Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs Other IDs Associated diseases
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

Show/Hide all (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
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

Show/Hide all (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
MIRT006231	hsa-miR-219a-5p	ImmunohistochemistryLuciferase reporter assayqRT-PCRWestern blot	22449976
MIRT053054	hsa-miR-520c-3p	FlowLuciferase reporter assayWestern blot	23647462
MIRT053054	hsa-miR-520c-3p	Luciferase reporter assayQRTPCRWestern blot	23607462
MIRT053054	hsa-miR-520c-3p	qRT-PCRWestern blot	27633306
MIRT734767	hsa-miR-527	Western blottingMicroarray	33613718

Show/Hide all (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
GO:0005796	Component	Golgi lumen	TAS
GO:0005886	Component	Plasma membrane	IBA
GO:0005886	Component	Plasma membrane	IDA
GO:0005886	Component	Plasma membrane	IEA
GO:0005886	Component	Plasma membrane	ISS
GO:0005886	Component	Plasma membrane	TAS
GO:0007224	Process	Smoothened signaling pathway	IEA
GO:0008285	Process	Negative regulation of cell population proliferation	IEA
GO:0009617	Process	Response to bacterium	IEA
GO:0009653	Process	Anatomical structure morphogenesis	TAS	8589713
GO:0009887	Process	Animal organ morphogenesis	IEA
GO:0009948	Process	Anterior/posterior axis specification	IEA
GO:0009966	Process	Regulation of signal transduction	IEA
GO:0009986	Component	Cell surface	IBA
GO:0010171	Process	Body morphogenesis	IEA
GO:0016020	Component	Membrane	IEA
GO:0016477	Process	Cell migration	IBA
GO:0030282	Process	Bone mineralization	IEA
GO:0030316	Process	Osteoclast differentiation	IEA
GO:0030324	Process	Lung development	IEA
GO:0030414	Function	Peptidase inhibitor activity	IEA
GO:0030513	Process	Positive regulation of BMP signaling pathway	IEA
GO:0035116	Process	Embryonic hindlimb morphogenesis	IEA
GO:0040008	Process	Regulation of growth	IEA
GO:0042074	Process	Cell migration involved in gastrulation	ISS
GO:0043202	Component	Lysosomal lumen	IEA
GO:0043202	Component	Lysosomal lumen	TAS
GO:0045732	Process	Positive regulation of protein catabolic process	IEA
GO:0045732	Process	Positive regulation of protein catabolic process	ISS
GO:0045807	Process	Positive regulation of endocytosis	IEA
GO:0045807	Process	Positive regulation of endocytosis	ISS
GO:0045879	Process	Negative regulation of smoothened signaling pathway	IEA
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 D-glucose import	IEA
GO:0050673	Process	Epithelial cell proliferation	IEA
GO:0050680	Process	Negative regulation of epithelial cell proliferation	IEA
GO:0060070	Process	Canonical Wnt signaling pathway	IEA
GO:0060071	Process	Wnt signaling pathway, planar cell polarity pathway	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	IEA
GO:0060976	Process	Coronary vasculature development	ISS
GO:0072111	Process	Cell proliferation involved in kidney development	IEA
GO:0072111	Process	Cell proliferation involved in kidney development	ISS
GO:0072138	Process	Mesenchymal cell proliferation involved in ureteric bud development	IEA
GO:0072138	Process	Mesenchymal cell proliferation involved in ureteric bud development	ISS
GO:0072180	Process	Mesonephric duct morphogenesis	IEA
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
GO:0090263	Process	Positive regulation of canonical Wnt signaling pathway	IDA	24496449
GO:0098552	Component	Side of membrane	IEA
GO:1905475	Process	Regulation of protein localization to membrane	IBA
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

