The gene spans 32381 pb of DNA, comprising 9 exons.

1676 bp open reading frame.

The glypican-1 gene codes for a protein of 558 amino acids with a predicted molecular weight of 62 kDa. It is a cell surface, lipid-raft-associated heparan sulfate proteoglycan (HSPG), composed of a glycosylphosphatidylinositol (GPI)-anchored core protein substituted with a three chains of heparan sulfate near its C-terminus. It shares, along with all other glypicans, an N-terminal secretory signal, heparan sulfate attachment sites, 14 evolutionary conserved cysteine residues and hydrophobic domain near the C-terminus for the addition of the glycosylphosphatidylinositol (GPI) anchor. Also, the glypican-1 core protein contains two N-glycosylation sites at Asn79 & Asn116, which are found to be invariably occupied. The N-linked glycans at these sites affect Gpc-1 protein expression and heparan sulfate substitution. Nevertheless the protein is folded correctly even in the absence of N-linked glycans (Svensson et al., 2011). Recently, the structure of C-terminally truncated human N-glycosylated Gpc-1 core protein was determined at 2.55 Å resolution (Svensson et al., 2012; Awad et al., 2013), which revealed a highly extended, cylindrical (dimensions 120 x 30 x 30 Å), stable all-α-helical fold. Its structural similarity to the Dally-like protein from Drosophila (Kim et al., 2011) confirmed a conserved overall fold for the glypican family. The Gpc-1 structure consists of 14 α-helices (α1- α14) and three major loops (L1-L3). The extended helix α2 (83Å) traverses the whole protein, carrying two N-linked glycans close to its ends. The Gpc-1 structure revealed the complete arrangement of the 14 Cys residues conserved across the glypican family, in 7 disulfide bonds, 6 of them located near the molecule N terminus at a region termed "Cys-rich lobe". This lobe is followed by a region forms the heart of the structure called the "central lobe". This lobe is stabilized by evolutionary conserved hydrophobic centers. The last region of the Gpc-1 molecule is termed the "protease site lobe" because of the presence of a protease site in this part. No additional electron density was observed in the electron density maps from crystals of non-truncated glypican-1 containing the HS attachment region near the C-terminus, which suggests that this part is highly disordered. This extended long C terminus (50 residues) might thus give the core protein a freedom in its orientation when Gpc-1 is anchored to the cell membrane (Svensson et al., 2012).

GPC1 is expressed mainly in the central nervous system (CNS) and skeletal system during development but also in many other tissues in the adult.

GPC1 is a cell surface HSPG that can be internalized via a caveolin-1 associated pathway. GPC1 undergoes a recycling from cell surface to endosomes and back to the cell surface via Golgi. During recycling, the HS chains of GPC1 are degraded by heparanase and further on by a novel copper, nitric oxide and vitamin C-dependent deaminative cleavage. New HS chains are synthesized on the stubs remaining on the core protein (Cheng et al., 2002; Fransson and Mani, 2007).

Many of the functions of GPC1 are dependent on the HS side chains, which are capable of binding and/or activating and/or transporting a variety of growth factors (FGF2), cytokines, enzymes, viral proteins, and polyamines. It is known that both the core protein and the HS chains of GPC1 are important for brain function, as knock-out of GPC1 gene expression results in reduction of brain size by 30% (Jen et al., 2009) and errors in HS metabolism result in neurodegeneration and mental retardation accompanied by accumulation of amyloid β in human brain (Ohmi et al., 2011). A role for GPC1 in axonal guidance and regeneration via Slit has been proposed (Bloechlinger et al., 2004; Lau and Margolis, 2010). Several studies indicate involvement of Gpc1 in prion conversion and scrapie infection (Löfgren et al., 2008; Taylor et al., 2009; Hooper, 2011).

GPC1 belongs to the glypican family. To date, six different glypicans have been identified in vertebrates (GPC1, GPC2, GPC3, GPC4, GPC5, and GPC6), two in Drosophila melanogaster (Dally and Dally-like protein), two in C. elegans (Gpn-1 and Lon-2) and one in zebrafish (knypek). Based on sequence comparisons, vertebrate glypicans fall into two subfamilies: glypicans 1, 2, 4, 6 and glypicans 3 and 5, with approximately 25% amino acid identity between the groups.