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    GPC6 glypican 6 [ Homo sapiens (human) ]

    Gene ID: 10082, updated on 9-Dec-2024

    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
    NEW
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    Genomic context

    See GPC6 in Genome Data Viewer
    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_000013.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105370317 Neighboring gene long intergenic non-protein coding RNA 363 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr13:93870107-93870619 Neighboring gene ReSE screen-validated silencer GRCh37_chr13:93876144-93876329 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:93876296-93877246 Neighboring gene H3K27ac hESC enhancer GRCh37_chr13:93879653-93880495 Neighboring gene Sharpr-MPRA regulatory region 9831 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:93895692-93896504 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr13:93900477-93900978 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr13:93900979-93901478 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr13:93957026-93957578 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr13:94066135-94066677 Neighboring gene heterogeneous nuclear ribonucleoprotein A1 pseudogene 29 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:94125933-94126519 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:94148471-94149063 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr13:94213697-94214301 Neighboring gene NANOG hESC enhancer GRCh37_chr13:94267556-94268060 Neighboring gene NANOG hESC enhancer GRCh37_chr13:94470501-94471002 Neighboring gene Sharpr-MPRA regulatory region 9781 Neighboring gene GPC6 antisense RNA 2 Neighboring gene RNA, 5S ribosomal pseudogene 35 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr13:94795799-94796732 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr13:94840401-94841316 Neighboring gene GPC6 antisense RNA 1 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr13:94901699-94902296 Neighboring gene NANOG hESC enhancer GRCh37_chr13:94964513-94965082 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7864 Neighboring gene NANOG hESC enhancer GRCh37_chr13:94996270-94996868 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:95024062-95024724 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr13:95143673-95144872 Neighboring gene uncharacterized LOC124903191 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5434 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

    EBI GWAS Catalog

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

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • MGC126288

    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 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

    Preferred Names
    glypican-6
    Names
    glypican proteoglycan 6

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_011880.2 RefSeqGene

      Range
      15280..1196493
      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
      A8K279, Q96SG5, Q96SG8, Q9H1P4, Q9Y625
      Related
      ENSP00000366246.3, ENST00000377047.9
      Conserved Domains (1) summary
      pfam01153
      Location:22548
      Glypican

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000013.11 Reference GRCh38.p14 Primary Assembly

      Range
      93216529..94408020
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047429990.1XP_047285946.1  glypican-6 isoform X1

    2. XM_017020300.2XP_016875789.1  glypican-6 isoform X1

      Conserved Domains (1) summary
      pfam01153
      Location:1478
      Glypican; Glypican
    3. XM_017020302.2XP_016875791.1  glypican-6 isoform X2

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060937.1 Alternate T2T-CHM13v2.0

      Range
      92430763..93611616
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054373972.1XP_054229947.1  glypican-6 isoform X2