MIM	HGNC	e!Ensembl
300037	4451	ENSG00000147257

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

MAGTVRTACLVVAMLLSLDFPGQAQPPPPPPDATCHQVRSFFQRLQPGLKWVPETPVPGS
DLQVCLPKGPTCCSRKMEEKYQLTARLNMEQLLQSASMELKFLIIQNAAVFQEAFEIVVR
HAKNYTNAMFKNNYPSLTPQAFEFVGEFFTDVSLYILGSDINVDDMVNELFDSLFPVIYT
QLMNPGLPDSALDINECLRGARRDLKVFGNFPKLIMTQVSKSLQVTRIFLQALNLGIEVI
NTTDHLKFSKDCGRMLTRMWYCSYCQGLMMVKPCGGYCNVVMQGCMAGVVEIDKYWREYI
LSLEELVNGMYRIYDMENVLLGLFSTIHDSIQYVQKNAGKLTTTIGKLCAHSQQRQYRSA
YYPEDLFIDKKVLKVAHVEHEETLSSRRRELIQKLKSFISFYSALPGYICSHSPVAENDT
LCWNGQELVERYSQKAARNGMKNQFNLHELKMKGPEPVVSQIIDKLKHINQLLRTMSMPK
GRVLDKNLDEEGFESGDCGDDEDECIGGSGDGMIKVKNQLRFLAELAYDLDVDDAPGNSQ
QATPKDNEISTFHNLGNVHSPLKLLTSMAISVVCFFFLVH

Sequence length

580

Interactions

View interactions

1061

Show/Hide Causal Diseases (5)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
GPC3-related disorder	Pathogenic	rs2076400400	RCV004731100
Nonpapillary renal cell carcinoma	Pathogenic; Likely pathogenic	rs2124479966, rs2521354962	RCV005924247 RCV005937377
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 RCV002272947 RCV002286516 RCV000256430 RCV000012451 RCV000012453 RCV000012454 RCV000012455 RCV000012459 RCV000012460 RCV000012461 RCV003405203 RCV003990008 RCV000681476 RCV000755692
Thyroid cancer, nonmedullary, 1	Likely pathogenic; Pathogenic	rs2521895048, rs869025182, rs2071072322	RCV005928667 RCV005887454 RCV005912519
Wilms tumor 1	Pathogenic; Likely pathogenic	rs2124330798, rs2124479949, rs2124634791, rs2124401750, rs2124480362, rs267606850, rs2124479966, rs2124401794, rs2124655627, rs752194694, rs2521016626, rs2521895087, rs2071072751, rs2521356554, rs2521895048 View all (15 more)	RCV001378188 RCV001387823 RCV002541464 RCV002046444 RCV001970089 RCV002042596 RCV001960136 RCV002002382 RCV001970035 RCV005095840 RCV002580095 RCV002889561 RCV002889503 RCV002853146 RCV002872284 RCV000692634 RCV000012456 RCV000653751 RCV003501851 RCV003608081 RCV000532170 RCV000684891 RCV000697859 RCV000823186 RCV000812314 RCV001054387 RCV001211200 RCV001210467 RCV001211057 RCV001204028

Show/Hide Unknown Diseases (15)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Acute myeloid leukemia	Likely benign	rs147506479	RCV005917494
Cervical cancer	Benign	rs192870946, rs61754632	RCV005921681 RCV005899549
Clear cell carcinoma of kidney	Likely benign	rs373916851	RCV005899478
Familial cancer of breast	Benign; Likely benign	rs370737647	RCV005868101
Gastric cancer	Benign	rs61754632	RCV005899550
Glioma susceptibility 1	Benign; Likely benign	rs370737647	RCV005868102
Hereditary ataxia	Benign; Likely benign	rs182950534	RCV005625468
Hereditary cancer-predisposing syndrome	Conflicting classifications of pathogenicity; Likely benign; Benign; Uncertain significance	rs141100113, rs748391795, rs587778392, rs61754631, rs970592059, rs2124257249, rs370737647, rs375606908, rs751413609, rs182950534, rs61754633, rs2314298, rs148021273, rs780431445, rs373406834, rs748480657, rs201677091, rs765072095 View all (3 more)	RCV002258792 RCV002258242 RCV002257439 RCV002258807 RCV002258374 RCV002258645 RCV002258646 RCV002257500 RCV002258847 RCV002258846 RCV002257564 RCV002258848 RCV002257618 RCV002257625 RCV002257753 RCV002257840 RCV002258968 RCV002257916 RCV002257999 RCV002258010 RCV002258020 RCV002259073
History of neurodevelopmental disorder	Uncertain significance	rs749874149	RCV000718793
Intellectual disability	Benign; Likely benign; Conflicting classifications of pathogenicity; Uncertain significance	rs182950534, rs1556297827, rs2071691139	RCV005625467 RCV001260620 RCV001260621
Lung cancer	Benign	rs61754632	RCV005899552
Ovarian cancer	Benign; Likely benign	rs755733724	RCV003153624
Sarcoma	Likely benign	rs147506479	RCV005917495
Uterine carcinosarcoma	Benign	rs192870946	RCV005921682
Uterine corpus endometrial carcinoma	Benign	rs192870946	RCV005921683

