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 |
| Diagnoses - main ICD10: B37 Candidiasis |
0.000447 |
0.000149 |
0.0028 |
Inverse variance weighted |
2 |
trans |
NA |
| Diagnoses - main ICD10: B37 Candidiasis |
0.000447 |
0.000149 |
0.0028 |
Inverse variance weighted |
2 |
cis |
NA |
| Parkinson’s disease |
0.385 |
0.146 |
0.00825 |
Wald ratio |
1 |
trans |
NA |
| Body mass index (BMI) |
0.0159 |
0.00692 |
0.0211 |
Inverse variance weighted |
2 |
trans |
NA |
| Body mass index (BMI) |
0.0159 |
0.00692 |
0.0211 |
Inverse variance weighted |
2 |
cis |
NA |
| Pancreatic cancer |
-0.303 |
0.141 |
0.0308 |
Inverse variance weighted |
2 |
trans |
NA |
| Pancreatic cancer |
-0.303 |
0.141 |
0.0308 |
Inverse variance weighted |
2 |
cis |
NA |
| Non-cancer illness code self-reported: enlarged prostate |
-0.00163 |
0.000808 |
0.0439 |
Inverse variance weighted |
2 |
trans |
NA |
| Non-cancer illness code self-reported: enlarged prostate |
-0.00163 |
0.000808 |
0.0439 |
Inverse variance weighted |
2 |
cis |
NA |
| Amyotrophic lateral sclerosis |
0.0996 |
0.0507 |
0.0495 |
Inverse variance weighted |
2 |
trans |
NA |
| Amyotrophic lateral sclerosis |
0.0996 |
0.0507 |
0.0495 |
Inverse variance weighted |
2 |
cis |
NA |
| Diagnoses - main ICD10: S76 Injury of muscle and tendon at hip and thigh level |
-0.000286 |
0.00015 |
0.0561 |
Inverse variance weighted |
2 |
trans |
NA |
| …and 158 more outcomes (see JSON) |
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2. pQTL instrument availability (Tier-B probe)
| Dataset |
Trait |
Author |
Year |
prot-c-2974_61_2 |
contactin-1 |
Suhre K |
2019 |
3. GWAS Catalog results — traits with signal at this locus
83 association rows across 43 traits (49 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 CNTN1 levels |
3e-344 |
rs11177623 |
9 |
GCST90859934 |
no MR -> candidate analysis |
| CNTN1 protein levels |
2e-258 |
rs3904168 |
13 |
GCST90468803 |
no MR -> candidate analysis |
| CNTN1/EGFR protein level ratio |
2e-177 |
rs1965163 |
1 |
GCST90314162 |
no MR -> candidate analysis |
| ALCAM/CNTN1 protein level ratio |
6e-177 |
rs1965163 |
1 |
GCST90313235 |
no MR -> candidate analysis |
| Contactin-1 levels |
7e-64 |
rs12811939 |
6 |
GCST90247122 |
no MR -> candidate analysis |
| Parkinson’s disease |
2e-27 |
rs1442190 |
4 |
GCST002455 |
MR: beta=0.385, p=0.00825 (trans) |
| RELT-like protein 1 levels |
7e-17 |
rs7299744 |
1 |
GCST90422123 |
no MR -> candidate analysis |
| Serum levels of protein CNTN1 |
2e-12 |
rs11177623 |
1 |
GCST90088159 |
no MR -> candidate analysis |
| Blood protein levels |
1e-11 |
rs11177623 |
1 |
GCST006585 |
no MR -> candidate analysis |
| Precordial pain (PheCode 418.1) |
5e-11 |
rs150785851 |
1 |
GCST90480142 |
no MR -> candidate analysis |
| Gut microbial network clusters (Salmon (at 1 year) x Househo |
8e-11 |
rs117742571 |
2 |
GCST90569451 |
no MR -> candidate analysis |
| Total PHF-tau (SNP x SNP interaction) |
5e-10 |
rs10082977 x rs10754859 |
1 |
GCST010340 |
no MR -> candidate analysis |
| …and 31 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 910 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 |
| Compton-North congenital myopathy |
0.902 |
— |
established (curated) |
no MR -> candidate analysis |
| Congenital lethal myopathy, Compton-North type |
0.608 |
— |
established (curated) |
no MR -> candidate analysis |
| Parkinson disease |
0.555 |
— |
common-variant locus |
no MR -> candidate analysis |
| urinary system disorder |
0.536 |
— |
common-variant locus |
no MR -> candidate analysis |
| escherichia coli infection |
0.485 |
— |
common-variant locus |
no MR -> candidate analysis |
| exostosis |
0.417 |
— |
common-variant locus |
no MR -> candidate analysis |
| Hypercholesterolemia |
0.32 |
— |
common-variant locus |
MR: beta=-0.0207, p=0.0587 (trans) |
| hereditary disease |
0.318 |
— |
established (curated) |
no MR -> candidate analysis |
| retinal disorder |
0.317 |
— |
common-variant locus |
no MR -> candidate analysis |
| Precordial pain |
0.311 |
— |
common-variant locus |
no MR -> candidate analysis |
| inflammatory bowel disease |
0.22 |
— |
common-variant locus |
no MR -> candidate analysis |
| cervical carcinoma |
0.214 |
— |
common-variant locus |
no MR -> candidate analysis |
| arthropathy |
0.203 |
— |
common-variant locus |
no MR -> candidate analysis |
| Crohn disease |
0.198 |
— |
common-variant locus |
no MR -> candidate analysis |
Of the 14 rows above, 13 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 |
0 known modulators (Contactin-1) |
| gnomAD constraint |
pLI=1, LOEUF=0.394 — LoF-INTOLERANT |
| GWAS Catalog |
109 unique SNPs / 182 rows |
| ClinVar |
752 records; 1 pathogenic in sample of 30 |
| PharmGKB/ClinPGx |
no annotations |
phenome — Top 30 of 910 associated diseases by overall score. genetic_association aggregates GWAS common-variant AND rare-variant evidence. These are ASSOCIATIONS (loci), not causal claims.chembl — ChEMBL target matched by text search on ‘CNTN1’ and resolved to ‘Contactin-1’ — confirm this is the intended target.clinvar — Pathogenic count is over the 30 record(s) retrieved, NOT over all 752 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 43 traits by best p-value, aggregated from 83 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/Q12860 — 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/ENSG00000018236/associations — Open Targets data release 26.06chembl: https://www.ebi.ac.uk/chembl/target_report_card/CHEMBL6067142/ — ChEMBL_37 (released 2026-05-01)gnomad: https://gnomad.broadinstitute.org/gene/CNTN1 — gnomAD constraint via GraphQL API (reference genome GRCh38)gwas: https://www.ebi.ac.uk/gwas/genes/CNTN1 — GWAS Catalog REST (live; release not exposed by this endpoint)clinvar: https://www.ncbi.nlm.nih.gov/clinvar/?term=CNTN1%5Bgene%5D — ClinVar build Build260809-1055.1gwas_traits: https://www.ebi.ac.uk/gwas/genes/CNTN1 — GWAS Catalog search API (live; release not exposed)
Provenance
- Generated: 2026-08-14T01:55:23 · 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