GPC1 - ENSG00000063660
glypican 1
Also known as: glypican
Location: chr2:241,375,088-241,407,493
Gene Type: protein coding
- NCBI Gene
- 2817
- HUGO
- HGNC:4449
- Ensembl
- ENSG00000063660
- VEGA
- OTTHUMG00000133349
- OMIM
- 600395
- UniProtKB
- P35052
Genomic Context
The genome browser snapshot is fully interactive. Mouse over track elements for more information. Click and drag to move tracks. Click and drag on top positional guide to zoom to a sub-region.
To add tracks, use the provided link to switch to the full genome browser view.
The genome browser snapshot is fully interactive. Mouse over track elements for more information. Click and drag to move tracks. Click and drag on top positional guide to zoom to a sub-region.
To add tracks, use the provided link to switch to the full genome browser view.
Gene-based Trait Associations
ADSP WES: Alzheimer's Disease Results from gene-level rare and functional variant aggregation tests for association to AD supported by significane of p < 0.5 / #genes.
Individual score test statistics for rare, predicted functional, and loss of function variants colocated with the gene were aggregated to compute gene level p-values.
See NIAGADS Accession NG00065 for more information.
Results from gene-level rare and functional variant aggregation tests for association to AD supported by significane of p < 0.5 / #genes.
Individual score test statistics for rare, predicted functional, and loss of function variants colocated with the gene were aggregated to compute gene level p-values.
See NIAGADS Accession NG00065 for more information.
| Accession | Population | N SNPs | p-value | Sign. Level | rho | CMAF | CMAC | Covariates | Variant Filter | Caveats |
|---|---|---|---|---|---|---|---|---|---|---|
| NG00065 | European | 2 | 0.179 | N/A | 1 | 9.6e-05 | 2.0 | PCs and sequencing center | LOF | |
| NG00065 | European | 2 | 0.179 | N/A | 1 | 9.6e-05 | 2.0 | PCs and sequencing center | VEP HIGH | |
| NG00065 | Meta | 81 | 0.357 | N/A | 0 | 0.071 | 1528.0 | PCs, sequencing center, sex, age at AD onset or last-known dementia-free age (for controls), and APOE E2 and E4 genotypes | VEP MOD-HIGH | N/A |
| NG00065 | Meta | 81 | 0.409 | N/A | 0 | 0.071 | 1528.0 | PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) | VEP MOD-HIGH | N/A |
| NG00065 | European | 74 | 0.419 | N/A | 0 | 0.071 | 1484.0 | PCs, sequencing center, sex, age at AD onset or last-known dementia-free age (for controls), and APOE E2 and E4 genotypes | VEP MOD-HIGH | N/A |
| NG00065 | European | 74 | 0.462 | N/A | 0 | 0.071 | 1484.0 | PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) | VEP MOD-HIGH | N/A |
| NG00065 | Meta | 81 | 0.548 | N/A | 0 | 0.071 | 1528.0 | PCs and sequencing center | VEP MOD-HIGH | N/A |
| NG00065 | European | 2 | 0.611 | N/A | 1 | 9.6e-05 | 2.0 | PCs, sequencing center, sex, age at AD onset or last-known dementia-free age (for controls), and APOE E2 and E4 genotypes | VEP HIGH | |
| NG00065 | European | 2 | 0.611 | N/A | 1 | 9.6e-05 | 2.0 | PCs, sequencing center, sex, age at AD onset or last-known dementia-free age (for controls), and APOE E2 and E4 genotypes | LOF | |
| NG00065 | European | 74 | 0.618 | N/A | 0 | 0.071 | 1484.0 | PCs and sequencing center | VEP MOD-HIGH | N/A |
| NG00065 | European | 2 | 0.625 | N/A | 1 | 9.6e-05 | 2.0 | PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) | VEP HIGH | |
| NG00065 | European | 2 | 0.625 | N/A | 1 | 9.6e-05 | 2.0 | PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) | LOF | |
| NG00065 | Caribbean Hispanic | 11 | 0.801 | N/A | 1 | 0.056 | 44.1 | PCs and sequencing center | VEP MOD-HIGH | N/A |
| NG00065 | Caribbean Hispanic | 11 | 0.824 | N/A | 1 | 0.056 | 44.1 | PCs, sequencing center, sex, age at AD onset or last-known dementia-free age (for controls), and APOE E2 and E4 genotypes | VEP MOD-HIGH | N/A |
| NG00065 | Caribbean Hispanic | 11 | 0.852 | N/A | 1 | 0.056 | 44.1 | PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) | VEP MOD-HIGH | N/A |
Genetic Variation and Variant-based Trait Associations (GWAS)
Variants contained within the GPC1 gene.
