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    GYG1 glycogenin 1 [ Homo sapiens (human) ]

    Gene ID: 2992, updated on 27-Nov-2024

    Summary

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    Official Symbol
    GYG1provided by HGNC
    Official Full Name
    glycogenin 1provided by HGNC
    Primary source
    HGNC:HGNC:4699
    See related
    Ensembl:ENSG00000163754 MIM:603942; AllianceGenome:HGNC:4699
    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
    GYG; GSD15
    Summary
    This gene encodes a member of the glycogenin family. Glycogenin is a glycosyltransferase that catalyzes the formation of a short glucose polymer from uridine diphosphate glucose in an autoglucosylation reaction. This reaction is followed by elongation and branching of the polymer, catalyzed by glycogen synthase and branching enzyme, to form glycogen. This gene is expressed in muscle and other tissues. Mutations in this gene result in glycogen storage disease XV. This gene has pseudogenes on chromosomes 1, 8 and 13 respectively. Alternatively spliced transcript variants encoding different isoforms have been identified.[provided by RefSeq, Sep 2010]
    Expression
    Broad expression in bone marrow (RPKM 53.8), testis (RPKM 49.1) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See GYG1 in Genome Data Viewer
    Location:
    3q24
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (148991540..149031775)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (151742259..151782489)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (148709327..148749562)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107986045 Neighboring gene NANOG hESC enhancer GRCh37_chr3:148675298-148675799 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14802 Neighboring gene Sharpr-MPRA regulatory region 13788 Neighboring gene ubiquilin 4 pseudogene 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:148726195-148726695 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:148733083-148733712 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:148733713-148734340 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:148738584-148739234 Neighboring gene helicase like transcription factor Neighboring gene OCT4-NANOG-H3K27ac hESC enhancers GRCh37_chr3:148803647-148804164 and GRCh37_chr3:148804165-148804682 Neighboring gene HLTF antisense RNA 1 Neighboring gene mediator complex subunit 28 pseudogene 2 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:148847467-148847966 Neighboring gene HPS3 biogenesis of lysosomal organelles complex 2 subunit 1 Neighboring gene ceruloplasmin

    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. A new muscle glycogen storage disease associated with glycogenin-1 deficiency. Malfatti E, et al. Ann Neurol, 2014 Dec. PMID 25272951, Free PMC Article
    2. Characterization of rabbit skeletal muscle glycogenin. Tyrosine 194 is essential for function. Cao Y, et al. J Biol Chem, 1993 Jul 15. PMID 8325847
    3. The human intron-containing gene for glycogenin maps to chromosome 3, band q24. Lomako J, et al. Genomics, 1996 May 1. PMID 8661012
    4. Molecular pathogenesis of a new glycogenosis caused by a glycogenin-1 mutation. Nilsson J, et al. Biochim Biophys Acta, 2012 Apr. PMID 22198226
    5. Late-onset polyglucosan body myopathy in five patients with a homozygous mutation in GYG1. Akman HO, et al. Neuromuscul Disord, 2016 Jan. PMID 26652229, Free PMC Article

    See all (59) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The structural mechanism of human glycogen synthesis by the GYS1-GYG1 complex.
      Title: The structural mechanism of human glycogen synthesis by the GYS1-GYG1 complex.
    2. Crystal structure and mutational analysis of the human TRIM7 B30.2 domain provide insights into the molecular basis of its binding to glycogenin-1.
      Title: Crystal structure and mutational analysis of the human TRIM7 B30.2 domain provide insights into the molecular basis of its binding to glycogenin-1.
    3. Glycogenin is at the core of glycogen's structure and initiates its glucopolymerization.[review]
      Title: From the seminal discovery of proteoglycogen and glycogenin to emerging knowledge and research on glycogen biology.
    4. palladium-mediated enzyme activation suggests multiphase initiation of glycogenesis
      Title: Palladium-mediated enzyme activation suggests multiphase initiation of glycogenesis.
    5. we screened the susceptibility loci for Myocardial infarction (MI) using exome sequencing and validated candidate variants in replication sets. We identified that three genes (GYG1, DIS3L and DDRGK1) were associated with MI at the discovery and replication stages.
      Title: Genome-based exome sequencing analysis identifies GYG1, DIS3L and DDRGK1 are associated with myocardial infarction in Koreans.
    6. We present functional evidence for the pathogenicity of a novel GYG1 missense mutation located in the substrate binding domain.
      Title: Polyglucosan myopathy and functional characterization of a novel GYG1 mutation.
    7. This study found a single homozygous intronic mutation of GYG1 harbored by five patients, who, except for two siblings, appear to be unrelated but all five live in central or south Sardinian villages.
      Title: Late-onset polyglucosan body myopathy in five patients with a homozygous mutation in GYG1.
    8. Depletion of glycogenin-1 and impaired interaction with glycogen synthase underlies a new form of glycogen storage disease.
      Title: A new muscle glycogen storage disease associated with glycogenin-1 deficiency.
    9. The glucosylation of glycogenin-2 was enhanced to 2-4 glucose units by the co-presence of enzymatically active glycogenin-1.
      Title: LC-MS/MS characterization of combined glycogenin-1 and glycogenin-2 enzymatic activities reveals their self-glucosylation preferences.
    10. results explain the glycogen depletion in the patient expressing only Thr83Met glycogenin-1 and why heterozygous carriers without clinical symptoms show a small proportion of unglucosylated glycogenin-1
      Title: Molecular pathogenesis of a new glycogenosis caused by a glycogenin-1 mutation.
    Submit: New GeneRIF Correction See all GeneRIFs (13)

