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GPC6 glypican 6 [ Homo sapiens (human) ]

Gene ID: 10082, updated on 12-May-2019

Summary

Official Symbol
GPC6provided by HGNC
Official Full Name
glypican 6provided by HGNC
Primary source
HGNC:HGNC:4454
See related
Ensembl:ENSG00000183098 MIM:604404
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

Genomic context

See GPC6 in Genome Data Viewer
Location:
13q31.3-q32.1
Exon count:
15
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 13 NC_000013.11 (93226808..94408020)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (93879078..95060274)

Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105370317 Neighboring gene long intergenic non-protein coding RNA 363 Neighboring gene heterogeneous nuclear ribonucleoprotein A1 pseudogene 29 Neighboring gene GPC6 antisense RNA 2 Neighboring gene RNA, 5S ribosomal pseudogene 35 Neighboring gene GPC6 antisense RNA 1 Neighboring gene tRNA-Phe (anticodon GAA) 1-5 Neighboring gene dopachrome tautomerase

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Omodysplasia 1
MedGen: C1850318 OMIM: 258315 GeneReviews: Not available
Compare labs

NHGRI GWAS Catalog

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

Pathways from BioSystems

  • A tetrasaccharide linker sequence is required for GAG synthesis, organism-specific biosystem (from REACTOME)
    A tetrasaccharide linker sequence is required for GAG synthesis, organism-specific biosystemThe biosynthesis of dermatan sulfate/chondroitin sulfate and heparin/heparan sulfate glycosaminoglycans (GAGs) starts with the formation of a tetrasaccharide linker sequence to the core protein. The ...
  • Chondroitin sulfate/dermatan sulfate metabolism, organism-specific biosystem (from REACTOME)
    Chondroitin sulfate/dermatan sulfate metabolism, organism-specific biosystemChondroitin sulfate (CS) is a sulfated glycosaminoglycan (GAG). CS chains are unbranched polysaccharides of varying length containing two alternating monosaccharides: D-glucuronic acid (GlcA) and N-a...
  • Defective B3GALT6 causes EDSP2 and SEMDJL1, organism-specific biosystem (from REACTOME)
    Defective B3GALT6 causes EDSP2 and SEMDJL1, organism-specific biosystemThe biosynthesis of dermatan sulfate/chondroitin sulfate and heparin/heparan sulfate glycosaminoglycans (GAGs) starts with the formation of a tetrasaccharide linker sequence attached to the core prot...
  • Defective B3GAT3 causes JDSSDHD, organism-specific biosystem (from REACTOME)
    Defective B3GAT3 causes JDSSDHD, organism-specific biosystemGalactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferases1, 2 and 3 (B3GAT1-3) are involved in forming the linker tetrasaccharide present in heparan sulfate and chondroitin sulfate. Defects ...
  • Defective B4GALT7 causes EDS, progeroid type, organism-specific biosystem (from REACTOME)
    Defective B4GALT7 causes EDS, progeroid type, organism-specific biosystemEhlers?Danlos syndrome (EDS) is a group of inherited connective tissue disorders, caused by a defect in the synthesis of collagen types I or III. Abnormal collagen renders connective tissues more ela...
  • Defective EXT1 causes exostoses 1, TRPS2 and CHDS, organism-specific biosystem (from REACTOME)
    Defective EXT1 causes exostoses 1, TRPS2 and CHDS, organism-specific biosystemHeparan sulfate (HS) is involved in regulating various body functions functions during development, homeostasis and pathology including blood clotting, angiogenesis and metastasis of cancer cells. Ex...
  • Defective EXT2 causes exostoses 2, organism-specific biosystem (from REACTOME)
    Defective EXT2 causes exostoses 2, organism-specific biosystemHeparan sulfate (HS) is involved in regulating various body functions during development, homeostasis and pathology including blood clotting, angiogenesis and metastasis of cancer cells. Exostosin 1 ...
  • Disease, organism-specific biosystem (from REACTOME)
    Disease, organism-specific biosystemBiological processes are captured in Reactome by identifying the molecules (DNA, RNA, protein, small molecules) involved in them and describing the details of their interactions. From this molecular ...
  • Diseases associated with glycosaminoglycan metabolism, organism-specific biosystem (from REACTOME)
    Diseases associated with glycosaminoglycan metabolism, organism-specific biosystemA number of genetic disorders are caused by mutations in the genes encoding glycosyltransferases and sulfotransferases, enzymes responsible for the synthesis of glycosaminoglycans (GAGs) as well as ...
  • Diseases of glycosylation, organism-specific biosystem (from REACTOME)
    Diseases of glycosylation, organism-specific biosystemDiseases of glycosylation, usually referred to as congenital disorders of glycosylation (CDG), are rare inherited disorders ascribing defects of nucleotide-sugar biosynthesis and transport, glycosylt...
  • Glycosaminoglycan metabolism, organism-specific biosystem (from REACTOME)
    Glycosaminoglycan metabolism, organism-specific biosystemGlycosaminoglycans (GAGs) are long, unbranched polysaccharides containing a repeating disaccharide unit composed of a hexosamine (either N-acetylgalactosamine (GalNAc) or N-acetylglucosamine (GlcNAc)...
  • HS-GAG biosynthesis, organism-specific biosystem (from REACTOME)
    HS-GAG biosynthesis, organism-specific biosystemHeparan sulfate (HS) and heparin (sometimes collectively called HS-GAG) consist of the disaccharide unit GlcNAc-GlcA (N-acetylglucosamine-glucuronic acid) connected by a beta1,4 linkage. Heparin is e...
  • HS-GAG degradation, organism-specific biosystem (from REACTOME)
    HS-GAG degradation, organism-specific biosystemLysosomal degradation of glycoproteins is part of the cellular homeostasis of glycosylation (Winchester 2005). The steps outlined below describe the degradation of heparan sulfate/heparin. Complete d...
  • Heparan sulfate/heparin (HS-GAG) metabolism, organism-specific biosystem (from REACTOME)
    Heparan sulfate/heparin (HS-GAG) metabolism, organism-specific biosystemThe acronym HS-GAG is used to describe both heparin and heparan sulfate. HS-GAG is a member of the glycosaminoglycan family and consists of a variably sulfated repeating disaccharide unit, the most ...
  • Metabolism, organism-specific biosystem (from REACTOME)
    Metabolism, organism-specific biosystemMetabolic processes in human cells generate energy through the oxidation of molecules consumed in the diet and mediate the synthesis of diverse essential molecules not taken in the diet as well as th...
  • Metabolism of carbohydrates, organism-specific biosystem (from REACTOME)
    Metabolism of carbohydrates, organism-specific biosystemThese pathways together are responsible for: 1) the extraction of energy and carbon skeletons for biosyntheses from dietary sugars and related molecules; 2) the short-term storage of glucose in the b...
  • Metabolism of fat-soluble vitamins, organism-specific biosystem (from REACTOME)
    Metabolism of fat-soluble vitamins, organism-specific biosystemVitamins A, D, E, and K are classified as fat-soluble. Metabolic pathways by which dietary precursors of vitamins A (Harrison 2005) and K(Shearer et al. 2012) are converted to active forms, and by wh...
  • Metabolism of vitamins and cofactors, organism-specific biosystem (from REACTOME)
    Metabolism of vitamins and cofactors, organism-specific biosystemVitamins are a diverse group of organic compounds, classified according to their solubility, either fat-soluble or water-soluble, that are either not synthesized or synthesized only in limited amount...
  • Retinoid metabolism and transport, organism-specific biosystem (from REACTOME)
    Retinoid metabolism and transport, organism-specific biosystemVitamin A (all-trans-retinol) must be taken up, either as carotenes from plants, or as retinyl esters from animal food. The most prominent carotenes are alpha-carotene, lycopene, lutein, beta-cryptox...
  • Signal Transduction, organism-specific biosystem (from REACTOME)
    Signal Transduction, organism-specific biosystemSignal transduction is a process in which extracellular signals elicit changes in cell state and activity. Transmembrane receptors sense changes in the cellular environment by binding ligands, such a...
  • Visual phototransduction, organism-specific biosystem (from REACTOME)
    Visual phototransduction, organism-specific biosystemVisual phototransduction is the process by which photon absorption by visual pigment molecules in photoreceptor cells is converted to an electrical cellular response. The events in this process are p...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC126288

