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GPC3 glypican 3 [ Homo sapiens (human) ]

Gene ID: 2719, updated on 23-Dec-2018

Summary

Official Symbol
GPC3provided by HGNC
Official Full Name
glypican 3provided by HGNC
Primary source
HGNC:HGNC:4451
See related
Ensembl:ENSG00000147257 MIM:300037
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

Genomic context

See GPC3 in Genome Data Viewer
Location:
Xq26.2
Exon count:
11
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 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 glypican 4 Neighboring gene RNA, U6 small nuclear 203, pseudogene Neighboring gene ribosomal protein S24 pseudogene 19 Neighboring gene ribosomal protein SA pseudogene 63 Neighboring gene GPC3 antisense RNA 1 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 FunctionsWhat's a GeneRIF?

Phenotypes

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

Pathways from BioSystems

  • 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 B3GALT6 causes EDSP2 and SEMDJL1, organism-specific biosystem (from REACTOME)
    Defective B3GALT6 causes EDSP2 and SEMDJL1, organism-specific biosystemThe biosynthesis of dermatan sulfate/chondroitin sulfate and heparin/heparan sulfate glycosaminoglycans (GAGs) starts with the formation of a tetrasaccharide linker sequence attached to the core prot...
  • 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 biosystemEhlers?Danlos 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 ela...
  • 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...
  • Metabolism of fat-soluble vitamins, organism-specific biosystem (from REACTOME)
    Metabolism of fat-soluble vitamins, organism-specific biosystemVitamins A, D, E, and K are classified as fat-soluble. Metabolic pathways by which dietary precursors of vitamins A (Harrison 2005) and K(Shearer et al. 2012) are converted to active forms, and by wh...
  • Metabolism of vitamins and cofactors, organism-specific biosystem (from REACTOME)
    Metabolism of vitamins and cofactors, organism-specific biosystemVitamins are a diverse group of organic compounds, classified according to their solubility, either fat-soluble or water-soluble, that are either not synthesized or synthesized only in limited amount...
  • 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...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
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
 
cell migration involved in gastrulation ISS
Inferred from Sequence or Structural Similarity
more info
 
cell proliferation involved in kidney development ISS
Inferred from Sequence or Structural Similarity
more info
 
cell proliferation involved in metanephros development IEA
Inferred from Electronic Annotation
more info
 
cellular protein metabolic process TAS
Traceable Author Statement
more info
 
coronary vasculature development ISS
Inferred from Sequence or Structural Similarity
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
 
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 ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of canonical Wnt signaling pathway 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 ISS
Inferred from Sequence or Structural Similarity
more info
 
osteoclast differentiation IEA
Inferred from Electronic Annotation
more info
 
positive regulation of BMP signaling pathway IEA
Inferred from Electronic Annotation
more info
 
positive regulation of Wnt signaling pathway, planar cell polarity pathway IEA
Inferred from Electronic Annotation
more info
 
positive regulation of canonical Wnt signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of endocytosis ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of glucose import IEA
Inferred from Electronic Annotation
more info
 
positive regulation of protein catabolic process ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of smoothened signaling pathway IEA
Inferred from Electronic Annotation
more info
 
post-translational protein modification TAS
Traceable Author Statement
more info
 
regulation of canonical Wnt signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
regulation of non-canonical Wnt signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
response to bacterium IEA
Inferred from Electronic Annotation
more info
 
retinoid 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 ISS
Inferred from Sequence or Structural Similarity
more info
 
collagen-containing extracellular matrix IEA
Inferred from Electronic Annotation
more info
 
endoplasmic reticulum lumen TAS
Traceable Author Statement
more info
 
intrinsic 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
 

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)

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
    ENSP00000377836.2, ENST00000394299.6
    Conserved Domains (1) summary
    pfam01153
    Location:14600
    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, Q53H15
    Conserved Domains (1) summary
    pfam01153
    Location:14561
    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
    Related
    ENSP00000486325.1, ENST00000631057.2
    Conserved Domains (1) summary
    pfam01153
    Location:14523
    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/Swiss-Prot
    P51654
    UniProtKB/TrEMBL
    I6QTG3, Q53H15
    Related
    ENSP00000359854.3, ENST00000370818.7
    Conserved Domains (1) summary
    pfam01153
    Location:14577
    Glypican; Glypican

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000023.11 Reference GRCh38.p12 Primary Assembly

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

mRNA and Protein(s)

  1. XM_017029413.2XP_016884902.1  glypican-3 isoform X1

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