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GPC5 glypican 5 [ Homo sapiens (human) ]

Gene ID: 2262, updated on 4-Sep-2018

Summary

Official Symbol
GPC5provided by HGNC
Official Full Name
glypican 5provided by HGNC
Primary source
HGNC:HGNC:4453
See related
Ensembl:ENSG00000179399 MIM:602446; Vega:OTTHUMG00000017200
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

Genomic context

See GPC5 in Genome Data Viewer
Location:
13q31.3
Exon count:
14
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 13 NC_000013.11 (91398619..92867237)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (92050935..93519490)

Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107984617 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 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 Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat'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

NHGRI GWAS Catalog

Description
A genome-wide association study in 19 633 Japanese subjects identified LHX3-QSOX2 and IGF1 as adult height loci.
NHGRI GWA Catalog
Common variation in GPC5 is associated with acquired nephrotic syndrome.
NHGRI GWA Catalog
Gene-Smoking Interactions Identify Several Novel Blood Pressure Loci in the Framingham Heart Study.
NHGRI GWA Catalog
Genetic variants and risk of lung cancer in never smokers: a genome-wide association study.
NHGRI GWA Catalog
Genetics meets metabolomics: a genome-wide association study of metabolite profiles in human serum.
NHGRI GWA Catalog
Genome-wide association analysis of susceptibility and clinical phenotype in multiple sclerosis.
NHGRI GWA Catalog
Genome-wide association study identifies loci on 12q24 and 13q32 associated with tetralogy of Fallot.
NHGRI GWA Catalog
Genome-wide association study of chemotherapeutic agent-induced severe neutropenia/leucopenia for patients in Biobank Japan.
NHGRI GWA Catalog
Host determinants of HIV-1 control in African Americans.
NHGRI GWA Catalog
Hundreds of variants clustered in genomic loci and biological pathways affect human height.
NHGRI GWA Catalog
Meta-analysis of genome-wide association studies of adult height in East Asians identifies 17 novel loci.
NHGRI GWA Catalog
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
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...
  • Hedgehog ligand biogenesis, organism-specific biosystem (from REACTOME)
    Hedgehog ligand biogenesis, organism-specific biosystemMammalian genomes encode three Hedgehog ligands, Sonic Hedgehog (SHH), Indian Hedgehog (IHH) and Desert Hedgehog (DHH). These secreted morphogens can remain associated with lipid rafts on the surfac...
  • 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...
  • Release of Hh-Np from the secreting cell, organism-specific biosystem (from REACTOME)
    Release of Hh-Np from the secreting cell, organism-specific biosystemCholesterol and palmitoyl-modification of Hh-Np render the ligand highly hydrophobic and results in its close association with the plasma membrane of the producing cell after secretion. Hh-Np tether...
  • 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...
  • Signaling by Hedgehog, organism-specific biosystem (from REACTOME)
    Signaling by Hedgehog, organism-specific biosystemHedgehog (Hh) is a secreted morphogen that regulates developmental processes in vertebrates including limb bud formation, neural tube patterning, cell growth and differentiation (reviewed in Hui and ...
  • 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

Gene Ontology Provided by GOA

Process Evidence Code Pubs
glycosaminoglycan biosynthetic process TAS
Traceable Author Statement
more info
 
glycosaminoglycan catabolic process TAS
Traceable Author Statement
more info
 
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
 
collagen-containing extracellular matrix IEA
Inferred from Electronic Annotation
more info
 
extracellular region TAS
Traceable Author Statement
more info
 
extracellular space IEA
Inferred from Electronic Annotation
more info
 
integral component of membrane TAS
Traceable Author Statement
more info
PubMed 
lysosomal lumen TAS
Traceable Author Statement
more info
 
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)

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_009370.1 RefSeqGene

    Range
    4939..1473556
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_004466.5NP_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
    Related
    ENSP00000366267.3, OTTHUMP00000018551, ENST00000377067.8, OTTHUMT00000045454
    Conserved Domains (1) summary
    pfam01153
    Location:12569
    Glypican; Glypican

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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
    91398619..92867237
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017020435.2XP_016875924.1  glypican-5 isoform X1

  2. XM_011521054.3XP_011519356.1  glypican-5 isoform X2

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

    Conserved Domains (1) summary
    pfam01153
    Location:12423
    Glypican; Glypican
  4. XM_011521059.2XP_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_011521058.2XP_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_011521060.2XP_011519362.1  glypican-5 isoform X4

    Conserved Domains (1) summary
    pfam01153
    Location:12423
    Glypican; Glypican
  7. XM_017020436.2XP_016875925.1  glypican-5 isoform X3

    Conserved Domains (1) summary
    pfam01153
    Location:12423
    Glypican; Glypican
  8. XM_011521055.3XP_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_011521056.3XP_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_011521057.3XP_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
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