Protein Dossier — CPNE1 (Copine-1)
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 |
| Height |
-0.0522 |
0.00502 |
2.28e-25 |
Wald ratio |
1 |
cis |
0.808 |
| Weight |
-0.0271 |
0.00362 |
7.16e-14 |
Wald ratio |
1 |
cis |
8.23e-37 |
| Age at menopause |
0.154 |
0.0307 |
5.73e-07 |
Wald ratio |
1 |
cis |
NA |
| Total cholesterol |
0.0409 |
0.0087 |
2.53e-06 |
Wald ratio |
1 |
cis |
NA |
| Breast cancer (Combined Oncoarray; iCOGS; GWAS meta analysis) |
-0.0427 |
0.0105 |
5.15e-05 |
Wald ratio |
1 |
cis |
NA |
| Hippocampus volume |
-29.8 |
7.63 |
9.37e-05 |
Wald ratio |
1 |
cis |
NA |
| Diagnoses - main ICD10: M23 Internal derangement of knee |
0.0956 |
0.025 |
1.34e-04 |
Wald ratio |
1 |
cis |
NA |
| ER-positive Breast cancer (Combined Oncoarray; iCOGS; GWAS meta analysis) |
-0.0443 |
0.0126 |
4.31e-04 |
Wald ratio |
1 |
cis |
NA |
| Forced expiratory volume in 1-second (FEV1) |
-0.0117 |
0.00354 |
9.40e-04 |
Wald ratio |
1 |
cis |
NA |
| Non-cancer illness code self-reported: high cholesterol |
0.0325 |
0.0107 |
0.00243 |
Wald ratio |
1 |
cis |
NA |
| Ovarian cancer |
-0.0678 |
0.0224 |
0.00244 |
Wald ratio |
1 |
cis |
NA |
| Non-cancer illness code self-reported: asthma |
-0.0353 |
0.0119 |
0.00301 |
Wald ratio |
1 |
cis |
NA |
| …and 91 more outcomes (see JSON) |
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2. pQTL instrument availability (Tier-B probe)
| Dataset |
Trait |
Author |
Year |
prot-c-5346_24_3 |
CPNE1 |
Suhre K |
2019 |
3. GWAS Catalog results — traits with signal at this locus
33 association rows across 22 traits (32 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 |
| Copine-1 levels |
4e-988 |
rs6060524 |
3 |
GCST90247129 |
no MR -> candidate analysis |
| Low tan response |
7e-173 |
rs6142422 |
1 |
GCST005897 |
no MR -> candidate analysis |
| Copine-1 levels (CPNE1.5346.24.3) |
2e-146 |
rs12481228 |
2 |
GCST90240791 |
no MR -> candidate analysis |
| Height (baseline) |
4e-143 |
rs6060518 |
5 |
GCST90565843 |
no MR -> candidate analysis |
| Multi-trait sex score |
7e-33 |
rs10649224 |
1 |
GCST90270118 |
no MR -> candidate analysis |
| Hip circumference adjusted for BMI |
5e-29 |
rs10211771 |
2 |
GCST012227 |
no MR -> candidate analysis |
| Refractive error |
3e-27 |
rs6058288 |
1 |
GCST90841196 |
no MR -> candidate analysis |
| Hematological traits (multi-trait analysis) |
1e-25 |
rs7261284 |
1 |
GCST90838669 |
no MR -> candidate analysis |
| Body shape phenotype PC2 |
7e-16 |
rs151197637 |
1 |
GCST90832990 |
no MR -> candidate analysis |
| PROCR protein levels |
1e-14 |
rs2425068 |
1 |
GCST90453400 |
no MR -> candidate analysis |
| Physical function (baseline) |
7e-13 |
rs28634878 |
3 |
GCST90565837 |
no MR -> candidate analysis |
| Standing height (UKB data field 50) |
3e-12 |
rs111405612 |
1 |
GCST90468178 |
no MR -> candidate analysis |
| …and 10 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 142 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 |
| schizophrenia 19 |
0.718 |
— |
established (curated) |
no MR -> candidate analysis |
| cardioembolic stroke |
0.342 |
— |
common-variant locus |
MR: beta=-0.0568, p=0.287 (cis) |
| basal cell carcinoma |
0.338 |
— |
common-variant locus |
MR: beta=0.0571, p=0.158 (cis) |
| response to statin |
0.262 |
— |
common-variant locus |
no MR -> candidate analysis |
| coronary artery disorder |
0.26 |
— |
common-variant locus |
no MR -> candidate analysis |
| Abnormality of the skeletal system |
0.225 |
— |
common-variant locus |
no MR -> candidate analysis |
| Neurodevelopmental delay |
0.195 |
— |
established (curated) |
no MR -> candidate analysis |
| myopia |
0.189 |
— |
common-variant locus |
no MR -> candidate analysis |
| squamous cell carcinoma |
0.179 |
— |
common-variant locus |
no MR -> candidate analysis |
| ischemic stroke |
0.172 |
— |
common-variant locus |
MR: beta=-0.0379, p=0.164 (cis) |
| skin sensitivity to sun |
0.17 |
— |
common-variant locus |
no MR -> candidate analysis |
| intelligence |
0.118 |
— |
common-variant locus |
no MR -> candidate analysis |
| venous thromboembolism |
0.082 |
— |
common-variant locus |
no MR -> candidate analysis |
Of the 13 rows above, 10 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=1.4e-18, LOEUF=1.14 — LoF-tolerant |
| GWAS Catalog |
113 unique SNPs / 284 rows |
| ClinVar |
266 records; 1 pathogenic in sample of 30 |
| PharmGKB/ClinPGx |
no annotations |
phenome — Top 30 of 142 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 ‘CPNE1’.clinvar — Pathogenic count is over the 30 record(s) retrieved, NOT over all 266 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 22 traits by best p-value, aggregated from 33 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/Q99829 — 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/ENSG00000214078/associations — Open Targets data release 26.06gnomad: https://gnomad.broadinstitute.org/gene/CPNE1 — gnomAD constraint via GraphQL API (reference genome GRCh38)gwas: https://www.ebi.ac.uk/gwas/genes/CPNE1 — GWAS Catalog REST (live; release not exposed by this endpoint)clinvar: https://www.ncbi.nlm.nih.gov/clinvar/?term=CPNE1%5Bgene%5D — ClinVar build Build260809-1055.1gwas_traits: https://www.ebi.ac.uk/gwas/genes/CPNE1 — GWAS Catalog search API (live; release not exposed)
Provenance
- Generated: 2026-08-14T02:00:59 · 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