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PGAM2

gene
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Also known as PGAM-M

Summary

PGAM2 (phosphoglycerate mutase 2, HGNC:8889) is a protein-coding gene on chromosome 7p13, encoding Phosphoglycerate mutase 2 (P15259). Catalyzes the interconversion of 3- and 2-phosphoglycerate with 2,3-bisphosphoglycerate as the primer of the reaction.

Phosphoglycerate mutase (PGAM) catalyzes the reversible reaction of 3-phosphoglycerate (3-PGA) to 2-phosphoglycerate (2-PGA) in the glycolytic pathway. The PGAM is a dimeric enzyme containing, in different tissues, different proportions of a slow-migrating muscle (MM) isozyme, a fast-migrating brain (BB) isozyme, and a hybrid form (MB). This gene encodes muscle-specific PGAM subunit. Mutations in this gene cause muscle phosphoglycerate mutase eficiency, also known as glycogen storage disease X.

Source: NCBI Gene 5224 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): glycogen storage disease due to phosphoglycerate mutase deficiency (Strong, GenCC)
  • Clinical variants (ClinVar): 21 total — 3 pathogenic
  • Phenotypes (HPO): 9
  • MANE Select transcript: NM_000290

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:8889
Approved symbolPGAM2
Namephosphoglycerate mutase 2
Location7p13
Locus typegene with protein product
StatusApproved
AliasesPGAM-M
Ensembl geneENSG00000164708
Ensembl biotypeprotein_coding
OMIM612931
Entrez5224

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000297283, ENST00000971360

RefSeq mRNA: 1 — MANE Select: NM_000290 NM_000290

CCDS: CCDS34624

Canonical transcript exons

ENST00000297283 — 3 exons

ExonStartEnd
ENSE000010868544406483244065012
ENSE000010868564406511644065567
ENSE000018508664406272744062930

Expression profiles

Bgee: expression breadth ubiquitous, 195 present calls, max score 99.76.

FANTOM5 (CAGE): breadth broad, TPM avg 7.0341 / max 1918.4688, expressed in 323 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter IDTPM avgSamples expressed
838316.5410280
838320.3492114
838290.087427
838300.056526

Top tissues by expression

289 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
apex of heartUBERON:000209899.76gold quality
hindlimb stylopod muscleUBERON:000425299.74gold quality
right atrium auricular regionUBERON:000663199.63gold quality
cardiac atriumUBERON:000208199.39gold quality
gastrocnemiusUBERON:000138899.28gold quality
biceps brachiiUBERON:000150799.15gold quality
triceps brachiiUBERON:000150999.14gold quality
skeletal muscle tissue of biceps brachiiUBERON:000450299.13gold quality
vastus lateralisUBERON:000137999.10gold quality
heart left ventricleUBERON:000208498.97gold quality
skeletal muscle tissue of rectus abdominisUBERON:000451198.96gold quality
cardiac ventricleUBERON:000208298.89gold quality
quadriceps femorisUBERON:000137798.75gold quality
heart right ventricleUBERON:000208098.44gold quality
skeletal muscle tissueUBERON:000113498.30gold quality
gluteal muscleUBERON:000200098.08gold quality
diaphragmUBERON:000110397.77gold quality
muscle organUBERON:000163097.75gold quality
skeletal muscle organUBERON:001489297.75gold quality
left testisUBERON:000453397.69gold quality
muscle of legUBERON:000138397.40gold quality
right testisUBERON:000453497.21gold quality
body of tongueUBERON:001187697.16gold quality
heartUBERON:000094896.57gold quality
myocardiumUBERON:000234996.49gold quality
cardiac muscle of right atriumUBERON:000337996.32gold quality
left ventricle myocardiumUBERON:000656694.60gold quality
deltoidUBERON:000147694.57gold quality
muscle tissueUBERON:000238594.50gold quality
testisUBERON:000047394.40gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

ExperimentMarker?Max mean expression
E-ANND-3no0.00

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): TP53

Literature-anchored findings (GeneRIF, showing 2)

  • These results reveal a mechanism of PGAM2 regulation and NADPH homeostasis in response to oxidative stress that impacts cell proliferation and tumor growth. (PMID:24786789)
  • Targeting the Metabolic Enzyme PGAM2 Overcomes Enzalutamide Resistance in Castration-Resistant Prostate Cancer by Inhibiting BCL2 Signaling. (PMID:37676279)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriopgam2ENSDARG00000057571
mus_musculusPgam2ENSMUSG00000020475
rattus_norvegicusPgam2ENSRNOG00000013532
drosophila_melanogasterPglym87FBGN0011270
drosophila_melanogasterPglym78FBGN0014869

