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Aliases for PYGM Gene

Aliases for PYGM Gene

  • Glycogen Phosphorylase, Muscle Associated 2 3 5
  • Myophosphorylase 2 3 4
  • Glycogen Phosphorylase, Muscle Form 2 3
  • Phosphorylase, Glycogen, Muscle 3
  • Glycogen Storage Disease Type V 2
  • Phosphorylase, Glycogen; Muscle 2
  • McArdle Syndrome 2
  • EC 4

External Ids for PYGM Gene

Previous GeneCards Identifiers for PYGM Gene

  • GC11M067029
  • GC11M066195
  • GC11M064289
  • GC11M064272
  • GC11M064513
  • GC11M060840

Summaries for PYGM Gene

Entrez Gene Summary for PYGM Gene

  • This gene encodes a muscle enzyme involved in glycogenolysis. Highly similar enzymes encoded by different genes are found in liver and brain. Mutations in this gene are associated with McArdle disease (myophosphorylase deficiency), a glycogen storage disease of muscle. Alternative splicing results in multiple transcript variants.[provided by RefSeq, Sep 2009]

GeneCards Summary for PYGM Gene

PYGM (Glycogen Phosphorylase, Muscle Associated) is a Protein Coding gene. Diseases associated with PYGM include Glycogen Storage Disease V and Glycogen Storage Disease. Among its related pathways are Galactose metabolism and DAG and IP3 signaling. Gene Ontology (GO) annotations related to this gene include nucleotide binding and phosphorylase activity. An important paralog of this gene is PYGB.

UniProtKB/Swiss-Prot for PYGM Gene

  • Phosphorylase is an important allosteric enzyme in carbohydrate metabolism. Enzymes from different sources differ in their regulatory mechanisms and in their natural substrates. However, all known phosphorylases share catalytic and structural properties.

Additional gene information for PYGM Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PYGM Gene

Genomics for PYGM Gene

GeneHancer (GH) Regulatory Elements for PYGM Gene

Promoters and enhancers for PYGM Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH11J064758 Promoter/Enhancer 1.8 EPDnew Ensembl ENCODE dbSUPER 650.7 -1.6 -1565 7 PKNOX1 ARID4B SIN3A FEZF1 ZNF2 POLR2B GLIS2 ZNF143 RUNX3 DEK GC11P064762 PYGM KAT5 MEN1 SF1 POLA2 ZFPL1 DPF2 PCNX3 VPS51
GH11J064553 Promoter/Enhancer 1.8 EPDnew FANTOM5 Ensembl ENCODE 5.4 +205.8 205817 3.2 ARID4B ZNF48 ARID2 ZNF143 DEK SP5 REST KAT8 ATF4 SMARCA4 SLC22A11 PYGM MEN1 NRXN2 MAJIN GC11P064541
GH11J065402 Enhancer 1.2 Ensembl ENCODE dbSUPER 5.1 -643.3 -643316 2.3 SOX13 KLF1 TEAD4 MAX CEBPG RARA ZKSCAN1 TCF12 CTBP1 POLR2A NEAT1 PYGM CDC42BPG GC11P065418 FRMD8
GH11J064717 Enhancer 0.5 dbSUPER 11.8 +42.8 42806 1.7 CTCF ZNF768 ZFHX2 MAX KDM1A ZIC2 EGR2 NRXN2 RASGRP2 PYGM ENSG00000237410
GH11J064697 Enhancer 0.5 dbSUPER 11.5 +63.2 63154 1.1 RFX1 NFATC1 REST PRDM1 NRXN2 RASGRP2 PYGM ENSG00000237410 SLC22A12 MIR1237 ENSG00000269038
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around PYGM on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PYGM gene promoter:
  • ATF
  • AREB6
  • YY1
  • GATA-2
  • Ik-2
  • CREB
  • deltaCREB
  • Pax-5
  • NF-1
  • Sox9

Genomic Locations for PYGM Gene

Genomic Locations for PYGM Gene
14,327 bases
Minus strand
14,327 bases
Minus strand

