Protein Dossier — GPC5 (Glypican-5)
MR feasibility tier: A — Published pQTL-MR estimates exist for this protein (retrieved below - not computed here).
1. Published MR estimates (retrieved, not computed)
| Outcome |
beta |
se |
p |
method |
nSNP |
cis/trans |
coloc |
| Thyroid cancer |
-0.643 |
0.11 |
5.83e-09 |
Wald ratio |
1 |
cis |
0.00105 |
| Fracture resulting from simple fall |
0.0248 |
0.00801 |
0.00197 |
Inverse variance weighted |
2 |
cis |
NA |
| Fracture resulting from simple fall |
0.0248 |
0.00801 |
0.00197 |
Inverse variance weighted |
2 |
cis |
NA |
| Non-cancer illness code self-reported: depression |
0.0359 |
0.0124 |
0.00373 |
Inverse variance weighted |
2 |
cis |
NA |
| Non-cancer illness code self-reported: depression |
0.0359 |
0.0124 |
0.00373 |
Inverse variance weighted |
2 |
cis |
NA |
| Age at menarche |
0.0219 |
0.00793 |
0.00578 |
Inverse variance weighted |
2 |
cis |
NA |
| Age at menarche |
0.0219 |
0.00793 |
0.00578 |
Inverse variance weighted |
2 |
cis |
NA |
| Breast cancer (Combined Oncoarray; iCOGS; GWAS meta analysis) |
0.0211 |
0.00799 |
0.00815 |
Inverse variance weighted |
2 |
cis |
NA |
| Breast cancer (Combined Oncoarray; iCOGS; GWAS meta analysis) |
0.0211 |
0.00799 |
0.00815 |
Inverse variance weighted |
2 |
cis |
NA |
| HDL cholesterol |
-0.0156 |
0.00643 |
0.0154 |
Inverse variance weighted |
2 |
cis |
NA |
| HDL cholesterol |
-0.0156 |
0.00643 |
0.0154 |
Inverse variance weighted |
2 |
cis |
NA |
| Non-cancer illness code self-reported: hyperthyroidism or thyrotoxicosis |
0.0692 |
0.0338 |
0.0406 |
Inverse variance weighted |
2 |
cis |
NA |
| …and 171 more outcomes (see JSON) |
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2. pQTL instrument availability (Tier-B probe)
| Dataset |
Trait |
Author |
Year |
prot-c-4991_12_1 |
GPC5 |
Suhre K |
2019 |
3. GWAS Catalog results — traits with signal at this locus
173 association rows across 92 traits (123 genome-wide significant rows). Associations are loci, not causal claims; the mapped gene at a locus is not necessarily the effector gene.
| Trait |
best p |
lead SNP |
n assoc |
study |
MR status |
| Circulating GPC5 levels |
4e-3718 |
rs342702 |
5 |
GCST90859713 |
no MR -> candidate analysis |
| Glypican-5 levels |
1e-781 |
rs342706 |
18 |
GCST90247759 |
no MR -> candidate analysis |
| Bone mineral density mean |
3e-299 |
rs117782072 |
3 |
GCST90321120 |
no MR -> candidate analysis |
| GPC5 protein levels |
4e-292 |
rs116990124 |
43 |
GCST90469387 |
no MR -> candidate analysis |
| Triglycerides x anxiety interaction (2df test) |
2e-258 |
rs72640234 |
2 |
GCST90570677 |
no MR -> candidate analysis |
| Glypican-5 levels (GPC5.4991.12.1) |
5e-233 |
rs342702 |
1 |
GCST90241309 |
no MR -> candidate analysis |
| Blood protein levels |
2e-218 |
rs342702 |
2 |
GCST006585 |
no MR -> candidate analysis |
| HDL x anxiety interaction (2df test) |
8e-118 |
rs72640234 |
2 |
GCST90570665 |
no MR -> candidate analysis |
| Serum levels of protein GPC5 |
2e-56 |
rs118000667 |
1 |
GCST90088851 |
no MR -> candidate analysis |
| Neurological blood protein biomarker levels |
1e-36 |
rs1929922 |
2 |
GCST008478 |
no MR -> candidate analysis |
| Cerebrospinal fluid protein GPC5 levels |
6e-29 |
rs345447 |
1 |
GCST90943437 |
no MR -> candidate analysis |
| Glypican-5 level in Chronic kidney disease with hypertension |
2e-22 |
rs342706 |
1 |
GCST90237780 |
no MR -> candidate analysis |
| …and 80 more traits (see JSON) |
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4. Phenome map — where this gene is a genetic locus, vs. where MR exists
Top diseases by Open Targets association (of 317 total). Associations are loci, not causal claims. The causal-status column is a four-state triage per pair: established (curated) = a curated clinical assertion exists (ClinGen/G2P/GEL/Orphanet/ClinVar — any validity level, MR adds little); exploratory rare-variant signal = ExWAS burden evidence without curation — a candidate NEW gene-disease relationship; common-variant locus = GWAS signal, classic pQTL-MR territory; multi-layer = burden+GWAS together, an allelic-series candidate (the strongest causal setup). Burden estimand is carrier-vs-noncarrier, not per-SD MR.
