MR feasibility tier: A — Published pQTL-MR estimates exist for this protein (retrieved below - not computed here).
| Outcome | beta | se | p | method | nSNP | cis/trans | coloc |
|---|---|---|---|---|---|---|---|
| Femoral neck bone mineral density | 0.142 | 0.0646 | 0.0279 | Wald ratio | 1 | trans | NA |
| Lumbar spine bone mineral density | 0.0983 | 0.073 | 0.178 | Wald ratio | 1 | trans | NA |
| Birth weight | -0.0341 | 0.0288 | 0.237 | Wald ratio | 1 | trans | NA |
| Low grade serous ovarian cancer | -0.351 | 0.298 | 0.239 | Wald ratio | 1 | trans | NA |
| Invasive mucinous ovarian cancer | 0.269 | 0.248 | 0.279 | Wald ratio | 1 | trans | NA |
| ER-negative Breast cancer (Combined Oncoarray; iCOGS; GWAS meta analysis) | 0.0864 | 0.0816 | 0.29 | Wald ratio | 1 | trans | NA |
| Ovarian cancer | 0.0797 | 0.0837 | 0.341 | Wald ratio | 1 | trans | NA |
| High grade serous ovarian cancer | 0.0785 | 0.0993 | 0.429 | Wald ratio | 1 | trans | NA |
| Breast cancer (Combined Oncoarray; iCOGS; GWAS meta analysis) | -0.0341 | 0.0437 | 0.435 | Wald ratio | 1 | trans | NA |
No prot-* pQTL GWAS dataset found for this protein (matched by UniProt accession and symbol).
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 |
|---|---|---|---|---|---|
| Late effect (PheCode 1012) | 1e-12 | rs532494959 | 1 | GCST90479760 | no MR -> candidate analysis |
| Heel bone mineral density | 2e-11 | rs62153852 | 1 | GCST006433 | no MR -> candidate analysis |
| ICD10 D25: Leiomyoma of uterus | 4e-11 | rs12475639 | 1 | GCST90454204 | no MR -> candidate analysis |
| IgG glycosylation | 4e-7 | rs2200578 | 1 | GCST001848 | no MR -> candidate analysis |
Top diseases by Open Targets association (of 35 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 |
|---|---|---|---|---|
| inflammatory bowel disease | 0.337 | — | common-variant locus | no MR -> candidate analysis |
| uterine corpus leiomyoma | 0.163 | — | common-variant locus | no MR -> candidate analysis |
| placental abruption | 0.081 | — | common-variant locus | no MR -> candidate analysis |
| Uterine leiomyoma | 0.057 | — | common-variant locus | no MR -> candidate analysis |
| male reproductive organ cancer | 0.049 | — | common-variant locus | no MR -> candidate analysis |
| mathematical ability | 0.048 | — | common-variant locus | no MR -> candidate analysis |
| Cachexia | 0.041 | — | common-variant locus | no MR -> candidate analysis |
| intelligence | 0.037 | — | common-variant locus | no MR -> candidate analysis |
| Splenomegaly | 0.032 | — | common-variant locus | no MR -> candidate analysis |
Of the 9 rows above, 9 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.
| Layer | Result |
|---|---|
| ChEMBL druggability | not available — no ChEMBL target (undrugged) |
| gnomAD constraint | pLI=1.9e-05, LOEUF=1.18 — LoF-tolerant |
| GWAS Catalog | 24 unique SNPs / 48 rows |
| ClinVar | 51 records; 3 pathogenic in sample of 30 |
| PharmGKB/ClinPGx | no annotations |
phenome — Top 30 of 35 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 ‘LYG1’.clinvar — Pathogenic count is over the 30 record(s) retrieved, NOT over all 51 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.uniprot: https://www.uniprot.org/uniprotkb/Q8N1E2 — 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/ENSG00000144214/associations — Open Targets data release 26.06gnomad: https://gnomad.broadinstitute.org/gene/LYG1 — gnomAD constraint via GraphQL API (reference genome GRCh38)gwas: https://www.ebi.ac.uk/gwas/genes/LYG1 — GWAS Catalog REST (live; release not exposed by this endpoint)clinvar: https://www.ncbi.nlm.nih.gov/clinvar/?term=LYG1%5Bgene%5D — ClinVar build Build260809-1055.1gwas_traits: https://www.ebi.ac.uk/gwas/genes/LYG1 — GWAS Catalog search API (live; release not exposed)