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PYGM glycogen phosphorylase, muscle associated [ Homo sapiens (human) ]

Gene ID: 5837, updated on 5-Mar-2024

Summary

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Official Symbol
PYGMprovided by HGNC
Official Full Name
glycogen phosphorylase, muscle associatedprovided by HGNC
Primary source
HGNC:HGNC:9726
See related
Ensembl:ENSG00000068976 MIM:608455; AllianceGenome:HGNC:9726
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
GSD5
Summary
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]
Expression
Biased expression in esophagus (RPKM 41.2), prostate (RPKM 24.2) and 6 other tissues See more
Orthologs
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Genomic context

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See PYGM in Genome Data Viewer
Location:
11q13.1
Exon count:
20
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (64746389..64760715, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (64739618..64754020, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (64513861..64528187, complement)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene neurexin 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:64414407-64414908 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:64414909-64415408 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:64415526-64416494 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:64419195-64419694 Neighboring gene NRXN2 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:64421037-64421537 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4906 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:64424149-64424650 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:64424651-64425150 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr11:64426961-64428160 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:64455312-64456232 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4907 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:64480596-64481379 Neighboring gene Sharpr-MPRA regulatory region 4107 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3481 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4908 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:64492769-64493607 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:64506559-64507108 Neighboring gene RAS guanyl releasing protein 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3482 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3483 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3484 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3485 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3486 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3487 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:64520964-64521574 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:64525447-64526151 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:64526152-64526855 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:64526856-64527560 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:64527561-64528263 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4909 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4910 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:64530587-64531460 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:64532334-64533208 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:64533209-64534081 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:64534082-64534955 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4914 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3488 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:64545791-64546392 Neighboring gene splicing factor 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:64557481-64557982 Neighboring gene Sharpr-MPRA regulatory region 11124 Neighboring gene MPRA-validated peak1298 silencer Neighboring gene Sharpr-MPRA regulatory region 2965 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4916 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4917 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3490 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3491 Neighboring gene mitogen-activated protein kinase kinase kinase kinase 2

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Whole-exome sequencing detects PYGM variants in two adults with McArdle disease. Thomas-Wilson A, et al. Cold Spring Harb Mol Case Stud, 2022 Feb. PMID 35022222, Free PMC Article
  2. Muscle Glycogen Phosphorylase and Its Functional Partners in Health and Disease. Migocka-Patrzałek M, et al. Cells, 2021 Apr 13. PMID 33924466, Free PMC Article
  3. PYGM mRNA expression in McArdle disease: Demographic, clinical, morphological and genetic features. Carvalho AAS, et al. PLoS One, 2020. PMID 32735634, Free PMC Article
  4. A New Glycogen Storage Disease Caused by a Dominant PYGM Mutation. Echaniz-Laguna A, et al. Ann Neurol, 2020 Aug. PMID 32386344
  5. Missense mutations have unexpected consequences: The McArdle disease paradigm. GarcĂ­a-Consuegra I, et al. Hum Mutat, 2018 Oct. PMID 30011114

See all (100) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Whole-exome sequencing detects PYGM variants in two adults with McArdle disease.
    Title: Whole-exome sequencing detects PYGM variants in two adults with McArdle disease.
  2. Muscle Glycogen Phosphorylase and Its Functional Partners in Health and Disease.
    Title: Muscle Glycogen Phosphorylase and Its Functional Partners in Health and Disease.
  3. A New Glycogen Storage Disease Caused by a Dominant PYGM Mutation.
    Title: A New Glycogen Storage Disease Caused by a Dominant PYGM Mutation.
  4. PYGM mRNA expression in McArdle disease: Demographic, clinical, morphological and genetic features.
    Title: PYGM mRNA expression in McArdle disease: Demographic, clinical, morphological and genetic features.
  5. The effect of muscle glycogen phosphorylase (Pygm) knockdown on zebrafish morphology.
    Title: The effect of muscle glycogen phosphorylase (Pygm) knockdown on zebrafish morphology.
  6. Bioinformatics-based discovery of PYGM and TNNC2 as potential biomarkers of head and neck squamous cell carcinoma.
    Title: Bioinformatics-based discovery of PYGM and TNNC2 as potential biomarkers of head and neck squamous cell carcinoma.
  7. These findings explain the lack of PYGM genotype-phenotype correlation and have important implications for the design of molecular-based therapeutic approaches.
    Title: Missense mutations have unexpected consequences: The McArdle disease paradigm.
  8. Results show that PYGM and RAC1 are altered in the dorsolateral prefrontal cortex in chronic schizophrenia and are controlled by NMDA signaling in the rodent cortex and cortical astrocytes suggesting an altered NMDA-dependent glycogenolysis in astrocytes in schizophrenia.
    Title: The glial phosphorylase of glycogen isoform is reduced in the dorsolateral prefrontal cortex in chronic schizophrenia.
  9. This report expands the phenotype and genotype of McArdle disease and suggests that PYGM mutations should be looked for in patients with very late-onset myopathy with no previous history of exercise intolerance
    Title: Novel variant in the PYGM gene causing late-onset limb-girdle myopathy, ptosis, and camptocormia.
  10. Because the NMD mechanism does not seem to operate in nonspecific cells, PBMCs were more suitable than muscle biopsies for detecting the pathogenicity of some PYGM mutations, notably the silent mutation whose effect in the splicing of intron 6 was unnoticed in previous muscle transcriptomic studies
    Title: Taking advantage of an old concept, "illegitimate transcription", for a proposed novel method of genetic diagnosis of McArdle disease.
Submit: New GeneRIF Correction See all GeneRIFs (40)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Glycogen storage disease, type V
MedGen: C0017924 OMIM: 232600 GeneReviews: Glycogen Storage Disease Type V
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EBI GWAS Catalog

