GPC6 glypican 6 [Homo sapiens (human)] - Gene

Summary

Official Symbol: GPC6provided by HGNC
Official Full Name: glypican 6provided by HGNC
Primary source: HGNC:HGNC:4454
See related: Ensembl:ENSG00000183098 MIM:604404; AllianceGenome:HGNC:4454
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: OMIMD1
Summary: The glypicans comprise a family of glycosylphosphatidylinositol-anchored heparan sulfate proteoglycans, and they have been implicated in the control of cell growth and cell division. The glypican encoded by this gene is a putative cell surface coreceptor for growth factors, extracellular matrix proteins, proteases and anti-proteases. Mutations in this gene are associated with omodysplasia 1. [provided by RefSeq, Nov 2016]
Expression: Broad expression in gall bladder (RPKM 6.5), urinary bladder (RPKM 3.9) and 21 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 13q31.3-q32.1

Exon count:: 12

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	13	NC_000013.11 (93216529..94408020)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	13	NC_060937.1 (92430763..93611616)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	13	NC_000013.10 (93879060..95060274)

Chromosome 13 - NC_000013.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues 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?

Five siblings expand the spectrum of GPC6-related skeletal dysplasia.
Title: Five siblings expand the spectrum of GPC6-related skeletal dysplasia.
Prognostic value of GPC5 polymorphism rs2352028 and clinical characteristics in Chinese lung cancer patients.
Title: Prognostic value of GPC5 polymorphism rs2352028 and clinical characteristics in Chinese lung cancer patients.
TDP-43 proteinopathy alters the ribosome association of multiple mRNAs including the glypican Dally-like protein (Dlp)/GPC6.
Title: TDP-43 proteinopathy alters the ribosome association of multiple mRNAs including the glypican Dally-like protein (Dlp)/GPC6.
Can Glypican-6 Level Predict Ejection Fraction Decline After Myocardial Infarction?
Title: Can Glypican-6 Level Predict Ejection Fraction Decline After Myocardial Infarction?
Hedgehog signaling activation required for glypican-6-mediated regulation of invasion, migration, and epithelial-mesenchymal transition of gastric cancer cells.
Title: Hedgehog signaling activation required for glypican-6-mediated regulation of invasion, migration, and epithelial-mesenchymal transition of gastric cancer cells.
GPC6 rs4773724 was associated with a decreased risk of LDH in allele model (OR = 0.82, 95% CI: 0.68-0.98, p = 0.026), whereas rs1008993 increased the LDH risk (OR = 1.34, 95% CI: 1.05-1.71, p = 0.020). rs4773724 and rs9523981 were associated with susceptibility of LDH among individuals whose age are less than 45. And rs1008993 was associated with increased LDH risk in males.
Title: Association of glypican-6 polymorphisms with lumbar disk herniation risk in the Han Chinese population.
findings identified GPC6 as an early biomarker for melanoma metastatic progression, one that can be regulated by miR-509-3p.
Title: Glypican 6 is a putative biomarker for metastatic progression of cutaneous melanoma.
Thus, GPC6 and TMEM132D may serve as predictors of CD8+ T-lymphocyte infiltration and as favorable prognostic markers in early stage ovarian cancer with important consequences for diagnosis.
Title: Overexpression of GPC6 and TMEM132D in Early Stage Ovarian Cancer Correlates with CD8+ T-Lymphocyte Infiltration and Increased Patient Survival.
Extracellular matrix proteins expression profiling in chemoresistant variants of the A2780 ovarian cancer cell line.
Title: Extracellular matrix proteins expression profiling in chemoresistant variants of the A2780 ovarian cancer cell line.
GPC6 promotes invasive migration by inhibition of canonical beta-catenin and Wnt signalling, and up-regulation of non-canonical Wnt5A signalling leading to the activation of JNK and p38 MAPK.
Title: NFAT promotes carcinoma invasive migration through glypican-6.

Submit: New GeneRIF Correction See all GeneRIFs (15)

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
Autosomal recessive omodysplasia MedGen: C1850318 OMIM: 258315 GeneReviews: Not available	Compare labs