| Disease |
genetic assoc. |
burden (ExWAS) |
causal status |
MR status |
| COVID-19 |
0.339 |
— |
common-variant locus |
no MR -> candidate analysis |
| type 2 diabetes mellitus |
0.636 |
— |
common-variant locus |
no MR -> candidate analysis |
| smoking initiation |
0.631 |
— |
common-variant locus |
no MR -> candidate analysis |
| ovarian dysfunction |
0.623 |
— |
common-variant locus |
no MR -> candidate analysis |
| diabetes mellitus |
0.617 |
— |
common-variant locus |
no MR -> candidate analysis |
| gastric cancer |
0.417 |
— |
established (curated) |
no MR -> candidate analysis |
| prostate carcinoma |
0.457 |
— |
common-variant locus |
no MR -> candidate analysis |
| intelligence |
0.528 |
— |
common-variant locus |
no MR -> candidate analysis |
| connective tissue disorder |
0.508 |
— |
common-variant locus |
no MR -> candidate analysis |
| Hypercholesterolemia |
0.508 |
— |
common-variant locus |
MR: beta=-0.0156, p=0.0154 (cis) |
| type 1 diabetes mellitus |
0.502 |
— |
common-variant locus |
no MR -> candidate analysis |
| placental abruption |
0.502 |
— |
common-variant locus |
no MR -> candidate analysis |
| arthropathy |
0.502 |
— |
common-variant locus |
no MR -> candidate analysis |
| mathematical ability |
0.491 |
— |
common-variant locus |
no MR -> candidate analysis |
| alcohol drinking |
0.42 |
— |
common-variant locus |
no MR -> candidate analysis |
Of the 15 rows above, 14 have no MR estimate in this resource. Across all retrieved diseases for this gene: 0 exploratory rare-variant signal(s), 0 multi-layer (allelic-series candidate) pair(s). Final triage still belongs to a statistical geneticist.
5. Downstream annotation (druggability & safety preview)
| Layer |
Result |
| ChEMBL druggability |
not available — no ChEMBL target (undrugged) |
| gnomAD constraint |
pLI=1.6e-14, LOEUF=1.11 — LoF-tolerant |
| GWAS Catalog |
172 unique SNPs / 431 rows |
| ClinVar |
236 records; 2 pathogenic in sample of 30 |
| PharmGKB/ClinPGx |
no annotations |
phenome — Top 30 of 317 associated diseases by overall score. genetic_association aggregates GWAS common-variant AND rare-variant evidence. These are ASSOCIATIONS (loci), not causal claims.chembl — No ChEMBL target for ‘GPC5’.clinvar — Pathogenic count is over the 30 record(s) retrieved, NOT over all 236 ClinVar records for this gene; it is a sample, not a rate.pharmgkb — No PharmGKB/ClinPGx clinical annotations (gene may not be a pharmacogene).gwas_traits — Top 20 of 92 traits by best p-value, aggregated from 173 association rows. These are GWAS ASSOCIATIONS (loci), not causal claims; mapped genes at a locus are not necessarily the effector gene.
Sources
uniprot: https://www.uniprot.org/uniprotkb/P78333 — UniProt release 2026_02 (10-June-2026)mr_outcomes: https://epigraphdb.org/pqtl/ — EpiGraphDB pQTL MR (Zheng et al., Nat Genet 2020) — pre-computed two-sample MR; retrieved, not computed by this agent; EpiGraphDB build 1.0, pQTL dataset v3.0phenome: https://platform.opentargets.org/target/ENSG00000179399/associations — Open Targets data release 26.06gnomad: https://gnomad.broadinstitute.org/gene/GPC5 — gnomAD constraint via GraphQL API (reference genome GRCh38)gwas: https://www.ebi.ac.uk/gwas/genes/GPC5 — GWAS Catalog REST (live; release not exposed by this endpoint)clinvar: https://www.ncbi.nlm.nih.gov/clinvar/?term=GPC5%5Bgene%5D — ClinVar build Build260809-1055.1gwas_traits: https://www.ebi.ac.uk/gwas/genes/GPC5 — GWAS Catalog search API (live; release not exposed)
Provenance
- Generated: 2026-08-14T02:53:02 · Tier: A
- Fully mechanical: every cell above is rendered from tool return values. No language model wrote any part of this dossier.
- MR estimates, where present, are retrieved from published work (EpiGraphDB pQTL, Zheng et al. Nat Genet 2020); nothing is computed here.
- Tool errors this run: none