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GPC5 glypican 5 [ Homo sapiens (human) ]

Gene ID: 2262, updated on 22-Sep-2022

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
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Genomic context

See GPC5 in Genome Data Viewer
Location:
13q31.3
Exon count:
14
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) 13 NC_000013.11 (91398621..92867237)
110 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (90601154..92070908)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (92050875..93519490)

Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903189 Neighboring gene miR-17-92a-1 cluster host gene Neighboring gene microRNA 92a-1 Neighboring gene RNA, U4atac small nuclear 3, pseudogene Neighboring gene fatty acid binding protein 5 pseudogene 4 Neighboring gene GPC5 antisense RNA 2 Neighboring gene uncharacterized LOC124903190 Neighboring gene GPC5 intronic transcript 1 Neighboring gene microRNA 548as Neighboring gene uncharacterized LOC105370315 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
  • 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

Homology

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
PubMed 
involved_in positive regulation of canonical Wnt signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in regulation of protein localization to membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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
PubMed 
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 extracellular space IEA
Inferred from Electronic Annotation
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
 

General protein information

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

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.

Genomic

  1. NG_009370.2 RefSeqGene

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

mRNA and Protein(s)

  1. NM_004466.6NP_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
    P78333, Q9BX27
    Related
    ENSP00000366267.3, ENST00000377067.9
    Conserved Domains (1) summary
    pfam01153
    Location:12569
    Glypican; Glypican

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 110 details...Open this link in a new tab

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_017020435.3XP_016875924.1  glypican-5 isoform X1

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

    Conserved Domains (1) summary
    pfam01153
    Location:12467
    Glypican; Glypican
  3. XM_017020437.2XP_016875926.1  glypican-5 isoform X3

    Conserved Domains (1) summary
    pfam01153
    Location:12423
    Glypican; Glypican
  4. XM_011521059.3XP_011519361.1  glypican-5 isoform X3

    See identical proteins and their annotated locations for XP_011519361.1

    Conserved Domains (1) summary
    pfam01153
    Location:12423
    Glypican; Glypican
  5. XM_011521058.3XP_011519360.1  glypican-5 isoform X3

    See identical proteins and their annotated locations for XP_011519360.1

    Conserved Domains (1) summary
    pfam01153
    Location:12423
    Glypican; Glypican
  6. XM_011521060.3XP_011519362.1  glypican-5 isoform X4

    Conserved Domains (1) summary
    pfam01153
    Location:12423
    Glypican; Glypican
  7. XM_017020436.3XP_016875925.1  glypican-5 isoform X3

    Conserved Domains (1) summary
    pfam01153
    Location:12423
    Glypican; Glypican
  8. XM_011521055.4XP_011519357.1  glypican-5 isoform X3

    See identical proteins and their annotated locations for XP_011519357.1

    Conserved Domains (1) summary
    pfam01153
    Location:12423
    Glypican; Glypican
  9. XM_011521056.4XP_011519358.1  glypican-5 isoform X3

    See identical proteins and their annotated locations for XP_011519358.1

    Conserved Domains (1) summary
    pfam01153
    Location:12423
    Glypican; Glypican
  10. XM_011521057.4XP_011519359.1  glypican-5 isoform X3

    See identical proteins and their annotated locations for XP_011519359.1

    Conserved Domains (1) summary
    pfam01153
    Location:12423
    Glypican; Glypican
  11. XM_047430153.1XP_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)