Show/Hide Text Mining Associations (108)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Abnormalities Drug Induced	Associate	32019583
Adenocarcinoma	Associate	21623236, 23348905
Adenocarcinoma Clear Cell	Associate	19329941
Adenocarcinoma Mucinous	Stimulate	25619476
Adenocarcinoma Mucinous	Associate	36676710
Adenocarcinoma of Lung	Associate	26345955, 34112123, 34580602, 35710585, 37960765
Adenocarcinoma Scirrhous	Associate	23348905
Beckwith Wiedemann Syndrome	Associate	23169491
Breast Neoplasms	Associate	11454708, 12819009, 29935166, 33742285, 35587107, 36676710
Breast Neoplasms	Inhibit	30267212
Calcifying Epithelial Odontogenic Tumor	Associate	36510965
Carcinogenesis	Associate	22449976, 25896897, 26722522, 31053802
Carcinoma	Associate	18264086, 21937079
Carcinoma Ductal Breast	Associate	35587107
Carcinoma Endometrioid	Associate	26722522
Carcinoma Hepatocellular	Stimulate	11247902, 12824919, 16227623, 17763368, 19329941, 23192642, 24369324, 25896897, 28207681, 28402954, 29569872, 36853298
Carcinoma Hepatocellular	Associate	15826317, 15920546, 15991281, 17006932, 18264086, 18536657, 18976006, 19038010, 19496787, 19517479, 20653060, 20845507, 20868507, 21040406, 21057160 View all (72 more)
Carcinoma Intraductal Noninfiltrating	Associate	36676710
Carcinoma Merkel Cell	Associate	35507536, 35937502
Carcinoma Non Small Cell Lung	Associate	34112123
Carcinoma Ovarian Epithelial	Associate	29933751
Carcinoma Pancreatic Ductal	Associate	27689616, 33302876
Carcinoma Renal Cell	Stimulate	19243386
Carcinoma Renal Cell	Inhibit	25168166
Carcinoma Renal Cell	Associate	34449964
Carcinoma Signet Ring Cell	Inhibit	27259271
Carcinoma Squamous Cell	Stimulate	18469798, 25896897, 37965271
Carcinoma Squamous Cell	Associate	21623236, 26345955, 34112123
Chemical and Drug Induced Liver Injury	Associate	33902495
Cholangiocarcinoma	Associate	27552844, 28028292, 29271183, 31567946, 34715880
Chromosome Disorders	Associate	30683921
Colorectal Neoplasms	Associate	15920546, 25619476, 35848476, 36434637
Death	Stimulate	35937502
Drug Related Side Effects and Adverse Reactions	Associate	37986544
Endodermal Sinus Tumor	Associate	19329941, 26076062, 27443515, 31375771, 37986544
Endometrial Neoplasms	Associate	26722522
Endometriosis	Associate	36930359
Fuchs' Endothelial Dystrophy	Stimulate	35239706
Gestational Trophoblastic Disease	Associate	20868507
Granulosa Cell Tumor	Associate	26076062
Hamartoma	Associate	21937079
Heart Defects Congenital	Associate	22318994
Hemangioblastoma	Associate	26768750
Hepatitis B	Associate	27286460
Hepatitis C	Stimulate	23532638
Hepatitis C	Associate	29577937
Hepatitis C Chronic	Stimulate	24369324
Hepatoblastoma	Associate	15920546, 21937079, 25735325, 28476031
Hyperostosis corticalis deformans juvenilis	Associate	36676710
