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Aliases for GPC3 Gene

Aliases for GPC3 Gene

  • Glypican 3 2 3 5
  • Intestinal Protein OCI-5 3 4
  • Glypican Proteoglycan 3 2 3
  • GTR2-2 3 4
  • MXR7 3 4
  • Heparan Sulphate Proteoglycan 3
  • Secreted Glypican-3 3
  • Glypican-3 3
  • OCI-5 3
  • SGBS1 3
  • DGSX 3
  • SGBS 3
  • SDYS 3
  • OCI5 4
  • SGB 3

External Ids for GPC3 Gene

Previous HGNC Symbols for GPC3 Gene

  • SDYS

Previous GeneCards Identifiers for GPC3 Gene

  • GC0XM127315
  • GC0XM129515
  • GC0XM130614
  • GC0XM131375
  • GC0XM132395
  • GC0XM132497
  • GC0XM132669
  • GC0XM122070

Summaries for GPC3 Gene

Entrez Gene Summary for GPC3 Gene

  • 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]

GeneCards Summary for GPC3 Gene

GPC3 (Glypican 3) is a Protein Coding gene. Diseases associated with GPC3 include Simpson-Golabi-Behmel Syndrome, Type 1 and Wilms Tumor 1. Among its related pathways are Chondroitin sulfate/dermatan sulfate metabolism and Metabolism. Gene Ontology (GO) annotations related to this gene include heparan sulfate proteoglycan binding and peptidyl-dipeptidase inhibitor activity. An important paralog of this gene is GPC5.

UniProtKB/Swiss-Prot for GPC3 Gene

  • Cell surface proteoglycan that bears heparan sulfate. Inhibits the dipeptidyl peptidase activity of DPP4. May be involved in the suppression/modulation of growth in the predominantly mesodermal tissues and organs. May play a role in the modulation of IGF2 interactions with its receptor and thereby modulate its function. May regulate growth and tumor predisposition.

Gene Wiki entry for GPC3 Gene

Additional gene information for GPC3 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for GPC3 Gene

Genomics for GPC3 Gene

GeneHancer (GH) Regulatory Elements for GPC3 Gene

Promoters and enhancers for GPC3 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH0XJ133978 Promoter/Enhancer 2 EPDnew Ensembl ENCODE dbSUPER 656.4 +3.3 3280 7.8 CTCF PKNOX1 USF1 SAP130 KAT7 YY1 ZNF335 ZFHX2 GLIS2 ZNF316 GPC3 GC0XP133899
GH0XJ133987 Enhancer 1 FANTOM5 dbSUPER 658.5 -1.6 -1551 0.3 DRAP1 ELF3 SOX13 FOXA2 SAP130 CEBPG THRB RARA ZKSCAN1 POLR2A GPC3 ENSG00000232068
GH0XJ134171 Promoter/Enhancer 1.7 FANTOM5 Ensembl ENCODE dbSUPER 5.6 -187.7 -187739 4.8 MXI1 USF1 MAX ZIC2 ETS1 ZNF335 ZFHX2 GLIS2 PATZ1 ZNF143 ENSG00000283638 CCDC160 GPC3 PHF6 GC0XM134222 GC0XM134224 MIR106A
GH0XJ134025 Enhancer 1.2 FANTOM5 Ensembl ENCODE 7.4 -40.6 -40591 1.9 ARID4B ZNF2 RAD21 ZNF335 ZNF143 THAP11 ZNF654 CEBPB REST CEBPA GPC3 ENSG00000232068 GC0XM134143 ENSG00000200572
GH0XJ134021 Enhancer 0.5 ENCODE 12.6 -35.6 -35630 0.6 CTCF ZNF654 SAP130 RAD21 ENSG00000232068 GPC3 GC0XM134143 ENSG00000200572
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around GPC3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the GPC3 gene promoter:

Genomic Locations for GPC3 Gene

Genomic Locations for GPC3 Gene
chrX:133,535,745-133,985,895
(GRCh38/hg38)
Size:
450,151 bases
Orientation:
Minus strand
chrX:132,669,773-133,119,922
(GRCh37/hg19)

Genomic View for GPC3 Gene

Genes around GPC3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
GPC3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for GPC3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for GPC3 Gene

Proteins for GPC3 Gene

  • Protein details for GPC3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P51654-GPC3_HUMAN
    Recommended name:
    Glypican-3
    Protein Accession:
    P51654
    Secondary Accessions:
    • C9JLE3
    • G3V1R0
    • Q2L880
    • Q2L882

    Protein attributes for GPC3 Gene

    Size:
    580 amino acids
    Molecular mass:
    65563 Da
    Quaternary structure:
    • Interacts with DPP4.