EBI GWAS Catalog

Description
A genome-wide association study of neuroticism in a population-based sample. EBI GWAS Catalog EBI GWAS CatalogPubMed
A genome-wide meta-analysis identifies novel loci associated with schizophrenia and bipolar disorder. EBI GWAS Catalog EBI GWAS CatalogPubMed
Framingham Heart Study 100K Project: genome-wide associations for blood pressure and arterial stiffness. EBI GWAS Catalog EBI GWAS CatalogPubMed
Gene-Smoking Interactions Identify Several Novel Blood Pressure Loci in the Framingham Heart Study. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genetic variants associated with breast size also influence breast cancer risk. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association for abdominal subcutaneous and visceral adipose reveals a novel locus for visceral fat in women. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study of peripheral neuropathy with D-drug-containing regimens in AIDS Clinical Trials Group protocol 384. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study of the rate of cognitive decline in Alzheimer's disease. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study on dimethylarginines reveals novel AGXT2 variants associated with heart rate variability but not with overall mortality. EBI GWAS Catalog EBI GWAS CatalogPubMed
Heritability and genome-wide association analysis of renal sinus fat accumulation in the Framingham Heart Study. EBI GWAS Catalog EBI GWAS CatalogPubMed
Molecular genetics of adult ADHD: converging evidence from genome-wide association and extended pedigree linkage studies. EBI GWAS Catalog EBI GWAS CatalogPubMed
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population. EBI GWAS Catalog EBI GWAS CatalogPubMed
Novel genetic variants associated with lumbar disc degeneration in northern Europeans: a meta-analysis of 4600 subjects. 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

D13S184E (e-PCR)
- UniSTS:85010

RH44781 (e-PCR)
- UniSTS:28946

GPC6 (e-PCR)
- UniSTS:505365

G62678 (e-PCR)
- UniSTS:139803

STS-AA007180 (e-PCR)
- UniSTS:49437

WI-20311 (e-PCR)
- UniSTS:64798

D13S184E (e-PCR)
- UniSTS:147489

SHGC-105244 (e-PCR)
- UniSTS:169250

RH65457 (e-PCR)
- UniSTS:5156

D8S2279 (e-PCR)
- UniSTS:473907

RH98501 (e-PCR)
- UniSTS:88890

G60425 (e-PCR)
- UniSTS:137531

D13S1665 (e-PCR)
- UniSTS:18245

SHGC-79124 (e-PCR)
- UniSTS:95817

RH118850 (e-PCR)
- UniSTS:138831

D13S167 (e-PCR)
- UniSTS:19281

WI-18223 (e-PCR)
- UniSTS:54103

RH68496 (e-PCR)
- UniSTS:39258

D13S1193 (e-PCR)
- UniSTS:6496

GPC6__6647 (e-PCR)
- UniSTS:464482

G63691 (e-PCR)
- UniSTS:140653

SHGC-78776 (e-PCR)
- UniSTS:101229

D13S197 (e-PCR)
- UniSTS:147566

D13S71 (e-PCR), detects polymorphism
- UniSTS:146806

SHGC-83667 (e-PCR)
- UniSTS:100983

RH44943 (e-PCR)
- UniSTS:28793

D13S1451 (e-PCR)
- UniSTS:63362

RH45636 (e-PCR)
- UniSTS:52612

D13S1093E (e-PCR)
- UniSTS:153222

SHGC-106184 (e-PCR)
- UniSTS:182667

A008V26 (e-PCR)
- UniSTS:11660

SHGC-106880 (e-PCR)
- UniSTS:182668

D13S129 (e-PCR)
- UniSTS:8594

D13S762 (e-PCR)
- UniSTS:6037

RH99121 (e-PCR)
- UniSTS:91553

RH44643 (e-PCR)
- UniSTS:46755

D13S1206 (e-PCR)
- UniSTS:16553

G49558 (e-PCR)
- UniSTS:109227

G49559 (e-PCR)
- UniSTS:109228

D12S1283 (e-PCR)
- UniSTS:30643

G62575 (e-PCR)
- UniSTS:139702

SHGC-58551 (e-PCR)
- UniSTS:94394

SHGC-155183 (e-PCR)
- UniSTS:182723

ATC-P10376 (e-PCR)
- UniSTS:47310

D13S1665 (e-PCR)
- UniSTS:54490

D13S281 (e-PCR), detects polymorphism
- UniSTS:10460

D13S775 (e-PCR), detects polymorphism
- UniSTS:35294

WI-17041 (e-PCR)
- UniSTS:22239

D13S281 (e-PCR), detects polymorphism
- UniSTS:74977

SHGC-81838 (e-PCR)
- UniSTS:182757

SHGC-84554 (e-PCR)
- UniSTS:102892

D13S125 (e-PCR)
- UniSTS:147189

SHGC-58318 (e-PCR)
- UniSTS:65019

WI-18121 (e-PCR)
- UniSTS:80383

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables coreceptor activity	NAS Non-traceable Author Statement more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in cell migration	IBA Inferred from Biological aspect of Ancestor more info
involved_in cell migration	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of neurotransmitter receptor localization to postsynaptic specialization membrane	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of signal transduction	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 extracellular region	IEA Inferred from Electronic Annotation more info
located_in glutamatergic synapse	IEA Inferred from Electronic Annotation more info
located_in lysosomal lumen	TAS Traceable Author Statement more info
located_in nucleus	HDA more info	PubMed
located_in plasma membrane	TAS Traceable Author Statement more info
located_in side of membrane	IEA Inferred from Electronic Annotation more info
is_active_in synapse	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: glypican-6

Names: glypican proteoglycan 6

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.