Paralogs (3): PGAM1 (ENSG00000171314), BPGM (ENSG00000172331), PGAM4 (ENSG00000226784)

Protein

Protein identifiers

Phosphoglycerate mutase 2 — P15259 (reviewed: P15259)

Alternative names: BPG-dependent PGAM 2, Muscle-specific phosphoglycerate mutase, Phosphoglycerate mutase isozyme M

All UniProt accessions (1): P15259

UniProt curated annotations — full annotation on UniProt →

Function. Catalyzes the interconversion of 3- and 2-phosphoglycerate with 2,3-bisphosphoglycerate as the primer of the reaction. Can also catalyze the interconversion of (2R)-2,3-bisphosphoglycerate and (2R)-3-phospho-glyceroyl phosphate, but with a reduced activity.

Subunit / interactions. Homodimer. Interacts with ENO1.

Tissue specificity. Expressed in the heart and muscle. Not found in the liver and brain.

Disease relevance. Glycogen storage disease 10 (GSD10) [MIM:261670] A metabolic disorder characterized by myoglobinuria, increased serum creatine kinase levels, decreased phosphoglycerate mutase activity, myalgia, muscle pain, muscle cramps, exercise intolerance. The disease is caused by variants affecting the gene represented in this entry.

Similarity. Belongs to the phosphoglycerate mutase family. BPG-dependent PGAM subfamily.

RefSeq proteins (1): NP_000281* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001345PG/BPGM_mutase_ASActive_site
IPR005952Phosphogly_mut1Family
IPR013078His_Pase_superF_clade-1Family
IPR029033His_PPase_superfamHomologous_superfamily

Pfam: PF00300

Enzyme classification (BRENDA):

  • EC 5.4.2.11 — phosphoglycerate mutase (2,3-diphosphoglycerate-dependent) (BRENDA: 20 organisms, 14 substrates, 85 inhibitors, 37 Km, 16 kcat entries)

Substrate kinetics (BRENDA)

4 substrates with measured Km, best-characterized 4. Km ranges are aggregated across organisms/conditions.

SubstrateKm (mM)Measurements
3-PHOSPHOGLYCERATE0.026–7.4618
3-PHOSPHO-D-GLYCERATE0.22–614
2-PHOSPHOGLYCERATE0.041–0.0673
2-PHOSPHO-D-GLYCERATE0.37–0.692

Catalyzed reactions (Rhea), 2 shown:

  • (2R)-2-phosphoglycerate = (2R)-3-phosphoglycerate (RHEA:15901)
  • (2R)-3-phospho-glyceroyl phosphate = (2R)-2,3-bisphosphoglycerate + H(+) (RHEA:17765)

UniProt features (27 total): modified residue 7, binding site 7, sequence conflict 6, sequence variant 3, active site 2, chain 1, site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P15259-F194.070.83

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Catalytic / active sites (3): 11 (tele-phosphohistidine intermediate); 186 (transition state stabilizer); 89 (proton donor/acceptor)

Ligand- & substrate-binding residues (7): 10–17; 23–24; 62; 89–92; 100; 116–117; 187–188

Post-translational modifications (7): 3, 14, 118, 132, 133, 135, 152

Function

Pathways and Gene Ontology

Reactome pathways

2 pathways

IDPathway
R-HSA-70171Glycolysis
R-HSA-70263Gluconeogenesis

MSigDB gene sets: 187 (showing top): GOBP_NUCLEOSIDE_DIPHOSPHATE_METABOLIC_PROCESS, GAANYNYGACNY_UNKNOWN, GOBP_CARBOHYDRATE_DERIVATIVE_CATABOLIC_PROCESS, GOBP_MONOSACCHARIDE_CATABOLIC_PROCESS, GOBP_ORGANOPHOSPHATE_METABOLIC_PROCESS, GOBP_MALE_GAMETE_GENERATION, KEGG_GLYCOLYSIS_GLUCONEOGENESIS, GOBP_MONOCARBOXYLIC_ACID_METABOLIC_PROCESS, GNF2_MYL3, GOBP_CARBOHYDRATE_DERIVATIVE_METABOLIC_PROCESS, GOBP_RESPONSE_TO_METAL_ION, GOBP_NUCLEOBASE_CONTAINING_SMALL_MOLECULE_METABOLIC_PROCESS, GOBP_GENERATION_OF_PRECURSOR_METABOLITES_AND_ENERGY, GOBP_SMALL_MOLECULE_BIOSYNTHETIC_PROCESS, MODULE_379