Hypoxia	Stimulate	33420124
Hypoxia	Associate	37131292
Hypoxia Brain	Associate	37131292
Idiopathic Noncirrhotic Portal Hypertension	Associate	18976006
Inflammation	Associate	33302876, 34580602
Leukemia Lymphocytic Chronic B Cell	Associate	23537217
Leukemia Myeloid Acute	Associate	19243386
Liposarcoma	Associate	35507536
Liver Cirrhosis	Associate	18536657, 36853298
Liver Diseases	Associate	11247902
Liver Failure	Associate	23114924
Liver Neoplasms	Associate	21937079, 22606345
Liver Neoplasms	Stimulate	33902495
Lown Ganong Levine Syndrome	Associate	21057160
Lung Neoplasms	Associate	18469798, 26345955
Lymphatic Metastasis	Associate	26345955, 27286460, 29398870
Lymphatic Metastasis	Stimulate	27689616
Lymphoma Non Hodgkin	Associate	24498024
MASS syndrome	Associate	18976006
Melanoma	Stimulate	19329941
Melanoma	Associate	19517479, 25896897
Mesothelioma Malignant	Associate	17636483
Microvascular Angina	Associate	36973651
Musculoskeletal Abnormalities	Associate	9950367
Neoplasm Invasiveness	Associate	22654434
Neoplasm Metastasis	Associate	19243386, 21438004, 23532638, 24633918, 26977595, 27689616
Neoplasm Metastasis	Inhibit	27259271
Neoplasm Metastasis	Stimulate	35848476
Neoplasms	Associate	12819009, 18469798, 19243386, 20053773, 20868507, 21057160, 21668581, 22073364, 22098159, 22449976, 22606345, 22654434, 23537217, 25896897, 26107238 View all (28 more)
Neoplasms	Inhibit	24502776, 25168166
Neoplasms	Stimulate	26057582, 26722522, 27689616
Neoplasms Germ Cell and Embryonal	Associate	15083193
Neoplasms Squamous Cell	Stimulate	29935166
Neoplasms Squamous Cell	Associate	35507536
Neuroblastoma	Associate	15083193
Neuroendocrine Tumors	Associate	18264086
Odontogenic Tumors	Associate	36510965
Odontoma	Associate	39365497
Orofacial Cleft 1	Associate	40147726
Osteoarthritis	Associate	30947517
Osteoarthritis Knee	Associate	30947517
Osteosarcoma	Associate	35946078, 40433364
Ovarian Neoplasms	Associate	19329941, 21668581
Pancreatic Diseases	Associate	27689616
Pituitary Neoplasms	Associate	36686480
Portal Vein Cavernous Transformation Of	Associate	31141571
Prostatic Neoplasms	Associate	20053773
Retinal Dysplasia	Associate	27689616
Simpson Golabi Behmel syndrome	Associate	20868507, 23169491, 28600484, 30683921, 31651874, 9192268, 9950367
Soft Tissue Injuries	Associate	20868507
Squamous Cell Carcinoma of Head and Neck	Associate	29935166
Stomach Neoplasms	Associate	19243386, 27259271, 28028292, 33791386, 34706681, 35050429, 37036308
Tertiary Lymphoid Structures	Associate	26977595
Testicular Germ Cell Tumor	Stimulate	25896897
Thyroid Nodule	Associate	24498024
Trophoblastic Tumor Placental Site	Associate	20868507
Urethral Neoplasms	Associate	25896897
Uterine Cervical Dysplasia	Stimulate	27689616
Wilms Tumor	Associate	12085187, 15083193, 9950367

GPC3 (glypican 3)