    Alternative splice isoforms for GPC3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for GPC3 Gene

Post-translational modifications for GPC3 Gene

  • Glycosylation at isoforms=2, 3509, isoforms=2, 3495, Asn418, isoforms=2, 3359, Asn241, and isoforms=2, 3124
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for GPC3 Gene

Domains & Families for GPC3 Gene

Gene Families for GPC3 Gene

HGNC:
Human Protein Atlas (HPA):
  • Cancer-related genes
  • Disease related genes
  • Predicted intracellular proteins
  • Predicted membrane proteins

Protein Domains for GPC3 Gene

Blocks:
InterPro:
ProtoNet:

Graphical View of Domain Structure for InterPro Entry

P51654

UniProtKB/Swiss-Prot:

GPC3_HUMAN :
  • Belongs to the glypican family.
Family:
  • Belongs to the glypican family.
genes like me logo Genes that share domains with GPC3: view

Function for GPC3 Gene

Molecular function for GPC3 Gene

UniProtKB/Swiss-Prot Function:
Cell surface proteoglycan that bears heparan sulfate. Inhibits the dipeptidyl peptidase activity of DPP4. May be involved in the suppression/modulation of growth in the predominantly mesodermal tissues and organs. May play a role in the modulation of IGF2 interactions with its receptor and thereby modulate its function. May regulate growth and tumor predisposition.
GENATLAS Biochemistry:
glypican 3,60kDa,putative extracellular proteoglycan,involved in growth control in embryonic mesodermal tissues,complexing with and putative modulator of IGF2,juxtaposed to GPC4,with tumor suppression activity

Phenotypes From GWAS Catalog for GPC3 Gene

Gene Ontology (GO) - Molecular Function for GPC3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 17549790
GO:0030414 peptidase inhibitor activity IEA --
GO:0043395 heparan sulfate proteoglycan binding IEA --
GO:0060422 peptidyl-dipeptidase inhibitor activity IDA 17549790
genes like me logo Genes that share ontologies with GPC3: view
genes like me logo Genes that share phenotypes with GPC3: view

Human Phenotype Ontology for GPC3 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for GPC3 Gene

MGI Knock Outs for GPC3:

Animal Model Products

miRNA for GPC3 Gene

Clone Products

  • Addgene plasmids for GPC3

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for GPC3 Gene

Localization for GPC3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for GPC3 Gene

Cell membrane; Lipid-anchor, GPI-anchor; Extracellular side.
Secreted glypican-3: Secreted, extracellular space.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for GPC3 gene
Compartment Confidence
plasma membrane 5
extracellular 5
endoplasmic reticulum 5
golgi apparatus 5
lysosome 4
peroxisome 2
nucleus 2
cytoskeleton 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Plasma membrane (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for GPC3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region IEA --
GO:0005615 extracellular space IEA --
GO:0005764 lysosome IEA --
GO:0005788 endoplasmic reticulum lumen TAS --
GO:0005796 Golgi lumen TAS --
genes like me logo Genes that share ontologies with GPC3: view

Pathways & Interactions for GPC3 Gene

genes like me logo Genes that share pathways with GPC3: view

SIGNOR curated interactions for GPC3 Gene

Inactivates:

Gene Ontology (GO) - Biological Process for GPC3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001523 retinoid metabolic process TAS --
GO:0001658 branching involved in ureteric bud morphogenesis IEA --
GO:0001822 kidney development IEA --
GO:0006024 glycosaminoglycan biosynthetic process TAS --
GO:0006027 glycosaminoglycan catabolic process TAS --
genes like me logo Genes that share ontologies with GPC3: view

Drugs & Compounds for GPC3 Gene

(8) Drugs for GPC3 Gene - From: ClinicalTrials

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Fludarabine Approved Pharma DNA synthsis inhibitor 1231,1231
Cyclophosphamide Approved, Investigational Pharma Nitrogen mustard alkylating agent and prodrug. 3113
Alkylating Agents Pharma 5057
Antimetabolites Pharma 12587
Antimetabolites, Antineoplastic Pharma 7688

