GPC3 glypican 3 [Homo sapiens (human)] - Gene

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: mouse all
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Genomic context

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_000023.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Expression of Concern: Glypican-3 promotes cell proliferation and tumorigenesis through up-regulation of b-catenin expression in lung squamous cell carcinoma.
Title: Expression of Concern: Glypican-3 promotes cell proliferation and tumorigenesis through up-regulation of b-catenin expression in lung squamous cell carcinoma.
Predicting glypican-3 expression in hepatocellular carcinoma: A comprehensive analysis using combined contrast-enhanced ultrasound and clinical factors.
Title: Predicting glypican-3 expression in hepatocellular carcinoma: A comprehensive analysis using combined contrast-enhanced ultrasound and clinical factors.
GPC3 and PEG10 peptides associated with placental gp96 elicit specific T cell immunity against hepatocellular carcinoma.
Title: GPC3 and PEG10 peptides associated with placental gp96 elicit specific T cell immunity against hepatocellular carcinoma.
GPC3 Promotes Lung Squamous Cell Carcinoma Progression and HLA-A2-Restricted GPC3 Antigenic Peptide-Modified Dendritic Cell-Induced Cytotoxic T Lymphocytes to Kill Lung Squamous Cell Carcinoma Cells.
Title: GPC3 Promotes Lung Squamous Cell Carcinoma Progression and HLA-A2-Restricted GPC3 Antigenic Peptide-Modified Dendritic Cell-Induced Cytotoxic T Lymphocytes to Kill Lung Squamous Cell Carcinoma Cells.
Biological and clinical significance of the glypican-3 gene in human lung adenocarcinoma: An in silico analysis.
Title: Biological and clinical significance of the glypican-3 gene in human lung adenocarcinoma: An in silico analysis.
[The clinical value of serum GPC3 level in predicting recurrence of patients with primary hepatocellular carcinoma].
Title: [The clinical value of serum GPC3 level in predicting recurrence of patients with primary hepatocellular carcinoma].
Structural and Functional Impact of Posttranslational Modification of Glypican-3 on Liver Carcinogenesis.
Title: Structural and Functional Impact of Posttranslational Modification of Glypican-3 on Liver Carcinogenesis.
Evaluation of Intrafollicular Syndecan 1, Glypican 3, and Spermidine Levels in Women with Diminished Ovarian Reserve.
Title: Evaluation of Intrafollicular Syndecan 1, Glypican 3, and Spermidine Levels in Women with Diminished Ovarian Reserve.
Glypican-3, Vascular Endothelial Growth Factor and Golgi Protein-73 for Differentiation between Liver Cirrhosis and Hepatocellular Carcinoma.
Title: Glypican-3, Vascular Endothelial Growth Factor and Golgi Protein-73 for Differentiation between Liver Cirrhosis and Hepatocellular Carcinoma.
Immunohistochemical expression of Ki-67 and Glypican-3 to distinguish aggressive from nonaggressive benign odontogenic tumors.
Title: Immunohistochemical expression of Ki-67 and Glypican-3 to distinguish aggressive from nonaggressive benign odontogenic tumors.

Submit: New GeneRIF Correction See all GeneRIFs (213)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Simpson-Golabi-Behmel syndrome type 1 MedGen: C0796154 OMIM: 312870 GeneReviews: Simpson-Golabi-Behmel Syndrome Type 1, Wilms Tumor Predisposition	Compare labs
Wilms tumor 1 MedGen: CN033288 OMIM: 194070 GeneReviews: Wilms Tumor Predisposition, PAX6-Related Aniridia, WT1 Disorder	Compare labs

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 EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH16248 (e-PCR)
- UniSTS:75008

SHGC-52514 (e-PCR)
- UniSTS:11019

L77881 (e-PCR)
- UniSTS:44043

RH79181 (e-PCR)
- UniSTS:24

AL032559 (e-PCR)
- UniSTS:93210

DXS1414 (e-PCR)
- UniSTS:148771

L77880 (e-PCR)
- UniSTS:3642

DXS7764 (e-PCR)
- UniSTS:37434

NoName (e-PCR)
- UniSTS:99645

AL032585 (e-PCR)
- UniSTS:93260

G33003 (e-PCR)
- UniSTS:117580

AL032586 (e-PCR)
- UniSTS:93261

RH18522 (e-PCR)
- UniSTS:10581

AL008948 (e-PCR)
- UniSTS:72801

L76269 (e-PCR)
- UniSTS:47713

DXS9777 (e-PCR)
- UniSTS:18029

DXS7596 (e-PCR)
- UniSTS:75126

SHGC-35437 (e-PCR)
- UniSTS:58492

DXS7315 (e-PCR)
- UniSTS:39065

WI-16747 (e-PCR)
- UniSTS:38043

A009Z03 (e-PCR)
- UniSTS:5021

RH70004 (e-PCR)
- UniSTS:31416

SHGC-34872 (e-PCR)
- UniSTS:30914

DXS6842 (e-PCR)
- UniSTS:99778

RH17563 (e-PCR)
- UniSTS:37314

SHGC-35150 (e-PCR)
- UniSTS:81091

G66652 (e-PCR)
- UniSTS:166853

G66657 (e-PCR)
- UniSTS:166856

RH36204 (e-PCR)
- UniSTS:26313

G66656 (e-PCR)
- UniSTS:166858

G66651 (e-PCR)
- UniSTS:166859

DXS7314 (e-PCR)
- UniSTS:20177

L77882 (e-PCR)
- UniSTS:4819

L47619 (e-PCR)
- UniSTS:53459

RH68769 (e-PCR)
- UniSTS:48342

L77883 (e-PCR)
- UniSTS:18904

AL008945 (e-PCR)
- UniSTS:23776

SHGC-34460 (e-PCR)
- UniSTS:29920

G66688 (e-PCR)
- UniSTS:166883

G66690 (e-PCR)
- UniSTS:166885

G66691 (e-PCR)
- UniSTS:166886

G66692 (e-PCR)
- UniSTS:166889

RH45404 (e-PCR)
- UniSTS:54249

G18198 (e-PCR)
- UniSTS:1003

STS-H93110 (e-PCR)
- UniSTS:74476

L77878 (e-PCR)
- UniSTS:48364

L77879 (e-PCR)
- UniSTS:23277

GDB:182527 (e-PCR)
- UniSTS:155386

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 D-glucose import	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 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

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Preferred Names: glypican-3

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

NCBI Reference Sequences (RefSeq)

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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

NG_009286.1 RefSeqGene

Range

4994..454894

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_505

mRNA and Protein(s)

NM_001164617.2 → NP_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:14 → 600

Glypican; Glypican
NM_001164618.2 → NP_001158090.1 glypican-3 isoform 3 precursor

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:14 → 561

Glypican; Glypican
NM_001164619.2 → NP_001158091.1 glypican-3 isoform 4 precursor

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:14 → 523

Glypican
NM_004484.4 → NP_004475.1 glypican-3 isoform 2 precursor

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:14 → 577

Glypican; Glypican