Gene Ontology Provided by GOA

Function Evidence Code Pubs
coreceptor activity involved in Wnt signaling pathway, planar cell polarity pathway NAS
Non-traceable Author Statement
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
Wnt signaling pathway, planar cell polarity pathway IEA
Inferred from Electronic Annotation
more info
 
cell migration IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cell migration IDA
Inferred from Direct Assay
more info
PubMed 
glycosaminoglycan biosynthetic process TAS
Traceable Author Statement
more info
 
glycosaminoglycan catabolic process TAS
Traceable Author Statement
more info
 
regulation of neurotransmitter receptor localization to postsynaptic specialization membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of protein localization to membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of signal transduction IEA
Inferred from Electronic Annotation
more info
 
retinoid metabolic process TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
Golgi lumen TAS
Traceable Author Statement
more info
 
anchored component of plasma membrane IEA
Inferred from Electronic Annotation
more info
 
cell surface IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
collagen-containing extracellular matrix IEA
Inferred from Electronic Annotation
more info
 
extracellular region IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
extracellular space IEA
Inferred from Electronic Annotation
more info
 
glutamatergic synapse IEA
Inferred from Electronic Annotation
more info
 
lysosomal lumen TAS
Traceable Author Statement
more info
 
nucleus HDA PubMed 
plasma membrane TAS
Traceable Author Statement
more info
 
synapse IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

Preferred Names
glypican-6
Names
glypican proteoglycan 6

NCBI Reference Sequences (RefSeq)

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

  1. NG_011880.1 RefSeqGene

    Range
    4984..1186197
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_005708.5NP_005699.1  glypican-6 precursor

    See identical proteins and their annotated locations for NP_005699.1

    Status: REVIEWED

    Source sequence(s)
    AF111178, AK290144, AL137144, AL354811, AY358462, BQ009005, BX640888, DA267422
    Consensus CDS
    CCDS9469.1
    UniProtKB/Swiss-Prot
    Q9Y625
    Related
    ENSP00000366246.3, ENST00000377047.9
    Conserved Domains (1) summary
    pfam01153
    Location:22548
    Glypican; Glypican

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000013.11 Reference GRCh38.p12 Primary Assembly

    Range
    93226808..94408020
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017020299.2XP_016875788.1  glypican-6 isoform X1

    Conserved Domains (1) summary
    pfam01153
    Location:1478
    Glypican; Glypican
  2. XM_011521044.2XP_011519346.1  glypican-6 isoform X1

    Conserved Domains (1) summary
    pfam01153
    Location:1478
    Glypican; Glypican
  3. XM_017020300.1XP_016875789.1  glypican-6 isoform X1

    Conserved Domains (1) summary
    pfam01153
    Location:1478
    Glypican; Glypican
  4. XM_017020298.1XP_016875787.1  glypican-6 isoform X1

    Conserved Domains (1) summary
    pfam01153
    Location:1478
    Glypican; Glypican
  5. XM_017020301.1XP_016875790.1  glypican-6 isoform X2

  6. XM_017020302.1XP_016875791.1  glypican-6 isoform X3

    Related
    ENSP00000477667.1, ENST00000617456.1
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