(5) Additional Compounds for GPC3 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with GPC3: view

Transcripts for GPC3 Gene

Unigene Clusters for GPC3 Gene

Glypican 3:
Representative Sequences:

Clone Products

  • Addgene plasmids for GPC3

Alternative Splicing Database (ASD) splice patterns (SP) for GPC3 Gene

No ASD Table

Relevant External Links for GPC3 Gene

GeneLoc Exon Structure for
GPC3
ECgene alternative splicing isoforms for
GPC3

Expression for GPC3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for GPC3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for GPC3 Gene

This gene is overexpressed in Lung (x7.5), Adipose - Subcutaneous (x6.3), Nerve - Tibial (x4.6), Adipose - Visceral (Omentum) (x4.1), and Breast - Mammary Tissue (x4.0).

Protein differential expression in normal tissues from HIPED for GPC3 Gene

This gene is overexpressed in Urine (52.6) and Placenta (6.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for GPC3 Gene



Protein tissue co-expression partners for GPC3 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of GPC3 Gene:

GPC3

SOURCE GeneReport for Unigene cluster for GPC3 Gene:

Hs.644108

mRNA Expression by UniProt/SwissProt for GPC3 Gene:

P51654-GPC3_HUMAN
Tissue specificity: Highly expressed in lung, liver and kidney.

Evidence on tissue expression from TISSUES for GPC3 Gene

  • Liver(4.6)
  • Lung(2.9)
  • Kidney(2.8)
  • Gall bladder(2.1)
  • Blood(2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for GPC3 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • endocrine
  • integumentary
  • lymphatic
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
  • urinary
Regions:
Head and neck:
  • brain
  • cerebellum
  • cerebrospinal fluid
  • ear
  • eye
  • eyelid
  • face
  • head
  • jaw
  • lip
  • mandible
  • maxilla
  • meninges
  • mouth
  • neck
  • nose
  • outer ear
  • skull
  • tongue
  • tooth
Thorax:
  • breast
  • chest wall
  • clavicle
  • diaphragm
  • esophagus
  • heart
  • heart valve
  • lung
  • rib
  • rib cage
  • scapula
  • sternum
Abdomen:
  • abdominal wall
  • adrenal gland
  • appendix
  • biliary tract
  • duodenum
  • intestine
  • kidney
  • large intestine
  • liver
  • pancreas
  • small intestine
  • spleen
  • stomach
Pelvis:
  • pelvis
  • penis
  • placenta
  • testicle
  • ureter
  • urethra
  • uterus
Limb:
  • ankle
  • arm
  • digit
  • elbow
  • femur
  • fibula
  • finger
  • foot
  • forearm
  • hand
  • hip
  • humerus
  • knee
  • lower limb
  • nail
  • radius
  • shin
  • shoulder
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
  • wrist
General:
  • blood
  • blood vessel
  • peripheral nerve
  • peripheral nervous system
  • skin
  • spinal column
  • sweat gland
  • vertebrae
genes like me logo Genes that share expression patterns with GPC3: view

Orthologs for GPC3 Gene

This gene was present in the common ancestor of animals.

Orthologs for GPC3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia GPC3 34 33
  • 99.14 (n)
OneToOne
cow
(Bos Taurus)
Mammalia GPC3 34 33
  • 93.28 (n)
OneToOne
dog
(Canis familiaris)
Mammalia GPC3 34 33
  • 92.18 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Gpc3 33
  • 90.78 (n)
mouse
(Mus musculus)
Mammalia Gpc3 16 34 33
  • 90.73 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia GPC3 34
  • 74 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia GPC3 34
  • 70 (a)
OneToOne
chicken
(Gallus gallus)
Aves GPC3 34 33
  • 69.84 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia GPC3 34
  • 59 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia gpc3 33
  • 63.69 (n)
zebrafish
(Danio rerio)
Actinopterygii gpc3 34 33
  • 53.76 (n)
OneToOne
-- 33
fruit fly
(Drosophila melanogaster)
Insecta dally 34
  • 19 (a)
OneToMany
Species where no ortholog for GPC3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for GPC3 Gene

ENSEMBL:
Gene Tree for GPC3 (if available)
TreeFam:
Gene Tree for GPC3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for GPC3: view image

