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GPC3 glypican 3 [ Homo sapiens (human) ]

Gene ID: 2719, updated on 5-Jul-2025
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
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See GPC3 in Genome Data Viewer
Location:
Xq26.2
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (133535745..133985594, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (131860879..132310724, complement)
RS_2024_09 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

  • Project title: Tissue-specific circular RNA induction during human fetal development
  • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
  • BioProject: PRJNA270632
  • Publication: PMID 26076956
  • Analysis date: Mon Apr 2 22:54:59 2018

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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
Products Interactant Other Gene Complex Source Pubs Description

Markers

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables peptidase inhibitor activity IEA
Inferred from Electronic Annotation
more info
 
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
acts_upstream_of 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 
acts_upstream_of_or_within animal organ morphogenesis IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within anterior/posterior axis specification IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within body morphogenesis IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within bone mineralization IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within branching involved in ureteric bud morphogenesis IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of 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
 
acts_upstream_of_or_within cell proliferation involved in kidney development IEA
Inferred from Electronic Annotation
more info
 
involved_in cell proliferation involved in kidney development ISS
Inferred from Sequence or Structural Similarity
more info
 
acts_upstream_of_or_within cell proliferation involved in metanephros development IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within coronary vasculature development IEA
Inferred from Electronic Annotation
more info
 
involved_in coronary vasculature development ISS
Inferred from Sequence or Structural Similarity
more info
 
acts_upstream_of_or_within embryonic hindlimb morphogenesis IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of epithelial cell proliferation IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within kidney development IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within lung development IEA
Inferred from Electronic Annotation
more info
 
involved_in mesenchymal cell proliferation involved in ureteric bud 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
 
acts_upstream_of_or_within mesonephric duct morphogenesis IEA
Inferred from Electronic Annotation
more info
 
involved_in mesonephric duct morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
acts_upstream_of_or_within negative regulation of canonical Wnt signaling pathway IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within negative regulation of cell population proliferation IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within negative regulation of epithelial cell proliferation IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within negative regulation of growth IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within negative regulation of smoothened signaling pathway IEA
Inferred from Electronic Annotation
more info
 
involved_in negative regulation of smoothened signaling pathway ISS
Inferred from Sequence or Structural Similarity
more info
 
acts_upstream_of_or_within osteoclast differentiation IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within positive regulation of BMP signaling pathway IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within positive regulation of D-glucose import IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within 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 
acts_upstream_of_or_within positive regulation of endocytosis IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of endocytosis ISS
Inferred from Sequence or Structural Similarity
more info
 
acts_upstream_of_or_within positive regulation of protein catabolic process IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of protein catabolic process ISS
Inferred from Sequence or Structural Similarity
more info
 
acts_upstream_of_or_within 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 
acts_upstream_of_or_within regulation of growth IEA
Inferred from Electronic Annotation
more info
 
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 regulation of signal transduction IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within response to bacterium IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of 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 endoplasmic reticulum lumen TAS
Traceable Author Statement
more info
 
located_in lysosomal lumen IEA
Inferred from Electronic Annotation
more info
 
located_in lysosomal lumen TAS
Traceable Author Statement
more info
 
located_in lysosome IEA
Inferred from Electronic Annotation
more info
 
located_in membrane IEA
Inferred from Electronic Annotation
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 IEA
Inferred from Electronic Annotation
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
 
Preferred Names
glypican-3
Names
glypican proteoglycan 3
heparan sulphate proteoglycan
intestinal protein OCI-5
secreted glypican-3

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_2024_08

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