Variants contained within the GPC1 gene.
The GPC1 gene contains 2,896 variants records (corresponding to 2,760 unique genomic positions).
The following variants, contained within ±100kb of GPC1, have been found to be associated with Alzheimer's disease in a GWAS study:
NIAGADS GWAS: Alzheimer's Disease
Variants contained within ±100kb of GPC1 that have genome-wide significance in a NIAGADS Alzheimer's Disease GWAS summary statistics dataset; supported by a p-value < 5 x 10-8. For exome array studies, a cutoff of p-value < 1 x 10-3 was used.
Click on accession numbers to view a detailed report about the dataset or to request access to the data.
Variants contained within ±100kb of GPC1 that have genome-wide significance in a NIAGADS Alzheimer's Disease GWAS summary statistics dataset; supported by a p-value < 5 x 10-8. For exome array studies, a cutoff of p-value < 1 x 10-3 was used.
Click on accession numbers to view a detailed report about the dataset or to request access to the data.
Login in to select variants and add them to your basket.
| Relative Position | Variant | ADSP? | Allele | p-Value | Track | Accession |
|---|---|---|---|---|---|---|
| downstream | N/A | 6.2e-20 | ADSP Single-Variant Risk Association: European (Model 1) | NG00065 | ||
| downstream | N/A | 6.2e-20 | ADSP Single-Variant Risk Association: Caribbean Hispanic (Model 1) | NG00065 | ||
| downstream | N/A | 6.2e-20 | ADSP Single-Variant Risk Association: meta analysis (Model 1) | NG00065 | ||
| downstream | N/A | 4.1e-16 | ADSP Single-Variant Risk Association: European (Model 2) | NG00065 | ||
| downstream | N/A | 4.1e-16 | ADSP Single-Variant Risk Association: Caribbean Hispanic (Model 2) | NG00065 | ||
| downstream | N/A | 4.1e-16 | ADSP Single-Variant Risk Association: meta analysis (Model 2) | NG00065 | ||
| in gene | N/A | 1.0e-8 | ADSP Single-Variant Risk Association: meta analysis (Model 1) | NG00065 | ||
| in gene | N/A | 1.0e-8 | ADSP Single-Variant Risk Association: European (Model 1) | NG00065 | ||
| in gene | N/A | 1.0e-8 | ADSP Single-Variant Risk Association: Caribbean Hispanic (Model 1) | NG00065 | ||
| in gene | N/A | 1.0e-8 | ADSP Single-Variant Risk Association: European (Model 1) | NG00065 | ||
| in gene | N/A | 1.0e-8 | ADSP Single-Variant Risk Association: meta analysis (Model 1) | NG00065 | ||
| in gene | N/A | 1.0e-8 | ADSP Single-Variant Risk Association: Caribbean Hispanic (Model 1) | NG00065 |
NHGRI GWAS: Alzheimer's Disease
Variants contained within ±100kb of GPC1 that are associated with Alzheimer's disease in the NHGRI GWAS Catalog.
Variants contained within ±100kb of GPC1 that are associated with Alzheimer's disease in the NHGRI GWAS Catalog.
The following variants, contained within ±100kb of GPC1, have been associated with AD-relevant neuropathologies in a GWAS study:
NIAGADS GWAS: AD biomarkers and related neuropathologies
Variants contained within ±100kb of GPC1 that have genome-wide significance in a NIAGADS GWAS summary statistics dataset; supported by a p-value < 5 x 10-8. For exome array studies, a cutoff of p-value < 1 x 10-3 was used.
