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GPC6 glypican 6 [ Homo sapiens (human) ]

Gene ID: 10082, updated on 1-Jun-2020

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
109.20200522 current GRCh38.p13 (GCF_000001405.39) 13 NC_000013.11 (93226807..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 Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Autosomal recessive omodysplasia
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

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 presynapse assembly 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
 
synaptic membrane adhesion IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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
    4983..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 Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000013.11 Reference GRCh38.p13 Primary Assembly

    Range
    93226807..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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