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

    Gene ID: 5837, updated on 10-Dec-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
    mouse all
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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_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (64746389..64760715, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (64739618..64754020, complement)
    RS_2024_09 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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    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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    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
    		not available

    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)

    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 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 maltodextrin 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_2024_08

    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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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