Genomic View for PYGM Gene

Genes around PYGM on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PYGM Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PYGM Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PYGM Gene

Proteins for PYGM Gene

  • Protein details for PYGM Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Glycogen phosphorylase, muscle form
    Protein Accession:
    Secondary Accessions:
    • A0AVK1
    • A6NDY6

    Protein attributes for PYGM Gene

    842 amino acids
    Molecular mass:
    97092 Da
    Name=pyridoxal 5-phosphate; Xref=ChEBI:CHEBI:597326;
    Quaternary structure:
    • Homodimer. Dimers associate into a tetramer to form the enzymatically active phosphorylase A.

    Three dimensional structures from OCA and Proteopedia for PYGM Gene

    Alternative splice isoforms for PYGM Gene


neXtProt entry for PYGM Gene

Post-translational modifications for PYGM Gene

  • Phosphorylation of Ser-15 converts phosphorylase B (unphosphorylated) to phosphorylase A.
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for PYGM Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for PYGM Gene

Domains & Families for PYGM Gene

Gene Families for PYGM Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Enzymes
  • Plasma proteins
  • Potential drug targets
  • Predicted intracellular proteins

Protein Domains for PYGM Gene

Suggested Antigen Peptide Sequences for PYGM Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the glycogen phosphorylase family.
  • Belongs to the glycogen phosphorylase family.
genes like me logo Genes that share domains with PYGM: view

Function for PYGM Gene

Molecular function for PYGM Gene

UniProtKB/Swiss-Prot Function:
Phosphorylase is an important allosteric enzyme in carbohydrate metabolism. Enzymes from different sources differ in their regulatory mechanisms and in their natural substrates. However, all known phosphorylases share catalytic and structural properties.
UniProtKB/Swiss-Prot CatalyticActivity:
((1->4)-alpha-D-glucosyl)(n) + phosphate = ((1->4)-alpha-D-glucosyl)(n-1) + alpha-D-glucose 1-phosphate.
UniProtKB/Swiss-Prot EnzymeRegulation:
Activity of phosphorylase is controlled both by allosteric means (through the noncovalent binding of metabolites) and by covalent modification. Thus AMP allosterically activates, whereas ATP, ADP, and glucose-6-phosphate allosterically inhibit, phosphorylase B.
GENATLAS Biochemistry:
phosphorylase,glycogen catabolism,muscle

Enzyme Numbers (IUBMB) for PYGM Gene

Phenotypes From GWAS Catalog for PYGM Gene

Gene Ontology (GO) - Molecular Function for PYGM Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000166 nucleotide binding IEA --
GO:0003824 catalytic activity IEA --
GO:0004645 phosphorylase activity IEA --
GO:0005515 protein binding IPI 25416956
GO:0008184 glycogen phosphorylase activity TAS,IBA --
genes like me logo Genes that share ontologies with PYGM: view
genes like me logo Genes that share phenotypes with PYGM: view

Human Phenotype Ontology for PYGM Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

CRISPR Products

miRNA for PYGM Gene

miRTarBase miRNAs that target PYGM

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PYGM

Clone Products

No data available for Animal Models , Transcription Factor Targets and HOMER Transcription for PYGM Gene

Localization for PYGM Gene

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for PYGM gene
Compartment Confidence
extracellular 5
cytosol 5
mitochondrion 2
nucleus 1

Gene Ontology (GO) - Cellular Components for PYGM Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IBA --
GO:0005829 cytosol TAS --
GO:0070062 extracellular exosome HDA 23533145
genes like me logo Genes that share ontologies with PYGM: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot and Subcellular locations from the Human Protein Atlas (HPA) for PYGM Gene

Pathways & Interactions for PYGM Gene

genes like me logo Genes that share pathways with PYGM: view

Gene Ontology (GO) - Biological Process for PYGM Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005975 carbohydrate metabolic process IEA --
GO:0005977 glycogen metabolic process TAS 9633816
GO:0005980 glycogen catabolic process IEA,TAS --
GO:0008152 metabolic process IEA --
genes like me logo Genes that share ontologies with PYGM: view

