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    GPC3 glypican 3 [ Homo sapiens (human) ]

    Gene ID: 2719, updated on 26-Jul-2015
    Official Symbol
    GPC3provided by HGNC
    Official Full Name
    glypican 3provided by HGNC
    Primary source
    HGNC:HGNC:4451
    See related
    Ensembl:ENSG00000147257; HPRD:02074; MIM:300037; Vega:OTTHUMG00000022448
    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
    SGB; DGSX; MXR7; SDYS; SGBS; OCI-5; SGBS1; GTR2-2
    Summary
    Cell surface heparan sulfate proteoglycans are composed of a membrane-associated protein core substituted with a variable number of heparan sulfate chains. Members of the glypican-related integral membrane proteoglycan family (GRIPS) contain a core protein anchored to the cytoplasmic membrane via a glycosyl phosphatidylinositol linkage. These proteins may play a role in the control of cell division and growth regulation. The protein encoded by this gene can bind to and inhibit the dipeptidyl peptidase activity of CD26, and it can induce apoptosis in certain cell types. Deletion mutations in this gene are associated with Simpson-Golabi-Behmel syndrome, also known as Simpson dysmorphia syndrome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2009]
    Orthologs
    See GPC3 in Epigenomics, MapViewer
    Location:
    Xq26.1
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    107 current GRCh38.p2 (GCF_000001405.28) X NC_000023.11 (133535745..133985646, complement)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (132669773..133119673, complement)

    Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene transcription factor Dp family, member 3 Neighboring gene glypican 4 Neighboring gene ribosomal protein S24 pseudogene 19 Neighboring gene ribosomal protein SA pseudogene 63 Neighboring gene translocase of inner mitochondrial membrane 8B pseudogene 2 Neighboring gene microRNA 363

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated (2012-04-26)

    ClinGen Genome Curation Page
    Haploinsufficency

    Sufficient evidence for dosage pathogenicity (Last evaluated (2012-04-26)

