GPC3 (glypican 3)

Gene

• Entrez ID: 2719
• Gene name: Glypican 3
• Gene symbol: GPC3
• Synonyms: DGSX, GTR2-2, MXR7, OCI-5, SDYS, SGB, SGBS, SGBS1
• Chromosome: X
• Chromosome location: Xq26.2
• 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 protei

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs104894854	A>T	Pathogenic	Coding sequence variant, missense variant
rs104894855	G>A	Pathogenic	Coding sequence variant, stop gained
rs122453119	G>A	Pathogenic	Coding sequence variant, missense variant
rs122453120	C>T	Pathogenic	Coding sequence variant, missense variant, genic downstream transcript variant
rs122453121	G>A	Pathogenic	Coding sequence variant, stop gained
rs138450923	G>A	Likely-benign, conflicting-interpretations-of-pathogenicity	Coding sequence variant, synonymous variant
rs141100113	C>A,T	Likely-benign, conflicting-interpretations-of-pathogenicity	Coding sequence variant, missense variant
rs267606850	C>T	Likely-pathogenic, pathogenic	Missense variant, coding sequence variant, genic downstream transcript variant
rs398124166	C>T	Conflicting-interpretations-of-pathogenicity	Synonymous variant, coding sequence variant
rs745968470	C>T	Conflicting-interpretations-of-pathogenicity	Synonymous variant, genic downstream transcript variant, coding sequence variant
rs753210097	G>A,T	Likely-pathogenic, likely-benign	Synonymous variant, coding sequence variant, stop gained, genic downstream transcript variant
rs869025181	CCCTTAGGGAGAC>-	Pathogenic	Intron variant, frameshift variant, coding sequence variant
rs869025182	C>A	Pathogenic	Splice donor variant
rs869025183	C>T	Pathogenic	Intron variant, splice donor variant
rs886039384	AT>-	Pathogenic	Intron variant, frameshift variant, coding sequence variant
rs886039473	G>-	Pathogenic	Genic downstream transcript variant, frameshift variant, coding sequence variant
rs886039489	C>T	Pathogenic	Splice donor variant
rs886039908	A>-	Likely-pathogenic	Genic downstream transcript variant, frameshift variant, coding sequence variant
rs1057517739	C>A	Pathogenic	Coding sequence variant, stop gained
rs1556263859	G>A	Likely-pathogenic	Stop gained, coding sequence variant
rs1556297749	CTGGGTCATAATAAGCTTGGGGAAAT>TGCAAG	Pathogenic	Frameshift variant, coding sequence variant
rs1569392947	C>A	Pathogenic	Coding sequence variant, stop gained, genic downstream transcript variant
rs1569408743	G>-	Pathogenic	Coding sequence variant, frameshift variant, genic downstream transcript variant
rs1569426054	G>T	Likely-pathogenic	Coding sequence variant, stop gained
rs1602581162	->G	Pathogenic	Coding sequence variant, frameshift variant
rs1603240717	->A	Pathogenic	Coding sequence variant, stop gained

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT006231	hsa-miR-219a-5p	Immunohistochemistry, Luciferase reporter assay, qRT-PCR, Western blot	22449976
MIRT006231	hsa-miR-219a-5p	Immunohistochemistry, Luciferase reporter assay, qRT-PCR, Western blot	22449976
MIRT006231	hsa-miR-219a-5p	Immunohistochemistry, Luciferase reporter assay, qRT-PCR, Western blot	22449976
MIRT006231	hsa-miR-219a-5p	Immunohistochemistry, Luciferase reporter assay, qRT-PCR, Western blot	22449976
MIRT006231	hsa-miR-219a-5p	Immunohistochemistry, Luciferase reporter assay, qRT-PCR, Western blot	22449976
MIRT006231	hsa-miR-219a-5p	Immunohistochemistry, Luciferase reporter assay, qRT-PCR, Western blot	22449976
MIRT053054	hsa-miR-520c-3p	Flow, Luciferase reporter assay, Western blot	23647462
MIRT053054	hsa-miR-520c-3p	Luciferase reporter assay, QRTPCR, Western blot	23607462
MIRT053054	hsa-miR-520c-3p	qRT-PCR, Western blot	27633306
MIRT734767	hsa-miR-527	Western blotting, Microarray	33613718