GO Biological Process (7): gluconeogenesis (GO:0006094), glycolytic process (GO:0006096), striated muscle contraction (GO:0006941), Notch signaling pathway (GO:0007219), spermatogenesis (GO:0007283), response to mercury ion (GO:0046689), canonical glycolysis (GO:0061621)

GO Molecular Function (8): bisphosphoglycerate mutase activity (GO:0004082), phosphoglycerate mutase activity (GO:0004619), hydrolase activity (GO:0016787), identical protein binding (GO:0042802), catalytic activity (GO:0003824), protein binding (GO:0005515), isomerase activity (GO:0016853), intramolecular phosphotransferase activity (GO:0016868)

GO Cellular Component (3): nucleus (GO:0005634), cytosol (GO:0005829), extracellular exosome (GO:0070062)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
Glucose metabolism2

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
intramolecular phosphotransferase activity2
catalytic activity2
glucose metabolic process1
hexose biosynthetic process1
phosphoglycerate kinase activity1
phosphoglycerate mutase activity1
phosphopyruvate hydratase activity1
pyruvate kinase activity1
pyruvate metabolic process1
generation of precursor metabolites and energy1
aerobic respiration1
carbohydrate catabolic process1
pyridine nucleotide catabolic process1
glyceraldehyde-3-phosphate dehydrogenase [NAD(P)+] (phosphorylating) activity1
ADP catabolic process1
ATP metabolic process1
nicotinamide nucleotide metabolic process1
muscle contraction1
cell surface receptor signaling pathway1
developmental process involved in reproduction1
male gamete generation1
response to metal ion1
glucokinase activity1
glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity1
glucose catabolic process1
glycolytic process through glucose-6-phosphate1
protein binding1
molecular_function1
binding1
intramolecular transferase activity1
intracellular membrane-bounded organelle1
cytoplasm1
cellular anatomical structure1
extracellular vesicle1

Protein interactions and networks

STRING

2087 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
PGAM2PKMP14618844
PGAM2ENO3P13929741
PGAM2HOXA4Q00056715
PGAM2PKLRP11973713
PGAM2TPI1P00938697
PGAM2PGAM4Q8N0Y7697
PGAM2PGAM1P18669695
PGAM2PFKMP08237656
PGAM2MBP02144649
PGAM2ALDOAP04075634
PGAM2J3KPS3J3KPS3629
PGAM2OGDHQ02218628
PGAM2PYGMP11217627
PGAM2PGK1P00558623
PGAM2GPIP06744609

IntAct

67 interactions, top by confidence:

ABTypeScore
CCM2KRIT1psi-mi:“MI:0914”(association)0.960
SULT1A1SULT2B1psi-mi:“MI:0914”(association)0.830
PGAM2BPGMpsi-mi:“MI:0914”(association)0.740
BPGMPGAM2psi-mi:“MI:0915”(physical association)0.740
CFTRESYT2psi-mi:“MI:0914”(association)0.710
TCIRG1ATP6AP2psi-mi:“MI:0914”(association)0.640
CFTRHAX1psi-mi:“MI:0914”(association)0.610
PGAM2PGAM2psi-mi:“MI:0915”(physical association)0.560
PGAM2CLVS2psi-mi:“MI:0915”(physical association)0.560
PGAM2KATNAL1psi-mi:“MI:0915”(physical association)0.560
PGAM2DYNC1LI1psi-mi:“MI:0915”(physical association)0.560
VASPGTPBP1psi-mi:“MI:0914”(association)0.530
DCAF5PFDN6psi-mi:“MI:0914”(association)0.530
CAMK2DELP1psi-mi:“MI:0914”(association)0.530
PGAM2P4HBpsi-mi:“MI:0915”(physical association)0.400
TNNC2PGAM2psi-mi:“MI:0915”(physical association)0.400
LRRIQ3PGAM2psi-mi:“MI:0915”(physical association)0.400
PXMP4PGAM2psi-mi:“MI:0915”(physical association)0.400
DNAJC4PGAM2psi-mi:“MI:0915”(physical association)0.400
VDAC1PGAM2psi-mi:“MI:0915”(physical association)0.400
PLPP3PGAM2psi-mi:“MI:0915”(physical association)0.400
ENGIGKV2-28psi-mi:“MI:0914”(association)0.350
USP15KRT35psi-mi:“MI:0914”(association)0.350
SH3GLB1psi-mi:“MI:0914”(association)0.350
GABARAPL1psi-mi:“MI:0914”(association)0.350
FAM167AIFT56psi-mi:“MI:0914”(association)0.350
CLEC4EESYT2psi-mi:“MI:0914”(association)0.350