    ClinGen Genome Curation Page

    NHGRI GWAS Catalog

    Description
    Common variants in left/right asymmetry genes and pathways are associated with relative hand skill.
    NHGRI GWA Catalog
    • A tetrasaccharide linker sequence is required for GAG synthesis, organism-specific biosystem (from REACTOME)
      A tetrasaccharide linker sequence is required for GAG synthesis, organism-specific biosystemThe biosynthesis of dermatan sulfate/chondroitin sulfate and heparin/heparan sulfate glycosaminoglycans (GAGs) starts with the formation of a tetrasaccharide linker sequence to the core protein. The ...
    • Chondroitin sulfate/dermatan sulfate metabolism, organism-specific biosystem (from REACTOME)
      Chondroitin sulfate/dermatan sulfate metabolism, organism-specific biosystemChondroitin sulfate (CS) is a sulfated glycosaminoglycan (GAG). CS chains are unbranched polysaccharides of varying length containing two alternating monosaccharides: D-glucuronic acid (GlcA) and N-a...
    • Defective B3GAT3 causes JDSSDHD, organism-specific biosystem (from REACTOME)
      Defective B3GAT3 causes JDSSDHD, organism-specific biosystemGalactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferases1, 2 and 3 (B3GAT1-3) are involved in forming the linker tetrasaccharide present in heparan sulfate and chondroitin sulfate. Defects ...
    • Defective B4GALT7 causes EDS, progeroid type, organism-specific biosystem (from REACTOME)
      Defective B4GALT7 causes EDS, progeroid type, organism-specific biosystemEhlersDanlos syndrome (EDS) is a group of inherited connective tissue disorders, caused by a defect in the synthesis of collagen types I or III. Abnormal collagen renders connective tissues more elas...
    • Defective EXT1 causes exostoses 1, TRPS2 and CHDS, organism-specific biosystem (from REACTOME)
      Defective EXT1 causes exostoses 1, TRPS2 and CHDS, organism-specific biosystemHeparan sulfate (HS) is involved in regulating various body functions functions during development, homeostasis and pathology including blood clotting, angiogenesis and metastasis of cancer cells. Ex...
    • Defective EXT2 causes exostoses 2, organism-specific biosystem (from REACTOME)
      Defective EXT2 causes exostoses 2, organism-specific biosystemHeparan sulfate (HS) is involved in regulating various body functions during development, homeostasis and pathology including blood clotting, angiogenesis and metastasis of cancer cells. Exostosin 1 ...
    • Disease, organism-specific biosystem (from REACTOME)
      Disease, organism-specific biosystemBiological processes are captured in Reactome by identifying the molecules (DNA, RNA, protein, small molecules) involved in them and describing the details of their interactions. From this molecular ...
    • Diseases associated with glycosaminoglycan metabolism, organism-specific biosystem (from REACTOME)
      Diseases associated with glycosaminoglycan metabolism, organism-specific biosystemA number of genetic disorders are caused by mutations in the genes encoding glycosyltransferases and sulfotransferases, enzymes responsible for the synthesis of glycosaminoglycans (GAGs) as well as ...
    • Diseases of glycosylation, organism-specific biosystem (from REACTOME)
      Diseases of glycosylation, organism-specific biosystemDiseases of glycosylation, usually referred to as congenital disorders of glycosylation (CDG), are rare inherited disorders ascribing defects of nucleotide-sugar biosynthesis and transport, glycosylt...
    • Glycosaminoglycan metabolism, organism-specific biosystem (from REACTOME)
      Glycosaminoglycan metabolism, organism-specific biosystemGlycosaminoglycans (GAGs) are long, unbranched polysaccharides containing a repeating disaccharide unit composed of a hexosamine (either N-acetylgalactosamine (GalNAc) or N-acetylglucosamine (GlcNAc)...
    • Glypican 3 network, organism-specific biosystem (from Pathway Interaction Database)
      Glypican 3 network, organism-specific biosystem
      Glypican 3 network
    • Glypican pathway, organism-specific biosystem (from Pathway Interaction Database)
      Glypican pathway, organism-specific biosystem
      Glypican pathway
    • HS-GAG biosynthesis, organism-specific biosystem (from REACTOME)
      HS-GAG biosynthesis, organism-specific biosystemHeparan sulfate (HS) and heparin (sometimes collectively called HS-GAG) consist of the disaccharide unit GlcNAc-GlcA (N-acetylglucosamine-glucuronic acid) connected by a beta1,4 linkage. Heparin is e...
    • HS-GAG degradation, organism-specific biosystem (from REACTOME)
      HS-GAG degradation, organism-specific biosystemLysosomal degradation of glycoproteins is part of the cellular homeostasis of glycosylation (Winchester 2005). The steps outlined below describe the degradation of heparan sulfate/heparin. Complete d...
    • Heparan sulfate/heparin (HS-GAG) metabolism, organism-specific biosystem (from REACTOME)
      Heparan sulfate/heparin (HS-GAG) metabolism, organism-specific biosystemThe acronym HS-GAG is used to describe both heparin and heparan sulfate. HS-GAG is a member of the glycosaminoglycan family and consists of a variably sulfated repeating disaccharide unit, the most ...
    • Metabolism, organism-specific biosystem (from REACTOME)
      Metabolism, organism-specific biosystemMetabolic processes in human cells generate energy through the oxidation of molecules consumed in the diet and mediate the synthesis of diverse essential molecules not taken in the diet as well as th...
    • Metabolism of carbohydrates, organism-specific biosystem (from REACTOME)
      Metabolism of carbohydrates, organism-specific biosystemThese pathways together are responsible for: 1) the extraction of energy and carbon skeletons for biosyntheses from dietary sugars and related molecules; 2) the short-term storage of glucose in the b...
    • Proteoglycans in cancer, organism-specific biosystem (from KEGG)
      Proteoglycans in cancer, organism-specific biosystemMany proteoglycans (PGs) in the tumor microenvironment have been shown to be key macromolecules that contribute to biology of various types of cancer including proliferation, adhesion, angiogenesis a...
    • Proteoglycans in cancer, conserved biosystem (from KEGG)
      Proteoglycans in cancer, conserved biosystemMany proteoglycans (PGs) in the tumor microenvironment have been shown to be key macromolecules that contribute to biology of various types of cancer including proliferation, adhesion, angiogenesis a...
    • Retinoid metabolism and transport, organism-specific biosystem (from REACTOME)
      Retinoid metabolism and transport, organism-specific biosystemVitamin A (all-trans-retinol) must be taken up, either as carotenes from plants, or as retinyl esters from animal food. The most prominent carotenes are alpha-carotene, lycopene, lutein, beta-cryptox...
    • Signal Transduction, organism-specific biosystem (from REACTOME)
      Signal Transduction, organism-specific biosystemSignal transduction is a process in which extracellular signals elicit changes in cell state and activity. Transmembrane receptors sense changes in the cellular environment by binding ligands, such a...
    • Visual phototransduction, organism-specific biosystem (from REACTOME)
      Visual phototransduction, organism-specific biosystemVisual phototransduction is the process by which photon absorption by visual pigment molecules in photoreceptor cells is converted to an electrical cellular response. The events in this process are p...
    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    heparan sulfate proteoglycan binding IEA
    Inferred from Electronic Annotation
    more info
     
    peptidyl-dipeptidase inhibitor activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    anatomical structure morphogenesis TAS
    Traceable Author Statement
    more info
    PubMed 
    anterior/posterior axis specification IEA
    Inferred from Electronic Annotation
    more info
     
    body morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    bone mineralization IEA
    Inferred from Electronic Annotation
    more info
     
    branching involved in ureteric bud morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    carbohydrate metabolic process TAS
    Traceable Author Statement
    more info
     
    cell proliferation involved in metanephros development IEA
    Inferred from Electronic Annotation
    more info
     
    chondroitin sulfate metabolic process TAS
    Traceable Author Statement
    more info
     