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0001523	Process	Retinoid metabolic process	TAS
GO:0001658	Process	Branching involved in ureteric bud morphogenesis	IEA
GO:0005515	Function	Protein binding	IPI	17549790, 29162697
GO:0005788	Component	Endoplasmic reticulum lumen	TAS
GO:0005796	Component	Golgi lumen	TAS
GO:0005886	Component	Plasma membrane	IDA
GO:0005886	Component	Plasma membrane	TAS
GO:0006024	Process	Glycosaminoglycan biosynthetic process	TAS
GO:0006027	Process	Glycosaminoglycan catabolic process	TAS
GO:0009617	Process	Response to bacterium	IEA
GO:0009653	Process	Anatomical structure morphogenesis	TAS	8589713
GO:0009948	Process	Anterior/posterior axis specification	IEA
GO:0009986	Component	Cell surface	IBA	21873635
GO:0010171	Process	Body morphogenesis	IEA
GO:0010466	Process	Negative regulation of peptidase activity	IEA
GO:0016477	Process	Cell migration	IBA	21873635
GO:0030282	Process	Bone mineralization	IEA
GO:0030316	Process	Osteoclast differentiation	IEA
GO:0030324	Process	Lung development	IEA
GO:0030513	Process	Positive regulation of BMP signaling pathway	IEA
GO:0031226	Component	Intrinsic component of plasma membrane	TAS
GO:0035116	Process	Embryonic hindlimb morphogenesis	IEA
GO:0042074	Process	Cell migration involved in gastrulation	ISS
GO:0043202	Component	Lysosomal lumen	TAS
GO:0043687	Process	Post-translational protein modification	TAS
GO:0044267	Process	Cellular protein metabolic process	TAS
GO:0045732	Process	Positive regulation of protein catabolic process	ISS
GO:0045807	Process	Positive regulation of endocytosis	ISS
GO:0045879	Process	Negative regulation of smoothened signaling pathway	ISS
GO:0045880	Process	Positive regulation of smoothened signaling pathway	IEA
GO:0045926	Process	Negative regulation of growth	IEA
GO:0046326	Process	Positive regulation of glucose import	IEA
GO:0046658	Component	Anchored component of plasma membrane	IBA	21873635
GO:0046658	Component	Anchored component of plasma membrane	ISS
GO:0050680	Process	Negative regulation of epithelial cell proliferation	IEA
GO:0060422	Function	Peptidyl-dipeptidase inhibitor activity	IDA	17549790
GO:0060828	Process	Regulation of canonical Wnt signaling pathway	IDA	14610063
GO:0060976	Process	Coronary vasculature development	ISS
GO:0062023	Component	Collagen-containing extracellular matrix	IEA
GO:0072111	Process	Cell proliferation involved in kidney development	ISS
GO:0072138	Process	Mesenchymal cell proliferation involved in ureteric bud development	ISS
GO:0072180	Process	Mesonephric duct morphogenesis	ISS
GO:0072203	Process	Cell proliferation involved in metanephros development	IEA
GO:0090090	Process	Negative regulation of canonical Wnt signaling pathway	IEA
GO:0090263	Process	Positive regulation of canonical Wnt signaling pathway	IBA	21873635
GO:0090263	Process	Positive regulation of canonical Wnt signaling pathway	IDA	24496449
GO:1905475	Process	Regulation of protein localization to membrane	IBA	21873635
GO:2000050	Process	Regulation of non-canonical Wnt signaling pathway	IDA	14610063
GO:2000096	Process	Positive regulation of Wnt signaling pathway, planar cell polarity pathway	IEA

Other IDs

• MIM: 300037
• HGNC: 4451
• e!Ensembl: ENSG00000147257

Protein

• UniProt ID: P51654
• Protein name: Glypican-3 (GTR2-2) (Intestinal protein OCI-5) (MXR7) [Cleaved into: Glypican-3 alpha subunit; Glypican-3 beta subunit]
• Protein function: Cell surface proteoglycan (PubMed:14610063). Negatively regulates the hedgehog signaling pathway when attached via the GPI-anchor to the cell surface by competing with the hedgehog receptor PTC1 for binding to hedgehog proteins (By similarity).
• PDB: 7ZA1, 7ZAW
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF01153	Glypican	14 → 578	Glypican	Family

• Sequence:

  MAGTVRTACLVVAMLLSLDFPGQAQPPPPPPDATCHQVRSFFQRLQPGLKWVPETPVPGS
  DLQVCLPKGPTCCSRKMEEKYQLTARLNMEQLLQSASMELKFLIIQNAAVFQEAFEIVVR
  HAKNYTNAMFKNNYPSLTPQAFEFVGEFFTDVSLYILGSDINVDDMVNELFDSLFPVIYT
  QLMNPGLPDSALDINECLRGARRDLKVFGNFPKLIMTQVSKSLQVTRIFLQALNLGIEVI
  NTTDHLKFSKDCGRMLTRMWYCSYCQGLMMVKPCGGYCNVVMQGCMAGVVEIDKYWREYI
  LSLEELVNGMYRIYDMENVLLGLFSTIHDSIQYVQKNAGKLTTTIGKLCAHSQQRQYRSA
  YYPEDLFIDKKVLKVAHVEHEETLSSRRRELIQKLKSFISFYSALPGYICSHSPVAENDT
  LCWNGQELVERYSQKAARNGMKNQFNLHELKMKGPEPVVSQIIDKLKHINQLLRTMSMPK
  GRVLDKNLDEEGFESGDCGDDEDECIGGSGDGMIKVKNQLRFLAELAYDLDVDDAPGNSQ
  QATPKDNEISTFHNLGNVHSPLKLLTSMAISVVCFFFLVH

• Sequence length: 580