No data available for SIGNOR curated interactions for PYGM Gene

Drugs & Compounds for PYGM Gene

(64) Drugs for PYGM Gene - From: DrugBank, DGIdb, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Pyridoxal Phosphate Approved, Investigational Nutra Target, cofactor 17
Gluconolactone Approved, Experimental Pharma 0
Phosphoric acid Approved Pharma 0
Adenosine monophosphate Approved, Investigational Nutra 0
Glucose 1-phosphate Experimental Pharma Target 0

(6) Additional Compounds for PYGM Gene - From: Novoseek and HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
  • (1,4-alpha-D-Glucosyl)N
  • (1,4-alpha-D-Glucosyl)n+1
  • (1,4-alpha-D-Glucosyl)N-1
  • (1,4-alpha-delta-Glucosyl)N
  • (1,4-alpha-delta-Glucosyl)n+1
  • [po(OH)3]
  • Acide phosphorique
  • Acidum phosphoricum
  • H3PO4
  • Orthophosphoric acid
genes like me logo Genes that share compounds with PYGM: view

Transcripts for PYGM Gene

mRNA/cDNA for PYGM Gene

Unigene Clusters for PYGM Gene

Phosphorylase, glycogen, muscle:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PYGM

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for PYGM Gene

No ASD Table

Relevant External Links for PYGM Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for PYGM Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PYGM Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for PYGM Gene

This gene is overexpressed in Muscle - Skeletal (x44.6).

Protein differential expression in normal tissues from HIPED for PYGM Gene

This gene is overexpressed in Blymphocyte (33.9), Tlymphocyte (18.4), and Neutrophil (10.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for PYGM Gene

NURSA nuclear receptor signaling pathways regulating expression of PYGM Gene:


SOURCE GeneReport for Unigene cluster for PYGM Gene:


Evidence on tissue expression from TISSUES for PYGM Gene

  • Muscle(4.9)
  • Heart(4.2)
  • Liver(3.1)
  • Nervous system(3.1)
  • Thyroid gland(2.4)
  • Blood(2.3)
  • Eye(2.3)
  • Pancreas(2.1)

Phenotype-based relationships between genes and organs from Gene ORGANizer for PYGM Gene

Germ Layers:
  • mesoderm
  • skeletal muscle
  • urinary
  • kidney
genes like me logo Genes that share expression patterns with PYGM: view

No data available for Protein tissue co-expression partners and mRNA Expression by UniProt/SwissProt for PYGM Gene

Orthologs for PYGM Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for PYGM Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia PYGM 34 33
  • 99.6 (n)
(Bos Taurus)
Mammalia PYGM 34 33
  • 91.96 (n)
(Canis familiaris)
Mammalia PYGM 34 33
  • 91.21 (n)
(Mus musculus)
Mammalia Pygm 16 34 33
  • 89.47 (n)
(Rattus norvegicus)
Mammalia Pygm 33
  • 89.03 (n)
(Monodelphis domestica)
Mammalia PYGM 34
  • 89 (a)
(Ornithorhynchus anatinus)
Mammalia PYGM 34
  • 78 (a)
(Anolis carolinensis)
Reptilia PYGM 34
  • 83 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100491051 33
  • 74.73 (n)
(Danio rerio)
Actinopterygii pygmb 34
  • 82 (a)
pygma 34 33
  • 76.11 (n)
fruit fly
(Drosophila melanogaster)
Insecta GlyP 34 35 33
  • 71.79 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP007939 33
  • 69.28 (n)
(Caenorhabditis elegans)
Secernentea T22F3.3 34 33
  • 67.62 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes GPH1 36 34
  • 44 (a)
thale cress
(Arabidopsis thaliana)
eudicotyledons PHS2 33
  • 51.84 (n)
(Oryza sativa)
Liliopsida Os01g0851700 33
  • 52.4 (n)
(Hordeum vulgare)
Liliopsida Hv.4591 33
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 61 (a)
Species where no ortholog for PYGM was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for PYGM Gene

