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    GPC5 glypican 5 [ Homo sapiens (human) ]

    Gene ID: 2262, updated on 17-Sep-2024

    Summary

    Official Symbol
    GPC5provided by HGNC
    Official Full Name
    glypican 5provided by HGNC
    Primary source
    HGNC:HGNC:4453
    See related
    Ensembl:ENSG00000179399 MIM:602446; AllianceGenome:HGNC:4453
    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
    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 protein anchored to the cytoplasmic membrane via a glycosyl phosphatidylinositol linkage. These proteins may play a role in the control of cell division and growth regulation. [provided by RefSeq, Jul 2008]
    Expression
    Biased expression in brain (RPKM 1.8), testis (RPKM 1.4) and 7 other tissues See more
    Orthologs
    NEW
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    Try the new Transcript table

    Genomic context

    See GPC5 in Genome Data Viewer
    Location:
    13q31.3
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 13 NC_000013.11 (91398621..92867237)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (90601154..92070908)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (92050875..93519490)

    Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7863 Neighboring gene uncharacterized LOC124903189 Neighboring gene Sharpr-MPRA regulatory region 6090 Neighboring gene miR-17-92a-1 cluster host gene Neighboring gene microRNA 92a-1 Neighboring gene RNA, U4atac small nuclear 3, pseudogene Neighboring gene NANOG hESC enhancer GRCh37_chr13:92870965-92871466 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:92932846-92933346 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:92933347-92933847 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:92943271-92943775 Neighboring gene fatty acid binding protein 5 pseudogene 4 Neighboring gene GPC5 antisense RNA 2 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr13:93089056-93089650 Neighboring gene Sharpr-MPRA regulatory region 998 Neighboring gene uncharacterized LOC124903190 Neighboring gene GPC5 intronic transcript 1 Neighboring gene microRNA 548as Neighboring gene uncharacterized LOC105370315 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:93404424-93405150 Neighboring gene GPC5 antisense RNA 1 Neighboring gene uncharacterized LOC105370317 Neighboring gene long intergenic non-protein coding RNA 363

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Copy number response

    Description
    Copy number response
    Haploinsufficency

    No evidence available (Last evaluated 2012-03-08)

    ClinGen Genome Curation Page
    Triplosensitivity

    No evidence available (Last evaluated 2012-03-08)

    ClinGen Genome Curation Page

    EBI GWAS Catalog

    Description
    A genome-wide association study in 19 633 Japanese subjects identified LHX3-QSOX2 and IGF1 as adult height loci.
    EBI GWAS Catalog
    Common variation in GPC5 is associated with acquired nephrotic syndrome.
    EBI GWAS Catalog
    Gene-Smoking Interactions Identify Several Novel Blood Pressure Loci in the Framingham Heart Study.
    EBI GWAS Catalog
    Genetic variants and risk of lung cancer in never smokers: a genome-wide association study.
    EBI GWAS Catalog
    Genetics meets metabolomics: a genome-wide association study of metabolite profiles in human serum.
    EBI GWAS Catalog
    Genome-wide association analysis of susceptibility and clinical phenotype in multiple sclerosis.
    EBI GWAS Catalog
    Genome-wide association study identifies loci on 12q24 and 13q32 associated with tetralogy of Fallot.
    EBI GWAS Catalog
    Genome-wide association study of chemotherapeutic agent-induced severe neutropenia/leucopenia for patients in Biobank Japan.
    EBI GWAS Catalog
    Host determinants of HIV-1 control in African Americans.
    EBI GWAS Catalog
    Hundreds of variants clustered in genomic loci and biological pathways affect human height.
    EBI GWAS Catalog
    Meta-analysis of genome-wide association studies of adult height in East Asians identifies 17 novel loci.
    EBI GWAS Catalog
    Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    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 positive regulation of canonical Wnt signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in regulation of protein localization to membrane IBA
    Inferred from Biological aspect of Ancestor
    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 TAS
    Traceable Author Statement
    more info
     
    located_in lysosomal lumen TAS
    Traceable Author Statement
    more info
     
    located_in membrane TAS
    Traceable Author Statement
    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
     

