Protein Dossier — LCMT1 (Leucine carboxyl methyltransferase 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 |
| Serum creatinine (eGFRcrea) |
-0.0142 |
0.00307 |
3.44e-06 |
Wald ratio |
1 |
trans |
NA |
| Diagnoses - main ICD10: K60 Fissure and fistula of anal and rectal regions |
0.344 |
0.0886 |
1.03e-04 |
Wald ratio |
1 |
trans |
NA |
| Diagnoses - main ICD10: Z09 Follow-up examination after treatment for conditions other than malignant neoplasms |
0.15 |
0.0588 |
0.0106 |
Wald ratio |
1 |
trans |
NA |
| Type 2 diabetes |
-0.107 |
0.0426 |
0.0121 |
Wald ratio |
1 |
trans |
NA |
| Non-cancer illness code self-reported: pulmonary embolism (with or without) dvt |
-0.314 |
0.13 |
0.0154 |
Wald ratio |
1 |
trans |
NA |
| Fracture resulting from simple fall |
-0.0547 |
0.0235 |
0.0199 |
Wald ratio |
1 |
trans |
NA |
| Fractured or broken bones in last 5 years |
-0.058 |
0.0277 |
0.036 |
Wald ratio |
1 |
trans |
NA |
| Diagnoses - main ICD10: N20 Calculus of kidney and ureter |
0.171 |
0.0846 |
0.0431 |
Wald ratio |
1 |
trans |
NA |
| Eye problems or disorders: Glaucoma |
0.123 |
0.0622 |
0.0485 |
Wald ratio |
1 |
trans |
NA |
| Caudate volume |
32.5 |
16.7 |
0.0515 |
Wald ratio |
1 |
trans |
NA |
| Neo-openness to experience |
-0.437 |
0.229 |
0.0559 |
Wald ratio |
1 |
trans |
NA |
| Haemoglobin concentration |
-0.0408 |
0.0217 |
0.0603 |
Wald ratio |
1 |
trans |
NA |
| …and 100 more outcomes (see JSON) |
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2. pQTL instrument availability (Tier-B probe)
| Dataset |
Trait |
Author |
Year |
prot-c-4237_70_3 |
LCMT1 |
Suhre K |
2019 |
3. GWAS Catalog results — traits with signal at this locus
4 association rows across 4 traits (3 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 |
| Height |
2e-12 |
rs17774085 |
1 |
GCST90245848 |
MR: beta=0.00986, p=0.349 (trans) |
| Protein quantitative trait loci (liver) |
2e-8 |
rs111254682 |
1 |
GCST011427 |
no MR -> candidate analysis |
| Alzheimer’s disease or family history of Alzheimer’s disease |
4e-8 |
rs1248734336 |
1 |
GCST90624094 |
no MR -> candidate analysis |
| Color vision defects (Tritan) |
5e-8 |
rs60713925 |
1 |
GCST90301671 |
no MR -> candidate analysis |
4. Phenome map — where this gene is a genetic locus, vs. where MR exists
Top diseases by Open Targets association (of 103 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 |
| arthropathy |
0.528 |
— |
common-variant locus |
no MR -> candidate analysis |
| kidney disorder |
0.401 |
— |
common-variant locus |
no MR -> candidate analysis |
| gestational diabetes |
0.401 |
— |
common-variant locus |
no MR -> candidate analysis |
| bile duct disorder |
0.372 |
— |
common-variant locus |
no MR -> candidate analysis |
| Abnormality of the gastrointestinal tract |
0.355 |
— |
common-variant locus |
no MR -> candidate analysis |
Of the 5 rows above, 5 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=1e-07, LOEUF=0.9 — LoF-tolerant |
| GWAS Catalog |
19 unique SNPs / 38 rows |
| ClinVar |
102 records; 1 pathogenic in sample of 30 |
| PharmGKB/ClinPGx |
no annotations |
phenome — Top 30 of 103 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 ‘LCMT1’.clinvar — Pathogenic count is over the 30 record(s) retrieved, NOT over all 102 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 4 of 4 traits by best p-value, aggregated from 4 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/Q9UIC8 — 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/ENSG00000205629/associations — Open Targets data release 26.06gnomad: https://gnomad.broadinstitute.org/gene/LCMT1 — gnomAD constraint via GraphQL API (reference genome GRCh38)gwas: https://www.ebi.ac.uk/gwas/genes/LCMT1 — GWAS Catalog REST (live; release not exposed by this endpoint)clinvar: https://www.ncbi.nlm.nih.gov/clinvar/?term=LCMT1%5Bgene%5D — ClinVar build Build260809-1055.1gwas_traits: https://www.ebi.ac.uk/gwas/genes/LCMT1 — GWAS Catalog search API (live; release not exposed)
Provenance
- Generated: 2026-08-14T03:28:18 · 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