Protein Dossier — JAM3 (Junctional adhesion molecule C)
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 |
| Schizophrenia |
-0.243 |
0.0587 |
3.48e-05 |
Wald ratio |
1 |
cis |
NA |
| Pulse rate |
0.0795 |
0.0235 |
7.04e-04 |
Wald ratio |
1 |
cis |
NA |
| Microalbuminuria |
0.332 |
0.114 |
0.00368 |
Wald ratio |
1 |
cis |
NA |
| Diagnoses - main ICD10: Z09 Follow-up examination after treatment for conditions other than malignant neoplasms |
0.214 |
0.0879 |
0.0148 |
Wald ratio |
1 |
cis |
NA |
| Caudate volume |
62.5 |
26.6 |
0.0187 |
Wald ratio |
1 |
cis |
NA |
| Body mass index (BMI) |
0.0298 |
0.0133 |
0.0245 |
Wald ratio |
1 |
cis |
NA |
| HDL cholesterol |
-0.0587 |
0.0272 |
0.0308 |
Wald ratio |
1 |
cis |
NA |
| HOMA-B |
0.0408 |
0.019 |
0.0321 |
Wald ratio |
1 |
cis |
NA |
| Cancer code self-reported: small intestine or small bowel cancer |
0.733 |
0.345 |
0.0336 |
Wald ratio |
1 |
cis |
NA |
| Cardioembolic stroke |
-0.377 |
0.182 |
0.038 |
Wald ratio |
1 |
cis |
NA |
| Lung adenocarcinoma |
-0.326 |
0.16 |
0.0417 |
Wald ratio |
1 |
cis |
NA |
| Diagnoses - main ICD10: C50 Malignant neoplasm of breast |
0.176 |
0.0877 |
0.0442 |
Wald ratio |
1 |
cis |
NA |
| …and 94 more outcomes (see JSON) |
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|
2. pQTL instrument availability (Tier-B probe)
| Dataset |
Trait |
Author |
Year |
prot-c-2998_53_2 |
JAM-C |
Suhre K |
2019 |
3. GWAS Catalog results — traits with signal at this locus
22 association rows across 20 traits (20 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 |
| JAM2/RGMB protein level ratio |
6e-29 |
rs11223705 |
1 |
GCST90315237 |
no MR -> candidate analysis |
| JAM2 protein levels |
9e-23 |
rs12289084 |
1 |
GCST90469659 |
no MR -> candidate analysis |
| Cerebrospinal fluid dimethylmalonic acid levels |
5e-22 |
rs75201238 |
1 |
GCST90318077 |
no MR -> candidate analysis |
| Circulating JAM2 levels |
4e-19 |
rs12277151 |
1 |
GCST90859722 |
no MR -> candidate analysis |
| Serum levels of protein JAM3 |
3e-16 |
rs655627 |
1 |
GCST90088176 |
no MR -> candidate analysis |
| JAM3 protein levels |
1e-15 |
rs76745913 |
1 |
GCST90469660 |
no MR -> candidate analysis |
| Blood protein levels |
4e-14 |
rs655627 |
1 |
GCST006585 |
no MR -> candidate analysis |
| Height |
6e-13 |
rs470631 |
1 |
GCST90662911 |
no MR -> candidate analysis |
| White blood cell count |
3e-12 |
rs610829 |
1 |
GCST90662906 |
no MR -> candidate analysis |
| Atrial fibrillation |
2e-11 |
rs34732010 |
2 |
GCST90624411 |
MR: beta=0.193, p=0.0663 (cis) |
| Junctional adhesion molecule C levels |
4e-11 |
rs12270157 |
1 |
GCST90425568 |
no MR -> candidate analysis |
| Neutrophil count |
1e-10 |
rs7947419 |
2 |
GCST90002398 |
no MR -> candidate analysis |
| …and 8 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 2379 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 |
| porencephaly-microcephaly-bilateral congenital cataract syndrome |
0.846 |
— |
established (curated) |
no MR -> candidate analysis |
| atrial fibrillation |
0.571 |
— |
common-variant locus |
MR: beta=0.193, p=0.0663 (cis) |
| stroke disorder |
0.423 |
— |
common-variant locus |
no MR -> candidate analysis |
| alcohol drinking |
0.423 |
— |
common-variant locus |
no MR -> candidate analysis |
| nephrotic syndrome |
0.414 |
— |
common-variant locus |
no MR -> candidate analysis |
| temporomandibular joint disorder |
0.414 |
— |
common-variant locus |
no MR -> candidate analysis |
| blood vessel replacement |
0.389 |
— |
common-variant locus |
no MR -> candidate analysis |
| corneal dystrophy |
0.389 |
— |
common-variant locus |
no MR -> candidate analysis |
| bronchial disorder |
0.389 |
— |
common-variant locus |
no MR -> candidate analysis |
| hereditary disease |
0.317 |
— |
established (curated) |
no MR -> candidate analysis |
| Anxiety |
0.204 |
— |
common-variant locus |
no MR -> candidate analysis |
| schizophrenia |
0.182 |
— |
established (curated) |
MR: beta=-0.243, p=3.48e-05 (cis) |
Of the 12 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=4.8e-09, LOEUF=1.06 — LoF-tolerant |
| GWAS Catalog |
55 unique SNPs / 110 rows |
| ClinVar |
346 records; 7 pathogenic in sample of 30 |
| PharmGKB/ClinPGx |
no annotations |
phenome — Top 30 of 2379 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 ‘JAM3’.clinvar — Pathogenic count is over the 30 record(s) retrieved, NOT over all 346 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 20 traits by best p-value, aggregated from 22 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/Q9BX67 — 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/ENSG00000166086/associations — Open Targets data release 26.06gnomad: https://gnomad.broadinstitute.org/gene/JAM3 — gnomAD constraint via GraphQL API (reference genome GRCh38)gwas: https://www.ebi.ac.uk/gwas/genes/JAM3 — GWAS Catalog REST (live; release not exposed by this endpoint)clinvar: https://www.ncbi.nlm.nih.gov/clinvar/?term=JAM3%5Bgene%5D — ClinVar build Build260809-1055.1gwas_traits: https://www.ebi.ac.uk/gwas/genes/JAM3 — GWAS Catalog search API (live; release not exposed)
Provenance
- Generated: 2026-08-14T03:20:21 · 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