    General protein information

    Preferred Names
    glypican-5
    Names
    bA93M14.1
    glypican proteoglycan 5

    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_009370.2 RefSeqGene

      Range
      4941..1473557
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_004466.6 → NP_004457.1  glypican-5 precursor

      See identical proteins and their annotated locations for NP_004457.1

      Status: REVIEWED

      Source sequence(s)
      BC039730, DB100549, HY017486
      Consensus CDS
      CCDS9468.1
      UniProtKB/Swiss-Prot
      B2R726, O60436, P78333, Q9BX27
      Related
      ENSP00000366267.3, ENST00000377067.9
      Conserved Domains (1) summary
      pfam01153
      Location:12 → 569
      Glypican; 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
      91398621..92867237
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017020435.3 → XP_016875924.1  glypican-5 isoform X1

    2. XM_011521054.4 → XP_011519356.1  glypican-5 isoform X2

      Conserved Domains (1) summary
      pfam01153
      Location:12 → 467
      Glypican; Glypican
    3. XM_017020437.2 → XP_016875926.1  glypican-5 isoform X3

      Conserved Domains (1) summary
      pfam01153
      Location:12 → 423
      Glypican; Glypican
    4. XM_011521059.3 → XP_011519361.1  glypican-5 isoform X3

      See identical proteins and their annotated locations for XP_011519361.1

      Conserved Domains (1) summary
      pfam01153
      Location:12 → 423
      Glypican; Glypican
    5. XM_011521058.3 → XP_011519360.1  glypican-5 isoform X3

      See identical proteins and their annotated locations for XP_011519360.1

      Conserved Domains (1) summary
      pfam01153
      Location:12 → 423
      Glypican; Glypican
    6. XM_011521060.3 → XP_011519362.1  glypican-5 isoform X4

      Conserved Domains (1) summary
      pfam01153
      Location:12 → 423
      Glypican; Glypican
    7. XM_017020436.3 → XP_016875925.1  glypican-5 isoform X3

      Conserved Domains (1) summary
      pfam01153
      Location:12 → 423
      Glypican; Glypican
    8. XM_011521055.4 → XP_011519357.1  glypican-5 isoform X3

      See identical proteins and their annotated locations for XP_011519357.1

      Conserved Domains (1) summary
      pfam01153
      Location:12 → 423
      Glypican; Glypican
    9. XM_011521056.4 → XP_011519358.1  glypican-5 isoform X3

      See identical proteins and their annotated locations for XP_011519358.1

      Conserved Domains (1) summary
      pfam01153
      Location:12 → 423
      Glypican; Glypican
    10. XM_011521057.4 → XP_011519359.1  glypican-5 isoform X3

      See identical proteins and their annotated locations for XP_011519359.1

      Conserved Domains (1) summary
      pfam01153
      Location:12 → 423
      Glypican; Glypican
    11. XM_047430153.1 → XP_047286109.1  glypican-5 isoform X5

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060937.1 Alternate T2T-CHM13v2.0

      Range
      90601154..92070908
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054374222.1 → XP_054230197.1  glypican-5 isoform X1

    2. XM_054374223.1 → XP_054230198.1  glypican-5 isoform X2

    3. XM_054374228.1 → XP_054230203.1  glypican-5 isoform X3

    4. XM_054374229.1 → XP_054230204.1  glypican-5 isoform X3

    5. XM_054374227.1 → XP_054230202.1  glypican-5 isoform X3

    6. XM_054374230.1 → XP_054230205.1  glypican-5 isoform X4

    7. XM_054374224.1 → XP_054230199.1  glypican-5 isoform X3

    8. XM_054374225.1 → XP_054230200.1  glypican-5 isoform X3

    9. XM_054374226.1 → XP_054230201.1  glypican-5 isoform X3

    10. XM_054374231.1 → XP_054230206.1  glypican-5 isoform X5