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    GPC3 glypican 3 [ Homo sapiens (human) ]

    Gene ID: 2719, updated on 17-Jun-2024

    Summary

    Official Symbol
    GPC3provided by HGNC
    Official Full Name
    glypican 3provided by HGNC
    Primary source
    HGNC:HGNC:4451
    See related
    Ensembl:ENSG00000147257 MIM:300037; AllianceGenome:HGNC:4451
    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]
    Expression
    Biased expression in placenta (RPKM 205.3), lung (RPKM 44.2) and 3 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See GPC3 in Genome Data Viewer
    Location:
    Xq26.2
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (133535745..133985594, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (131860879..132310724, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (132669773..133119621, complement)

    Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:132439404-132439904 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:132440918-132441832 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:132446467-132446966 Neighboring gene NANOG hESC enhancer GRCh37_chrX:132484838-132485339 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:132501328-132501828 Neighboring gene glypican 4 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:132549756-132550256 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chrX:132551379-132551918 Neighboring gene NANOG hESC enhancer GRCh37_chrX:132568407-132568958 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chrX:132571583-132572295 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:132689082-132689878 Neighboring gene RNA, U6 small nuclear 203, pseudogene Neighboring gene NANOG hESC enhancer GRCh37_chrX:132712962-132713463 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chrX:132783454-132784145 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chrX:132808889-132809502 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chrX:132819803-132820460 Neighboring gene ribosomal protein S24 pseudogene 19 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29973 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29974 Neighboring gene ribosomal protein SA pseudogene 63 Neighboring gene NANOG hESC enhancer GRCh37_chrX:132999651-133000493 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29975 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29976 Neighboring gene GPC3 antisense RNA 1 Neighboring gene uncharacterized LOC124905220 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chrX:133115144-133115656 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:133118772-133119326 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:133119327-133119881 Neighboring gene MPRA-validated peak7430 silencer Neighboring gene ReSE screen-validated silencer GRCh37_chrX:133160773-133160986 Neighboring gene miR-106a-363 cluster host gene Neighboring gene translocase of inner mitochondrial membrane 8B pseudogene 2 Neighboring gene microRNA 363

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated 2021-01-27)

    ClinGen Genome Curation Page
    Haploinsufficency

    Sufficient evidence for dosage pathogenicity (Last evaluated 2021-01-27)

    ClinGen Genome Curation PagePubMed

    EBI GWAS Catalog

    Description
    Common variants in left/right asymmetry genes and pathways are associated with relative hand skill.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables peptidyl-dipeptidase inhibitor activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in Wnt signaling pathway, planar cell polarity pathway IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in anatomical structure morphogenesis TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in anterior/posterior axis specification IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in body morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in bone mineralization IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in branching involved in ureteric bud morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in canonical Wnt signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cell migration IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in cell migration involved in gastrulation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in cell proliferation involved in kidney development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in cell proliferation involved in metanephros development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in coronary vasculature development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in embryonic hindlimb morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in epithelial cell proliferation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in lung development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in mesenchymal cell proliferation involved in ureteric bud development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in mesonephric duct morphogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of canonical Wnt signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of epithelial cell proliferation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of growth IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of smoothened signaling pathway ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in osteoclast differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of BMP signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of Wnt signaling pathway, planar cell polarity pathway IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of canonical Wnt signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in positive regulation of canonical Wnt signaling pathway IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of endocytosis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of glucose import IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of protein catabolic process ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of smoothened signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of canonical Wnt signaling pathway IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in regulation of non-canonical Wnt signaling pathway IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in regulation of protein localization to membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in response to bacterium IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in smoothened signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    located_in Golgi lumen TAS
    Traceable Author Statement
    more info
     
    is_active_in cell surface IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in collagen-containing extracellular matrix IEA
    Inferred from Electronic Annotation
    more info
     
    located_in endoplasmic reticulum lumen TAS
    Traceable Author Statement
    more info
     
    located_in lysosomal lumen TAS
    Traceable Author Statement
    more info
     
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
     
    located_in plasma membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
     
    located_in side of membrane IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    glypican-3
    Names
    glypican proteoglycan 3
    heparan sulphate proteoglycan
    intestinal protein OCI-5
    secreted glypican-3

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_001164617.2NP_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/TrEMBL
      Q53H15, Q8IYG2
      Related
      ENSP00000377836.2, ENST00000394299.7
      Conserved Domains (1) summary
      pfam01153
      Location:14600
      Glypican; Glypican
    2. NM_001164618.2NP_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
      Consensus CDS
      CCDS94667.1
      UniProtKB/TrEMBL
      B4DTD8, Q53H15, Q8IYG2
      Related
      ENSP00000510438.1, ENST00000689310.1
      Conserved Domains (1) summary
      pfam01153
      Location:14561
      Glypican; Glypican
    3. NM_001164619.2NP_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/TrEMBL
      A0A1S5UZ08
      Related
      ENSP00000486325.1, ENST00000631057.2
      Conserved Domains (1) summary
      pfam01153
      Location:14523
      Glypican
    4. NM_004484.4NP_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/Swiss-Prot
      C9JLE3, G3V1R0, P51654, Q2L880, Q2L882
      UniProtKB/TrEMBL
      I6QTG3, Q53H15, Q8IYG2
      Related
      ENSP00000359854.3, ENST00000370818.8
      Conserved Domains (1) summary
      pfam01153
      Location:14577
      Glypican; Glypican

    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_000023.11 Reference GRCh38.p14 Primary Assembly

      Range
      133535745..133985594 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017029413.3XP_016884902.1  glypican-3 isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060947.1 Alternate T2T-CHM13v2.0

      Range
      131860879..132310724 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054326834.1XP_054182809.1  glypican-3 isoform X1