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF00162 PGK 9 406 Phosphoglycerate kinase Domain
Tissue specificity TISSUE SPECIFICITY: Mainly expressed in spermatogonia. Localized on the principle piece in the sperm (at protein level). Expression significantly decreased in the testis of elderly men. {ECO:0000269|PubMed:26677959}.
Sequence
Sequence length 417
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
  KEGG  Reactome
  Glycolysis / Gluconeogenesis
Metabolic pathways
Carbon metabolism
Biosynthesis of amino acids
HIF-1 signaling pathway
  Glycolysis
Gluconeogenesis
Manipulation of host energy metabolism
Associated diseases Disease associations from ClinVar categorized as Causal (Pathogenic/Likely Pathogenic) or Unknown.
136
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession
Glycogen storage disease due to phosphoglycerate kinase 1 deficiency Likely pathogenic; Pathogenic rs2149132078, rs137852528, rs137852529, rs431905501, rs137852531, rs137852532, rs137852533, rs137852535, rs137852536, rs137852537, rs137852538, rs431905503, rs137852539 RCV002250801
RCV000010620
RCV000010621
RCV000010622
RCV000010624
RCV000010625
RCV000010626
RCV000010629
RCV000010630
RCV000010631
RCV000010632
RCV000010633
RCV000010634
Male infertility due to obstructive azoospermia Likely pathogenic rs1569550773 RCV000767230
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession
Epilepsy Benign; Likely benign rs143031509 RCV005626743
Epileptic encephalopathy Uncertain significance rs1060499671 RCV000449521
Familial cancer of breast Likely benign; Benign rs138345294, rs370410785, rs78165041 RCV005916022
RCV005932058
RCV005904816
Hereditary skeletal muscle disorder Conflicting classifications of pathogenicity rs202138276 RCV005626448
Associations from Text MiningDisease associations identified through Pubtator
Disease Name Relationship Type References
Adenocarcinoma Associate 14573703, 34814273
Adenocarcinoma Stimulate 27150162
Adenocarcinoma of Lung Associate 14573703
Altitude Sickness Associate 33393624
Anemia Hemolytic Associate 16412025, 39787833
Astrocytoma Associate 22742733
Bone Diseases Metabolic Associate 22619369
Bone Marrow Diseases Associate 24376734
Brain Diseases Metabolic Inborn Associate 39787833
Breast Neoplasms Associate 16048908, 30537744, 31578148, 32028979, 32070368, 33597614, 34600547, 34790279, 34868337, 35441810, 36077333, 36860848, 37190091, 37986376, 39192221
View all (1 more)