Protein Dossier — LAG3 (Lymphocyte activation gene 3 protein)
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 |
| Eye problems or disorders: Injury or trauma resulting in loss of vision |
0.541 |
0.126 |
1.83e-05 |
Wald ratio |
1 |
cis |
NA |
| Diagnoses - main ICD10: K80 Cholelithiasis |
0.301 |
0.0848 |
3.80e-04 |
Wald ratio |
1 |
cis |
NA |
| Cigarettes smoked per day |
-2.25 |
0.642 |
4.54e-04 |
Wald ratio |
1 |
cis |
NA |
| Transferrin |
0.206 |
0.0695 |
0.00305 |
Wald ratio |
1 |
cis |
NA |
| Cancer code self-reported: malignant melanoma |
0.35 |
0.133 |
0.00868 |
Wald ratio |
1 |
cis |
NA |
| Femoral neck bone mineral density |
-0.136 |
0.0548 |
0.0132 |
Wald ratio |
1 |
cis |
NA |
| Thalamus volume |
100 |
41.2 |
0.0151 |
Wald ratio |
1 |
cis |
NA |
| Diagnoses - main ICD10: M16 Coxarthrosis [arthrosis of hip] |
0.256 |
0.107 |
0.0161 |
Wald ratio |
1 |
cis |
NA |
| Non-cancer illness code self-reported: hayfever or allergic rhinitis |
0.138 |
0.0587 |
0.0184 |
Wald ratio |
1 |
cis |
NA |
| Eczema |
0.241 |
0.115 |
0.0359 |
Wald ratio |
1 |
cis |
NA |
| Non-cancer illness code self-reported: gout |
0.23 |
0.11 |
0.037 |
Wald ratio |
1 |
cis |
NA |
| Pallidum volume |
25.5 |
12.7 |
0.0451 |
Wald ratio |
1 |
cis |
NA |
| …and 73 more outcomes (see JSON) |
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2. pQTL instrument availability (Tier-B probe)
| Dataset |
Trait |
Author |
Year |
prot-c-5099_14_3 |
LAG-3 |
Suhre K |
2019 |
3. GWAS Catalog results — traits with signal at this locus
38 association rows across 21 traits (37 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 LAG3 levels (id: OID01023_OID21315) |
4e-160 |
rs3782735 |
4 |
GCST90860248 |
no MR -> candidate analysis |
| LAG3 protein levels |
8e-160 |
rs3782735 |
3 |
GCST90469727 |
no MR -> candidate analysis |
| Circulating LAG3 levels (id: OID05553_OID21315) |
9e-159 |
rs3782735 |
4 |
GCST90860765 |
no MR -> candidate analysis |
| Circulating CD4 levels (id: OID00466_OID20584) |
2e-50 |
rs188343194 |
1 |
GCST90859827 |
no MR -> candidate analysis |
| Circulating CD4 levels (id: OID00776_OID20584) |
2e-47 |
rs188343194 |
1 |
GCST90860110 |
no MR -> candidate analysis |
| Lymphocyte activation gene 3 protein levels |
9e-32 |
rs3782735 |
1 |
GCST90248233 |
no MR -> candidate analysis |
| Sex hormone-binding globulin levels adjusted for BMI |
1e-21 |
rs3782735 |
3 |
GCST90012110 |
no MR -> candidate analysis |
| Sex hormone-binding globulin levels |
3e-18 |
rs3782735 |
7 |
GCST90012111 |
no MR -> candidate analysis |
| Phospholipids to Total Lipids in Very Large HDL percentage |
1e-16 |
rs3782735 |
1 |
GCST90501303 |
no MR -> candidate analysis |
| Gamma glutamyl transferase levels |
2e-16 |
rs3782735 |
1 |
GCST90428730 |
no MR -> candidate analysis |
| Gamma glutamyl transpeptidase |
6e-16 |
rs3782735 |
1 |
GCST90018954 |
no MR -> candidate analysis |
| Gamma glutamyltransferase levels (UKB data field 30730) |
8e-16 |
rs3782735 |
1 |
GCST90468070 |
no MR -> candidate analysis |
| …and 9 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 675 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 |
| Hashimoto thyroiditis |
0.198 |
— |
common-variant locus |
no MR -> candidate analysis |
Of the 1 rows above, 1 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 |
6 known modulators (Lymphocyte activation gene 3 protein) |
| gnomAD constraint |
pLI=7.5e-06, LOEUF=0.807 — LoF-tolerant |
| GWAS Catalog |
74 unique SNPs / 148 rows |
| ClinVar |
177 records; 5 pathogenic in sample of 30 |
| PharmGKB/ClinPGx |
no annotations |
phenome — Top 30 of 675 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 ‘LAG3’ and resolved to ‘Lymphocyte activation gene 3 protein’ — confirm this is the intended target.clinvar — Pathogenic count is over the 30 record(s) retrieved, NOT over all 177 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 21 traits by best p-value, aggregated from 38 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/P18627 — 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/ENSG00000089692/associations — Open Targets data release 26.06chembl: https://www.ebi.ac.uk/chembl/target_report_card/CHEMBL4630881/ — ChEMBL_37 (released 2026-05-01)gnomad: https://gnomad.broadinstitute.org/gene/LAG3 — gnomAD constraint via GraphQL API (reference genome GRCh38)gwas: https://www.ebi.ac.uk/gwas/genes/LAG3 — GWAS Catalog REST (live; release not exposed by this endpoint)clinvar: https://www.ncbi.nlm.nih.gov/clinvar/?term=LAG3%5Bgene%5D — ClinVar build Build260809-1055.1gwas_traits: https://www.ebi.ac.uk/gwas/genes/LAG3 — GWAS Catalog search API (live; release not exposed)
Provenance
- Generated: 2026-08-14T03:27:05 · 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