    coronary vasculature development IEA
    Inferred from Electronic Annotation
    more info
     
    embryonic hindlimb morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    glycosaminoglycan biosynthetic process TAS
    Traceable Author Statement
    more info
     
    glycosaminoglycan catabolic process TAS
    Traceable Author Statement
    more info
     
    glycosaminoglycan metabolic process TAS
    Traceable Author Statement
    more info
     
    lung development IEA
    Inferred from Electronic Annotation
    more info
     
    mesenchymal cell proliferation involved in ureteric bud development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    mesonephric duct morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    negative regulation of epithelial cell proliferation IEA
    Inferred from Electronic Annotation
    more info
     
    negative regulation of growth IEA
    Inferred from Electronic Annotation
    more info
     
    negative regulation of peptidase activity IEA
    Inferred from Electronic Annotation
    more info
     
    negative regulation of smoothened signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    osteoclast differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    phototransduction, visible light TAS
    Traceable Author Statement
    more info
     
    positive regulation of BMP signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of endocytosis IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of glucose import IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of protein catabolic process IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of smoothened signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    retinoid metabolic process TAS
    Traceable Author Statement
    more info
     
    small molecule metabolic process TAS
    Traceable Author Statement
    more info
     
    Component Evidence Code Pubs
    Golgi lumen TAS
    Traceable Author Statement
    more info
     
    anchored component of plasma membrane IEA
    Inferred from Electronic Annotation
    more info
     
    extracellular exosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    extracellular space IEA
    Inferred from Electronic Annotation
    more info
     
    integral component of plasma membrane TAS
    Traceable Author Statement
    more info
    PubMed 
    lysosomal lumen TAS
    Traceable Author Statement
    more info
     
    plasma membrane TAS
    Traceable Author Statement
    more info
     
    proteinaceous extracellular matrix IEA
    Inferred from Electronic Annotation
    more info
     
    Preferred Names
    glypican-3
    Names
    glypican proteoglycan 3
    heparan sulphate proteoglycan
    intestinal protein OCI-5
    secreted glypican-3

    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_009286.1 RefSeqGene

      Range
      4994..454894
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_505

    mRNA and Protein(s)

    1. NM_001164617.1NP_001158089.1  glypican-3 isoform 1 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AK222766, AL009174, BX329946, DB107651, DQ349138
      Consensus CDS
      CCDS55496.1
      UniProtKB/Swiss-Prot
      P51654
      UniProtKB/TrEMBL
      Q53H15
      Related
      ENSP00000377836, ENST00000394299
      Conserved Domains (1) summary
      pfam01153
      Location:11601
      Glypican; Glypican
    2. NM_001164618.1NP_001158090.1  glypican-3 isoform 3 precursor

      See identical proteins and their annotated locations for NP_001158090.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) uses an alternate in-frame splice site in the 5' coding region and lacks an alternate in-frame exon in the central coding region, compared to variant 1, resulting in an isoform (3) that is shorter than isoform 1.
      Source sequence(s)
      AK222766, AK300168, DB107651
      UniProtKB/TrEMBL
      B4DTD8
      UniProtKB/TrEMBL
      Q53H15
      Conserved Domains (1) summary
      pfam01153
      Location:11562
      Glypican; Glypican
    3. NM_001164619.1NP_001158091.1  glypican-3 isoform 4 precursor

      See identical proteins and their annotated locations for NP_001158091.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) lacks an alternate in-frame exon in both the 5' and central coding regions, compared to variant 1, resulting in an isoform (4) that is shorter than isoform 1.
      Source sequence(s)
      AK222766, AL009174, BX329946, DB107651, DQ349136
      Consensus CDS
      CCDS55495.1
      UniProtKB/Swiss-Prot
      P51654
      UniProtKB/TrEMBL
      Q53H15
      Conserved Domains (1) summary
      pfam01153
      Location:11524
      Glypican; Glypican
    4. NM_004484.3NP_004475.1  glypican-3 isoform 2 precursor

      See identical proteins and their annotated locations for NP_004475.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon in the central coding region, compared to variant 1, resulting in an isoform (2) that is shorter than isoform 1.
      Source sequence(s)
      AK222766, DB107651, L47176
      Consensus CDS
      CCDS14638.1
      UniProtKB/TrEMBL
      I6QTG3
      UniProtKB/Swiss-Prot
      P51654
      UniProtKB/TrEMBL
      Q53H15
      Related
      ENSP00000359854, OTTHUMP00000024058, ENST00000370818, OTTHUMT00000058356
      Conserved Domains (1) summary
      pfam01153
      Location:11578
      Glypican; Glypican

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 107

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

    Reference GRCh38.p2 Primary Assembly

    Genomic

    1. NC_000023.11 Reference GRCh38.p2 Primary Assembly

      Range
      133535745..133985646
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate CHM1_1.1

    Genomic

    1. NC_018934.2 Alternate CHM1_1.1

      Range
      132581479..133031377
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)