Gene Tree for PYGM (if available)
Gene Tree for PYGM (if available)
Evolutionary constrained regions (ECRs) for PYGM: view image

Paralogs for PYGM Gene

Paralogs for PYGM Gene

(2) SIMAP similar genes for PYGM Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with PYGM: view

Variants for PYGM Gene

Sequence variations from dbSNP and Humsavar for PYGM Gene

SNP ID Clin Chr 11 pos Variation AA Info Type
rs1005687078 storage disease 5 (GSD5) [MIM:232600] 64,753,928(-) A/G coding_sequence_variant, missense_variant
rs1056780 benign, Glycogen storage disease, type V 64,753,557(-) G/A/C/T coding_sequence_variant, synonymous_variant
rs1057516259 likely-pathogenic, Glycogen storage disease, type V 64,752,012(-) GGGG/GGG coding_sequence_variant, frameshift
rs1057516329 likely-pathogenic, Glycogen storage disease, type V 64,758,687(-) AGACAGGTAGTAGA/AGA coding_sequence_variant, frameshift, intron_variant
rs1057516349 likely-pathogenic, Glycogen storage disease, type V 64,759,695(-) C/T coding_sequence_variant, stop_gained

Structural Variations from Database of Genomic Variants (DGV) for PYGM Gene

Variant ID Type Subtype PubMed ID
nsv832189 CNV loss 17160897
nsv818842 CNV gain 17921354
nsv528506 CNV loss 19592680
nsv469962 CNV loss 18288195
esv3362683 CNV duplication 20981092
esv3337325 CNV insertion 20981092
esv1261955 CNV insertion 17803354
dgv1967n54 CNV loss 21841781
dgv1965n54 CNV loss 21841781
dgv153n27 CNV loss 19166990

Variation tolerance for PYGM Gene

Residual Variation Intolerance Score: 57.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.67; 72.92% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PYGM Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PYGM Gene

Disorders for PYGM Gene

MalaCards: The human disease database

(15) MalaCards diseases for PYGM Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search PYGM in MalaCards View complete list of genes associated with diseases


  • Glycogen storage disease 5 (GSD5) [MIM:232600]: A metabolic disorder resulting in myopathy characterized by exercise intolerance, cramps, muscle weakness and recurrent myoglobinuria. {ECO:0000269 PubMed:10382911, ECO:0000269 PubMed:10382912, ECO:0000269 PubMed:10417800, ECO:0000269 PubMed:10590419, ECO:0000269 PubMed:10681080, ECO:0000269 PubMed:10714589, ECO:0000269 PubMed:10899452, ECO:0000269 PubMed:11706962, ECO:0000269 PubMed:12031624, ECO:0000269 PubMed:7603523, ECO:0000269 PubMed:8316268, ECO:0000269 PubMed:8535454, ECO:0000269 PubMed:9506549}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for PYGM

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with PYGM: view

No data available for Genatlas for PYGM Gene

Publications for PYGM Gene

  1. Genotype modulators of clinical severity in McArdle disease. (PMID: 17630210) Rubio JC … Lucia A (Neuroscience letters 2007) 3 22 44 58
  2. Molecular heterogeneity of myophosphorylase deficiency (McArdle's disease): a genotype-phenotype correlation study. (PMID: 11706962) Martín MA … Arenas J (Annals of neurology 2001) 3 4 22 58
  3. A missense mutation W797R in the myophosphorylase gene in a Spanish patient with McArdle's disease. (PMID: 10590419) Rubio JC … Arenas J (Muscle & nerve 2000) 3 4 22 58
  4. Mutation analysis in myophosphorylase deficiency (McArdle's disease). (PMID: 9506549) Vorgerd M … Kilimann MW (Annals of neurology 1998) 3 4 22 58
  5. The molecular genetic basis of myophosphorylase deficiency (McArdle's disease). (PMID: 7603523) Tsujino S … DiMauro S (Muscle & nerve. Supplement 1995) 3 4 22 58

Products for PYGM Gene

Sources for PYGM Gene

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