Description
Genome-wide association study for serum urate concentrations and gout among African Americans identifies genomic risk loci and a novel URAT1 loss-of-function allele.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables SHG alpha-glucan phosphorylase activity IEA
Inferred from Electronic Annotation
more info
  
enables glycogen phosphorylase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables glycogen phosphorylase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables glycogen phosphorylase activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables linear malto-oligosaccharide phosphorylase activity IEA
Inferred from Electronic Annotation
more info
  
enables nucleotide binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables pyridoxal phosphate binding IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in glycogen catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in glycogen catabolic process IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in glycogen catabolic process IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in glycogen metabolic process TAS
Traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytosol TAS
Traceable Author Statement
more info
  
located_in extracellular exosome HDA PubMed 

General protein information

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Preferred Names
glycogen phosphorylase, muscle form
Names
myophosphorylase
phosphorylase, glycogen, muscle
NP_001158188.1
NP_005600.1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_013018.1 RefSeqGene

    Range
    5742..19318
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001164716.1 → NP_001158188.1  glycogen phosphorylase, muscle form isoform 2

    See identical proteins and their annotated locations for NP_001158188.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks two exons uses an alternate in-frame splice site in the 5' coding region compared to variant 1. The resulting protein (isoform 2) is shorter compared to isoform 1.
    Source sequence(s)
    AK056607, AP001462, BM987822
    Consensus CDS
    CCDS53659.1
    UniProtKB/TrEMBL
    B4DRW6
    Related
    ENSP00000366650.3, ENST00000377432.7
    Conserved Domains (2) summary
    cd04300
    Location:29 → 740
    GT1_Glycogen_Phosphorylase; This is a family of oligosaccharide phosphorylases. It includes yeast and mammalian glycogen phosphorylases, plant starch/glucan phosphorylase, as well as the maltodextrin phosphorylases of bacteria. The members of this family catalyze the breakdown of ...
    TIGR02093
    Location:32 → 740
    P_ylase; glycogen/starch/alpha-glucan phosphorylases

  2. NM_005609.4 → NP_005600.1  glycogen phosphorylase, muscle form isoform 1

    See identical proteins and their annotated locations for NP_005600.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer protein (isoform 1).
    Source sequence(s)
    AJ572752, BC130514
    Consensus CDS
    CCDS8079.1
    UniProtKB/Swiss-Prot
    A0AVK1, A6NDY6, P11217
    UniProtKB/TrEMBL
    A0A0M4FEM1, B2RB32
    Related
    ENSP00000164139.3, ENST00000164139.4
    Conserved Domains (2) summary
    cd04300
    Location:29 → 828
    GT1_Glycogen_Phosphorylase; This is a family of oligosaccharide phosphorylases. It includes yeast and mammalian glycogen phosphorylases, plant starch/glucan phosphorylase, as well as the maltodextrin phosphorylases of bacteria. The members of this family catalyze the breakdown of ...
    TIGR02093
    Location:32 → 828
    P_ylase; glycogen/starch/alpha-glucan phosphorylases

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    64746389..64760715 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    64739618..64754020 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P11217.6 GenPept UniProtKB/Swiss-Prot:P11217

Gene LinkOut

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