Gene Gene information from NCBI Gene database.
Entrez ID 2719
Gene name Glypican 3
Gene symbol GPC3
Synonyms (NCBI Gene)
DGSXGTR2-2MXR7OCI-5SDYSSGBSGBSSGBS1
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 information provided by dbSNP.
26
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
miRNA miRNA information provided by mirtarbase database.
10
miRTarBase ID miRNA Experiments Reference
MIRT006231 hsa-miR-219a-5p ImmunohistochemistryLuciferase reporter assayqRT-PCRWestern blot 22449976
MIRT006231 hsa-miR-219a-5p ImmunohistochemistryLuciferase reporter assayqRT-PCRWestern blot 22449976
MIRT006231 hsa-miR-219a-5p ImmunohistochemistryLuciferase reporter assayqRT-PCRWestern blot 22449976
MIRT006231 hsa-miR-219a-5p ImmunohistochemistryLuciferase reporter assayqRT-PCRWestern blot 22449976
MIRT006231 hsa-miR-219a-5p ImmunohistochemistryLuciferase reporter assayqRT-PCRWestern blot 22449976
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
63
GO ID Ontology Definition Evidence Reference
GO:0001658 Process Branching involved in ureteric bud morphogenesis IEA
GO:0001822 Process Kidney development IEA
GO:0005515 Function Protein binding IPI 17549790, 29162697, 39822733
GO:0005764 Component Lysosome IEA
GO:0005788 Component Endoplasmic reticulum lumen TAS
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
300037 4451 ENSG00000147257
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
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
Tissue specificity TISSUE SPECIFICITY: Detected in placenta (at protein level) (PubMed:32337544). Highly expressed in lung, liver and kidney. {ECO:0000269|PubMed:32337544, ECO:0000269|PubMed:8589713}.
Sequence
Sequence length 580
Interactions View interactions
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
28
Evidence Score: ★☆☆☆☆  Gene-disease association found in Text Mining only ★★☆☆☆  Found in Text Mining and Unknown/Other Associations ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession Evidence Score
GPC3-related disorder Pathogenic rs2076400400 RCV004731100
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Nonpapillary renal cell carcinoma Pathogenic; Likely pathogenic rs2124479966, rs2521354962 RCV005924247
RCV005937377
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Simpson-Golabi-Behmel syndrome type 1 Pathogenic; Likely pathogenic rs886039489, rs2071074944, rs2124634791, rs2071700502, rs2124401754, rs1206002281, rs2521895386, rs886039908, rs869025181, rs104894854, rs869025182, rs104894855, rs869025183, rs122453121, rs267606850
View all (4 more)
RCV001645005
RCV001782224
RCV001808025
RCV002077378
RCV002272751
View all (14 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Thyroid cancer, nonmedullary, 1 Likely pathogenic; Pathogenic rs2521895048, rs869025182, rs2071072322 RCV005928667
RCV005887454
RCV005912519
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Phenotype Name Clinical Significance Source Evidence Score
Acute myeloid leukemia Likely benign ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
CARCINOMA, HEPATOCELLULAR CTD
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Cervical cancer Benign ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Clear cell carcinoma of kidney Likely benign ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Associations from Text Mining Disease associations identified through text mining
Disease Name Disease (Merged) Source PMID Relationship Type Evidence Score
Accessory nipple Accessory Nipple BEFREE 11477610, 22807161
★☆☆☆☆
Found in Text Mining only
Accessory nipple Accessory Nipple HPO_DG
★☆☆☆☆
Found in Text Mining only
Adenocarcinoma Adenocarcinoma BEFREE 12816733, 18469798, 28315695, 30196987, 9371521
★☆☆☆☆
Found in Text Mining only
Adenocarcinoma of large intestine Colorectal Cancer BEFREE 25619476
★☆☆☆☆
Found in Text Mining only
Adenocarcinoma of lung (disorder) Lung adenocarcinoma BEFREE 12816733, 26345955
★☆☆☆☆
Found in Text Mining only
Adenocarcinoma, Clear Cell Adenocarcinoma BEFREE 19860840, 30036224
★☆☆☆☆
Found in Text Mining only
Adenoid Cystic Carcinoma Adenocarcinoma BEFREE 2408413
★☆☆☆☆
Found in Text Mining only
Adenoma Adenoma BEFREE 22914605, 23715166
★☆☆☆☆
Found in Text Mining only
Adult Hepatocellular Carcinoma Liver carcinoma BEFREE 21655958, 28207681
★☆☆☆☆
Found in Text Mining only
Adult Medulloblastoma Medulloblastoma BEFREE 11008203
★☆☆☆☆
Found in Text Mining only