BioGRID (101): PGAM1 (Affinity Capture-MS), PGAM4 (Affinity Capture-MS), BPGM (Affinity Capture-MS), NUTF2 (Co-fractionation), PGAM2 (Co-fractionation), PGAM2 (Co-fractionation), PGAM2 (Co-fractionation), TXN (Co-fractionation), PGAM4 (Affinity Capture-MS), BPGM (Affinity Capture-MS), PGAM1 (Affinity Capture-MS), PGAM2 (Affinity Capture-MS), PGAM2 (Affinity Capture-MS), PGAM2 (Affinity Capture-MS), PGAM2 (Two-hybrid)

ESM2 similar proteins: A1K9B9, A1TTW5, A1UZX9, A1VKR6, A1WBJ3, A2S625, A3MQ23, A3N5B0, A3NR09, A4JI45, A4SDM0, A9BUZ3, B1JZ61, B1Y3R5, B1YNA6, B2JC95, B2SX15, B2VBS6, B3QPN8, B3QVL0, B4EA64, B4S616, B9MEZ2, C5BJ25, C5CWV9, O70250, P15259, P16290, P18669, P25113, Q01YD0, Q0BBK5, Q21YW0, Q2T1H5, Q32KV0, Q39CN6, Q3AU60, Q3JWH7, Q3SZ62, Q5P7N4

Diamond homologs: A0AKV8, A1K9B9, A1KV25, A1TTW5, A1UZX9, A1VKR6, A1WBJ3, A1WWH7, A2RI67, A2S625, A3MQ23, A3N5B0, A3NR09, A4SDM0, A5VB15, A6VLV0, A9BUZ3, A9IFJ0, A9M1A2, B0KBW9, B0RQR7, B0SY17, B2AGP7, B2FHH6, B2SRM8, B2SX15, B3EN99, B3QPN8, B3QVL0, B4RZM6, B4S616, B4SEI0, B4SPL6, B6IYD3, B8DFA5, B8DLN4, B8GYN6, B9MEZ2, C0QV47, C1KXG0

SIGNOR signaling

4 interactions.

AEffectBMechanism
PGAM2“down-regulates quantity”3-phosphonato-D-glycerate(3-)“chemical modification”
PGAM2“up-regulates quantity”2-phosphonato-D-glycerate(3-)“chemical modification”
SIRT2“up-regulates activity”PGAM2deacetylation
PAK1“down-regulates quantity by destabilization”PGAM2phosphorylation

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 79 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

GO biological processes:

GO termPartnersFoldFDR
protein folding79.8×5e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

21 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic3
Likely pathogenic0
Uncertain significance8
Likely benign5
Benign1

Top pathogenic / likely-pathogenic (3)

Variant IDHGVSClassification
1073237NM_000290.4(PGAM2):c.331C>T (p.Gln111Ter)Pathogenic
2055208NM_000290.4(PGAM2):c.234G>A (p.Trp78Ter)Pathogenic
2422820NC_000007.13:g.(?44102363)(44105128_?)delPathogenic

SpliceAI

278 predictions. Top by Δscore:

VariantEffectΔscore
7:44064828:TCA:Tdonor_loss1.0000
7:44064829:CA:Cdonor_loss1.0000
7:44064830:ACCT:Adonor_loss1.0000
7:44064831:C:Adonor_loss1.0000
7:44065008:CGCTC:Cacceptor_gain1.0000
7:44065110:GCCCA:Gdonor_loss1.0000
7:44065111:CCCAC:Cdonor_loss1.0000
7:44065112:CCACC:Cdonor_loss1.0000
7:44065113:CAC:Cdonor_loss1.0000
7:44065114:A:ATdonor_loss1.0000
7:44065115:CCT:Cdonor_loss1.0000
7:44062926:CATCC:Cacceptor_gain0.9900
7:44062928:TCC:Tacceptor_gain0.9900
7:44062929:CCC:Cacceptor_gain0.9900
7:44062930:CCTA:Cacceptor_gain0.9900
7:44062937:C:CTacceptor_gain0.9900
7:44062938:G:Tacceptor_gain0.9900
7:44064830:A:ACdonor_gain0.9900
7:44064830:ACCTT:Adonor_gain0.9900
7:44064831:C:CCdonor_gain0.9900
7:44064831:CCTT:Cdonor_gain0.9900
7:44064831:CCTTC:Cdonor_gain0.9900
7:44064834:T:Adonor_gain0.9900
7:44065010:CTC:Cacceptor_gain0.9900
7:44065011:TCCT:Tacceptor_loss0.9900
7:44065013:C:CCacceptor_gain0.9900
7:44065014:T:Aacceptor_loss0.9900
7:44065115:CCTTG:Cdonor_gain0.9900
7:44062928:TCCC:Tacceptor_loss0.9800
7:44062929:CC:Cacceptor_gain0.9800