Click on accession numbers to view a detailed report about the dataset or to request access to the data.
Variants contained within ±100kb of GPC1 that have genome-wide significance in a NIAGADS GWAS summary statistics dataset; supported by a p-value < 5 x 10-8. For exome array studies, a cutoff of p-value < 1 x 10-3 was used.
Click on accession numbers to view a detailed report about the dataset or to request access to the data.
NHGRI GWAS: Other Traits (incl. related neuropathologies and AD biomarkers)
Variants contained within ±100kb of GPC1 that are associated with a trait in the NHGRI GWAS Catalog.
Variants contained within ±100kb of GPC1 that are associated with a trait in the NHGRI GWAS Catalog.
Functional Genomics
Explore all functional genomics annotations within the region of the GPC1 gene (chr2:241375088-241407493)
Transcription Factor Binding Site Overlap in Gene Promoter Region (ENCODE ChIP-SEQ)
ChIP-Seq sites for transcription factor binding (from selected brain-relevant ENCODE tracks) within the promoter region of this gene. See methods for more information.
ChIP-Seq sites for transcription factor binding (from selected brain-relevant ENCODE tracks) within the promoter region of this gene. See methods for more information.
Functional Annotation
Gene Ontology
Functional annotations were obtained from UniProt-GOA gene association files.
Click on a term accession number to view term details at the Gene Ontology Consortium.
Functional annotations were obtained from UniProt-GOA gene association files.
Click on a term accession number to view term details at the Gene Ontology Consortium.
| Ontology | GO Accession | Term | Evidence Code |
|---|---|---|---|
| BP | GO:0007411 | axon guidance | TAS |
| BP | GO:0006024 | glycosaminoglycan biosynthetic process | TAS |
| BP | GO:0006027 | glycosaminoglycan catabolic process | TAS |
| BP | GO:0030203 | glycosaminoglycan metabolic process | TAS |
| BP | GO:0030200 | heparan sulfate proteoglycan catabolic process | IDA |
| BP | GO:0050900 | leukocyte migration | TAS |
| BP | GO:0032288 | myelin assembly | ISS |
| BP | GO:0040037 | negative regulation of fibroblast growth factor receptor signaling pathway | IEA,ISS |
| BP | GO:2001016 | positive regulation of skeletal muscle cell differentiation | ISS,IEA |
| BP | GO:0001523 | retinoid metabolic process | TAS |
| BP | GO:0014037 | Schwann cell differentiation | ISS |
| CC | GO:0031225 | anchored component of membrane | IEA |
| CC | GO:0005829 | cytosol | IDA |
| CC | GO:0005768 | endosome | IEA |
| CC | GO:0070062 | extracellular exosome | IDA |
| CC | GO:0005576 | extracellular region | IEA |
| CC | GO:0005615 | extracellular space | IEA,TAS |
| CC | GO:0005796 | Golgi lumen | TAS |
| CC | GO:0005887 | integral component of plasma membrane | TAS |
| CC | GO:0043202 | lysosomal lumen | TAS |
| CC | GO:0016020 | membrane | IEA |
| CC | GO:0045121 | membrane raft | IDA,IEA,ISS |
| CC | GO:0005654 | nucleoplasm | IDA |
| CC | GO:0005886 | plasma membrane | IDA,TAS,IEA |
| CC | GO:0005578 | proteinaceous extracellular matrix | ISS,IEA |
| MF | GO:0005507 | copper ion binding | IDA |
| MF | GO:0017134 | fibroblast growth factor binding | IEA,ISS |
| MF | GO:0043395 | heparan sulfate proteoglycan binding | IEA |
| MF | GO:0043236 | laminin binding | ISS,IEA |
KEGG Pathways
Click on a pathway accession number to view term details at KEGG.
Click on the number in the Find Similar column to get a list of genes annotated by the associated pathway.
Click on a pathway accession number to view term details at KEGG.
Click on the number in the Find Similar column to get a list of genes annotated by the associated pathway.
| Pathway | KEGG Accession | Graph |
|---|---|---|
| Fluid shear stress and atherosclerosis | hsa05418 |
|
| Proteoglycans in cancer | hsa05205 |
|
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