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 (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
19
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
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
View all (8 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Male infertility due to obstructive azoospermia Likely pathogenic rs1569550773 RCV000767230
★★★★☆
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
ANEMIA, HEMOLYTIC Disgenet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
CARCINOMA, HEPATOCELLULAR CTD
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
CARCINOMA, RENAL CELL CTD
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Epilepsy Benign; Likely benign ClinVar
★★☆☆☆
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
Amyotrophic Lateral Sclerosis Amyotrophic Lateral Sclerosis BEFREE 31361595
★☆☆☆☆
Found in Text Mining only
Anemia Anemia BEFREE 1683796, 30951021
★☆☆☆☆
Found in Text Mining only
Anemia Hemolytic Hemolytic anemia Pubtator 16412025, 39787833 Associate
★☆☆☆☆
Found in Text Mining only
Anemia, Hemolytic Anemia BEFREE 16857429, 30975619
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Anemia, Hemolytic Anemia HPO_DG
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
ANOPHTHALMIA AND PULMONARY HYPOPLASIA Syndromic microphthalmia BEFREE 16493704, 31611300
★☆☆☆☆
Found in Text Mining only
Astrocytoma Astrocytoma Pubtator 22742733 Associate
★☆☆☆☆
Found in Text Mining only
Astrocytoma Astrocytoma BEFREE 24284928
★☆☆☆☆
Found in Text Mining only
Bone Diseases Metabolic Bone disease Pubtator 22619369 Associate
★☆☆☆☆
Found in Text Mining only
Bone Marrow Diseases Bone marrow diseases Pubtator 24376734 Associate
★☆☆☆☆
Found in Text Mining only