    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 XV
    MedGen: C3150754 OMIM: 613507 GeneReviews: Not available
    		Compare labs
    Polyglucosan body myopathy type 2
    MedGen: C4015452 OMIM: 616199 GeneReviews: Not available
    		Compare labs

    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 glycogenin glucosyltransferase activity EXP
    Inferred from Experiment
    more info
    		 PubMed 
    enables glycogenin glucosyltransferase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables glycosyltransferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables manganese ion binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein homodimerization activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in glycogen biosynthetic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in glycogen biosynthetic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in glycogen biosynthetic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in glycogen biosynthetic process TAS
    Traceable Author Statement
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in cytoplasm ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in cytoplasm ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    located_in extracellular region TAS
    Traceable Author Statement
    more info
    		  
    located_in ficolin-1-rich granule lumen TAS
    Traceable Author Statement
    more info
    		  
    located_in lysosomal lumen TAS
    Traceable Author Statement
    more info
    		  
    located_in membrane HDA PubMed 
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in secretory granule lumen TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    glycogenin-1
    Names
    GN-1
    glycogenin glucosyltransferase
    NP_001171649.1
    NP_001171650.1
    NP_004121.2
    XP_016861764.1
    XP_016861765.1
    XP_054202365.1
    XP_054202366.1

    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_027677.2 RefSeqGene

      Range
      5002..45237
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001184720.2 → NP_001171649.1  glycogenin-1 isoform 2

      See identical proteins and their annotated locations for NP_001171649.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an in-frame exon in the 3' CDS, as compared to variant 1. The resulting isoform (2) lacks an internal segment in the C-terminal region, as compared to isoform 1.
      Source sequence(s)
      AA191440, AC021059, BC000033, U31525
      Consensus CDS
      CCDS54654.1
      UniProtKB/TrEMBL
      Q8N5Y3
      Related
      ENSP00000296048.6, ENST00000296048.10
      Conserved Domains (2) summary
      cd02537
      Location:4 → 254
      GT8_Glycogenin; Glycogenin belongs the GT 8 family and initiates the biosynthesis of glycogen
      COG1442
      Location:92 → 221
      RfaJ; Lipopolysaccharide biosynthesis protein, LPS:glycosyltransferase [Cell wall/membrane/envelope biogenesis]

    2. NM_001184721.2 → NP_001171650.1  glycogenin-1 isoform 3

      See identical proteins and their annotated locations for NP_001171650.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks two consecutive exons in the 3' CDS, as compared to variant 1. The resulting isoform (3) is shorter and has a different C-terminus, as compared to isoform 1.
      Source sequence(s)
      AA191440, AC021059, BG702275, X79537
      Consensus CDS
      CCDS54655.1
      UniProtKB/Swiss-Prot
      P46976
      Related
      ENSP00000420683.1, ENST00000484197.5
      Conserved Domains (1) summary
      cd02537
      Location:4 → 201
      GT8_Glycogenin; Glycogenin belongs the GT 8 family and initiates the biosynthesis of glycogen

    3. NM_004130.4 → NP_004121.2  glycogenin-1 isoform 1

      See identical proteins and their annotated locations for NP_004121.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AA191440, AC021059, AF087942, BG702275
      Consensus CDS
      CCDS3139.1
      UniProtKB/Swiss-Prot
      D3DNH0, D3DNH1, D3DNH2, P46976, Q6FHZ1, Q9UNV0
      UniProtKB/TrEMBL
      B2R5R5
      Related
      ENSP00000340736.4, ENST00000345003.9
      Conserved Domains (2) summary
      cd02537
      Location:4 → 254
      GT8_Glycogenin; Glycogenin belongs the GT 8 family and initiates the biosynthesis of glycogen
      COG1442
      Location:92 → 221
      RfaJ; Lipopolysaccharide biosynthesis protein, LPS:glycosyltransferase [Cell wall/membrane/envelope biogenesis]

    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_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      148991540..149031775
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017006275.2 → XP_016861764.1  glycogenin-1 isoform X1

      UniProtKB/TrEMBL
      Q8N5Y3

    2. XM_017006276.2 → XP_016861765.1  glycogenin-1 isoform X2

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      151742259..151782489
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054346390.1 → XP_054202365.1  glycogenin-1 isoform X1

    2. XM_054346391.1 → XP_054202366.1  glycogenin-1 isoform X2

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P46976.4 GenPept UniProtKB/Swiss-Prot:P46976

    Gene LinkOut

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

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