AlphaMissense

1661 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
7:44064863:G:CN188K1.000
7:44064863:G:TN188K1.000
7:44065183:C:AR116M1.000
7:44065183:C:GR116T1.000
7:44065230:C:AK100N1.000
7:44065230:C:GK100N1.000
7:44065263:C:AE89D1.000
7:44065263:C:GE89D1.000
7:44065264:T:AE89V1.000
7:44065464:G:CF22L1.000
7:44065464:G:TF22L1.000
7:44065466:A:GF22L1.000
7:44062889:C:AG213W0.999
7:44064867:C:AG187V0.999
7:44064867:C:TG187E0.999
7:44064868:C:AG187W0.999
7:44064868:C:GG187R0.999
7:44064868:C:TG187R0.999
7:44064869:G:CH186Q0.999
7:44064869:G:TH186Q0.999
7:44065180:C:GR117P0.999
7:44065181:G:TR117S0.999
7:44065182:C:AR116S0.999
7:44065182:C:GR116S0.999
7:44065187:A:GW115R0.999
7:44065187:A:TW115R0.999
7:44065231:T:AK100M0.999
7:44065232:T:CK100E0.999
7:44065232:T:GK100Q0.999
7:44065252:C:TG93E0.999

dbSNP variants (sampled 300 via entrez): RS1000192172 (7:44063800 T>C), RS1000268209 (7:44063431 G>A,T), RS1000635929 (7:44064009 T>A), RS1000855245 (7:44064643 C>T), RS1001161504 (7:44064839 G>A,T), RS1001231252 (7:44062712 C>T), RS1001599028 (7:44062487 C>T), RS1002043242 (7:44064230 C>T), RS1002477505 (7:44064581 G>A,C), RS1002858188 (7:44066705 T>C,G), RS1003175850 (7:44066978 T>C), RS1003346363 (7:44066491 C>T), RS1003499099 (7:44065653 G>A,C), RS1003662509 (7:44062994 T>C,G), RS1003693539 (7:44063366 C>A,T)

Disease associations

OMIM: gene MIM:612931 | disease phenotypes: MIM:261670

GenCC curated gene-disease

DiseaseClassificationInheritance
glycogen storage disease due to phosphoglycerate mutase deficiencyStrongAutosomal recessive

Mondo (1): glycogen storage disease due to phosphoglycerate mutase deficiency (MONDO:0009865)

Orphanet (1): Glycogen storage disease due to phosphoglycerate mutase deficiency (Orphanet:97234)

HPO phenotypes

9 total (9 of 9 shown, HPO-id order):

HPOTerm
HP:0000007Autosomal recessive inheritance
HP:0000083Renal insufficiency
HP:0002913Myoglobinuria
HP:0003198Myopathy
HP:0003201Rhabdomyolysis
HP:0003236Elevated circulating creatine kinase concentration
HP:0003546Exercise intolerance
HP:0003710Exercise-induced muscle cramps
HP:0003738Exercise-induced myalgia

GWAS associations

0 associations (top):

MeSH disease descriptors (1)

DescriptorNameTree numbers
C536176Dimauro disease (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

15 total (human), top 15 by PubMed support.

ChemicalActions (top 5)PubMed papers
Doxorubicinaffects expression, decreases expression3
Valproic Acidaffects cotreatment, increases expression, increases methylation2
Particulate Matterincreases abundance, increases expression, decreases expression2
sodium arseniteincreases expression1
ferrous chloridedecreases expression1
Sunitinibdecreases expression1
Air Pollutantsincreases abundance, increases expression1
Benzo(a)pyreneaffects methylation, increases methylation1
Estradiolincreases expression, affects cotreatment1
Hydralazineaffects cotreatment, increases expression1
Smokedecreases expression1
Triclosandecreases expression1
Urethaneincreases expression1
Lactic Acidaffects expression1
Nanotubes, Carbonaffects expression1

Clinical trials (associated diseases)

1 trials via MONDO — disease-level, not drug-specific.

TrialPhaseStatusTitle
NCT02635269Not specifiedUNKNOWNFat and Sugar Metabolism During Exercise in Patients With Metabolic Myopathy

About this page

Generated deterministically by Sugi Atlas from primary biomedical databases via BioBTree. Every record on this page traces to a primary source.

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This page pulls from 75 datasets indexed by BioBTree:

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