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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
  • EC 2.4.1.1 4 56
  • Glycogen Storage Disease Type V 2
  • Phosphorylase, Glycogen; Muscle 2
  • Phosphorylase, Glycogen, Muscle 3
  • McArdle Syndrome 2

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 Glycosaminoglycan metabolism and Glycogen Metabolism. 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
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH11I064758 Promoter/Enhancer 1.8 EPDnew Ensembl ENCODE dbSUPER 550.8 -1.6 -1565 7 PKNOX1 ARID4B SIN3A FEZF1 ZNF2 POLR2B GLIS2 ZNF143 RUNX3 DEK PYGM GC11P064762 MEN1 SF1 POLA2 ZFPL1 PCNX3 VPS51 ENSG00000257086 SYVN1
GH11I064553 Promoter/Enhancer 1.8 EPDnew FANTOM5 Ensembl ENCODE 5.4 +205.8 205817 3.2 HDAC1 RB1 ARID4B ZNF48 ZSCAN9 RAD21 RARA ARID2 ZNF366 ZNF143 SLC22A11 PYGM MEN1 NRXN2 MAJIN GC11P064541
GH11I065402 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
GH11I064717 Enhancer 0.5 dbSUPER 11.8 +42.8 42806 1.7 CTCF ZFHX2 MAX KDM1A ZIC2 EGR2 NRXN2 RASGRP2 PYGM ENSG00000237410
GH11I064697 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:

Genomic Locations for PYGM Gene

Genomic Locations for PYGM Gene
chr11:64,746,389-64,760,715
(GRCh38/hg38)
Size:
14,327 bases
Orientation:
Minus strand
chr11:64,513,861-64,528,187
(GRCh37/hg19)

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:
    P11217-PYGM_HUMAN
    Recommended name:
    Glycogen phosphorylase, muscle form
    Protein Accession:
    P11217
    Secondary Accessions:
    • A0AVK1
    • A6NDY6

    Protein attributes for PYGM Gene

    Size:
    842 amino acids
    Molecular mass:
    97092 Da
    Cofactor:
    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

    UniProtKB/Swiss-Prot:

neXtProt entry for PYGM Gene

Selected DME Specific Peptides for PYGM Gene

P11217:
  • TLVKDRNV
  • DTQVVLA
  • TLYNRIK
  • IPELMRI
  • LKDFNVG
  • KCQEKVS
  • YAREIWGVEP
  • EEADDWLR
  • GKELRLKQ
  • GNPWEKARPEF
  • IGDVVNHDP
  • VAIQLNDTHP
  • APNDFNL
  • RWIRTQQHYY
  • DPKRIYYLSLE
  • GYGIRYEFGIF
  • GRTLQNTMVNL
  • HDRFKVFADYE
  • HMAKMII
  • TNGITPRRW
  • KRINMAHLCI
  • PEALERW
  • HAVNGVA
  • VGDRLRVIFLENYRVSL
  • YDTPVPGY
  • DLSEQIS
  • VNTMRLWSAKAP
  • KQISVRG
  • EYKVHINPNSLFD
  • LGNGGLGRLA
  • YIQAVLDRNLAENI
  • GYNAQEYYDRIPELR
  • NISRVLYP
  • FKDFYELEP
  • LDSMATL
  • NKTNGIT
  • RTVMIGGKA
  • FSSDRTI
  • EASGTGNMK
  • RDYYFALA
  • DVDRLRRMS
  • KRIHEYKRQL
  • WLRYGNPWEKARPE
  • NGALTIGT
  • FGCRDPVRT
  • LPRHLQII
  • ELRLKQEYF
  • FIFGMRVEDV
  • IFLENYRVSLAEKVIPA

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:

Domains & Families for PYGM Gene

Gene Families for PYGM Gene

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

Suggested Antigen Peptide Sequences for PYGM Gene

Graphical View of Domain Structure for InterPro Entry

P11217

UniProtKB/Swiss-Prot:

PYGM_HUMAN :
  • Belongs to the glycogen phosphorylase family.
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

GENATLAS Biochemistry:
phosphorylase,glycogen catabolism,muscle
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.
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.

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

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

Localization for PYGM Gene

Subcellular locations from

COMPARTMENTS
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,IDA 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: HMDB and Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
amylose
  • (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
9005-82-7
Phosphate
  • NFB Orthophosphate
  • O-Phosphoric acid
  • Ortho-phosphate
  • Orthophosphate (PO43-)
  • Orthophosphate(3-)
14265-44-2
genes like me logo Genes that share compounds with PYGM: view

Transcripts for PYGM Gene

Unigene Clusters for PYGM Gene

Phosphorylase, glycogen, muscle:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

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

No ASD Table

Relevant External Links for PYGM Gene

GeneLoc Exon Structure for
PYGM
ECgene alternative splicing isoforms for
PYGM

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, PaxDb, MaxQB, and MOPED for PYGM Gene



NURSA nuclear receptor signaling pathways regulating expression of PYGM Gene:

PYGM

SOURCE GeneReport for Unigene cluster for PYGM Gene:

Hs.154084

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
Systems:
  • skeletal muscle
  • urinary
Regions:
Abdomen:
  • kidney
genes like me logo Genes that share expression patterns with PYGM: view

Primer Products

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
chimpanzee
(Pan troglodytes)
Mammalia PYGM 33 34
  • 99.6 (n)
cow
(Bos Taurus)
Mammalia PYGM 33 34
  • 91.96 (n)
dog
(Canis familiaris)
Mammalia PYGM 33 34
  • 91.21 (n)
mouse
(Mus musculus)
Mammalia Pygm 33 16 34
  • 89.47 (n)
rat
(Rattus norvegicus)
Mammalia Pygm 33
  • 89.03 (n)
oppossum
(Monodelphis domestica)
Mammalia PYGM 34
  • 89 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia PYGM 34
  • 78 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia PYGM 34
  • 83 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100491051 33
  • 74.73 (n)
zebrafish
(Danio rerio)
Actinopterygii pygmb 34
  • 82 (a)
OneToMany
pygma 33 34
  • 76.11 (n)
fruit fly
(Drosophila melanogaster)
Insecta GlyP 35 33 34
  • 71.79 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP007939 33
  • 69.28 (n)
worm
(Caenorhabditis elegans)
Secernentea T22F3.3 33 34
  • 67.62 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes GPH1 34 36
  • 44 (a)
OneToMany
thale cress
(Arabidopsis thaliana)
eudicotyledons PHS2 33
  • 51.84 (n)
rice
(Oryza sativa)
Liliopsida Os01g0851700 33
  • 52.4 (n)
barley
(Hordeum vulgare)
Liliopsida Hv.4591 33
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 61 (a)
OneToMany
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

ENSEMBL:
Gene Tree for PYGM (if available)
TreeFam:
Gene Tree for PYGM (if available)

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

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)
PYGM
SNPedia medical, phenotypic, and genealogical associations of SNPs for
PYGM

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

(16) 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

UniProtKB/Swiss-Prot

PYGM_HUMAN
  • 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
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
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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