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GYG1 glycogenin 1 [ Homo sapiens (human) ]

Gene ID: 2992, updated on 3-Apr-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
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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_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (148991540..149031775)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (151742259..151782489)
105.20220307 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. From the seminal discovery of proteoglycogen and glycogenin to emerging knowledge and research on glycogen biology. Curtino JA, et al. Biochem J, 2019 Nov 15. PMID 31689353
  2. Polyglucosan myopathy and functional characterization of a novel GYG1 mutation. Hedberg-Oldfors C, et al. Acta Neurol Scand, 2018 Mar. PMID 29143313
  3. 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
  4. A new muscle glycogen storage disease associated with glycogenin-1 deficiency. Malfatti E, et al. Ann Neurol, 2014 Dec. PMID 25272951, Free PMC Article
  5. Molecular pathogenesis of a new glycogenosis caused by a glycogenin-1 mutation. Nilsson J, et al. Biochim Biophys Acta, 2012 Apr. PMID 22198226

See all (56) 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)

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 UDP-alpha-D-glucose:glucosyl-glycogenin alpha-D-glucosyltransferase activity IDA
Inferred from Direct Assay
more info
 PubMed 
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
  
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 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_2023_10

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

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