Paralogs for GPC3 Gene

Paralogs for GPC3 Gene

(1) SIMAP similar genes for GPC3 Gene using alignment to 5 proteins:

  • GPC3_HUMAN
  • H0Y3U6_HUMAN
  • I6QTG3_HUMAN
  • Q53H15_HUMAN
  • Q8IYG2_HUMAN
genes like me logo Genes that share paralogs with GPC3: view

Variants for GPC3 Gene

Sequence variations from dbSNP and Humsavar for GPC3 Gene

SNP ID Clin Chr 0X pos Variation AA Info Type
rs1048793393 likely-benign, Wilms tumor 1 133,754,100(-) A/G coding_sequence_variant, synonymous_variant
rs104894854 pathogenic, Simpson-Golabi-Behmel syndrome, Simpson-Golabi-Behmel syndrome 1 (SGBS1) [MIM:312870] 133,753,628(-) A/T coding_sequence_variant, missense_variant
rs104894855 pathogenic, Simpson-Golabi-Behmel syndrome, not provided 133,753,919(-) G/A coding_sequence_variant, stop_gained
rs1057522079 likely-benign, not specified, Wilms tumor 1 133,985,411(-) C/A coding_sequence_variant, synonymous_variant
rs1060502170 uncertain-significance, Wilms tumor 1 133,753,726(-) G/C coding_sequence_variant, missense_variant

Structural Variations from Database of Genomic Variants (DGV) for GPC3 Gene

Variant ID Type Subtype PubMed ID
esv2740486 CNV deletion 23290073
esv3559353 CNV deletion 23714750
esv3574595 CNV loss 25503493
esv3574596 CNV loss 25503493
esv3574597 CNV loss 25503493
esv3574599 CNV loss 25503493
esv3577259 CNV gain 25503493
esv3577260 CNV gain 25503493

Variation tolerance for GPC3 Gene

Residual Variation Intolerance Score: 44.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.60; 30.79% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for GPC3 Gene

Human Gene Mutation Database (HGMD)
GPC3
SNPedia medical, phenotypic, and genealogical associations of SNPs for
GPC3

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for GPC3 Gene

Disorders for GPC3 Gene

MalaCards: The human disease database

(39) MalaCards diseases for GPC3 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search GPC3 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

GPC3_HUMAN
  • Simpson-Golabi-Behmel syndrome 1 (SGBS1) [MIM:312870]: A condition characterized by pre- and postnatal overgrowth (gigantism), facial dysmorphism and a variety of inconstant visceral and skeletal malformations. Characteristic dysmorphic features include macrocephaly with coarse, distinctive facies with a large protruding jaw, broad nasal bridge and cleft palate. Cardiac defects are frequent. {ECO:0000269 PubMed:10814714}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for GPC3

genes like me logo Genes that share disorders with GPC3: view

No data available for Genatlas for GPC3 Gene

Publications for GPC3 Gene

  1. Mutations in GPC3, a glypican gene, cause the Simpson-Golabi-Behmel overgrowth syndrome. (PMID: 8589713) Pilia G … Schlessinger D (Nature genetics 1996) 2 3 4 22 58
  2. The Simpson-Golabi-Behmel syndrome causative glypican-3, binds to and inhibits the dipeptidyl peptidase activity of CD26. (PMID: 17549790) Davoodi J … MacKenzie AE (Proteomics 2007) 3 4 22 58
  3. Mutational analysis of the GPC3/GPC4 glypican gene cluster on Xq26 in patients with Simpson-Golabi-Behmel syndrome: identification of loss-of-function mutations in the GPC3 gene. (PMID: 10814714) Veugelers M … David G (Human molecular genetics 2000) 3 4 22 58
  4. GPC4, the gene for human K-glypican, flanks GPC3 on xq26: deletion of the GPC3-GPC4 gene cluster in one family with Simpson-Golabi-Behmel syndrome. (PMID: 9787072) Veugelers M … David G (Genomics 1998) 2 3 22 58
  5. Analysis of exon/intron structure and 400 kb of genomic sequence surrounding the 5'-promoter and 3'-terminal ends of the human glypican 3 (GPC3) gene. (PMID: 9339360) Huber R … Pilia G (Genomics 1997) 3 4 22 58

Products for GPC3 Gene

  • Addgene plasmids for GPC3

Sources for GPC3 Gene

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