Protein Dossier — PGLYRP1 (Peptidoglycan recognition protein 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 |
| Forced vital capacity (FVC) |
-0.0264 |
0.00967 |
0.00637 |
Wald ratio |
1 |
cis |
NA |
| Non-cancer illness code self-reported: vitiligo |
0.897 |
0.329 |
0.00648 |
Wald ratio |
1 |
cis |
NA |
| Forced expiratory volume in 1-second (FEV1) |
-0.0259 |
0.0102 |
0.011 |
Wald ratio |
1 |
cis |
NA |
| Non-cancer illness code self-reported: gout |
0.181 |
0.0831 |
0.0292 |
Wald ratio |
1 |
cis |
NA |
| Alzheimer’s disease |
-0.167 |
0.0793 |
0.0358 |
Wald ratio |
1 |
cis |
NA |
| Diagnoses - main ICD10: R35 Polyuria |
0.298 |
0.144 |
0.0376 |
Wald ratio |
1 |
cis |
NA |
| Diastolic blood pressure automated reading |
0.0251 |
0.0121 |
0.0379 |
Wald ratio |
1 |
cis |
NA |
| Fracture resulting from simple fall |
-0.0684 |
0.0333 |
0.0402 |
Wald ratio |
1 |
cis |
NA |
| Sleep duration |
-0.0186 |
0.0092 |
0.0431 |
Wald ratio |
1 |
cis |
NA |
| Heel bone mineral density (BMD) T-score automated |
-0.0306 |
0.0152 |
0.0448 |
Wald ratio |
1 |
cis |
NA |
| Non-cancer illness code self-reported: osteoporosis |
0.152 |
0.0819 |
0.064 |
Wald ratio |
1 |
cis |
NA |
| Non-cancer illness code self-reported: joint disorder |
-0.507 |
0.322 |
0.116 |
Wald ratio |
1 |
cis |
NA |
| …and 60 more outcomes (see JSON) |
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|
|
|
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2. pQTL instrument availability (Tier-B probe)
| Dataset |
Trait |
Author |
Year |
prot-c-3329_14_2 |
PGRP-S |
Suhre K |
2019 |
3. GWAS Catalog results — traits with signal at this locus
12 association rows across 11 traits (11 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 |
| LCN2/PGLYRP1 protein level ratio |
1e-819 |
rs12980641 |
1 |
GCST90315306 |
no MR -> candidate analysis |
| Circulating PGLYRP1 levels |
3e-571 |
rs35247686 |
1 |
GCST90859968 |
no MR -> candidate analysis |
| Peptidoglycan recognition protein 1 levels |
1e-39 |
rs12462367 |
1 |
GCST90248985 |
no MR -> candidate analysis |
| Serum levels of protein PGLYRP1 |
2e-22 |
rs12973391 |
1 |
GCST90088320 |
no MR -> candidate analysis |
| Blood protein levels |
1e-17 |
rs12980641 |
1 |
GCST006585 |
no MR -> candidate analysis |
| Peptidoglycan recognition protein 1 levels (PGLYRP1.3329.14. |
5e-17 |
rs8102493 |
1 |
GCST90242213 |
no MR -> candidate analysis |
| GLIPR1 protein levels |
1e-15 |
rs191272469 |
1 |
GCST90469357 |
no MR -> candidate analysis |
| Total PHF-tau (SNP x SNP interaction) |
4e-14 |
rs12663388 x rs12982353 |
2 |
GCST010340 |
no MR -> candidate analysis |
| Peptidoglycan recognition protein 1 (analyte X3329.14) level |
4e-11 |
rs12980641 |
1 |
GCST90425701 |
no MR -> candidate analysis |
| Cerebrospinal fluid protein PGLYRP1 levels |
5e-10 |
rs8102493 |
1 |
GCST90944855 |
no MR -> candidate analysis |
| Whole brain grey matter density |
3e-6 |
rs2005893 |
1 |
GCST009200 |
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 319 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 |
| dementia |
0.29 |
— |
common-variant locus |
no MR -> candidate analysis |
| neurodegenerative disease |
0.213 |
— |
common-variant locus |
no MR -> candidate analysis |
Of the 2 rows above, 2 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=2e-07, LOEUF=1.64 — LoF-tolerant |
| GWAS Catalog |
40 unique SNPs / 80 rows |
| ClinVar |
58 records; 1 pathogenic in sample of 30 |
| PharmGKB/ClinPGx |
no annotations |
phenome — Top 30 of 319 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 ‘PGLYRP1’.clinvar — Pathogenic count is over the 30 record(s) retrieved, NOT over all 58 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 11 of 11 traits by best p-value, aggregated from 12 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/O75594 — 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/ENSG00000008438/associations — Open Targets data release 26.06gnomad: https://gnomad.broadinstitute.org/gene/PGLYRP1 — gnomAD constraint via GraphQL API (reference genome GRCh38)gwas: https://www.ebi.ac.uk/gwas/genes/PGLYRP1 — GWAS Catalog REST (live; release not exposed by this endpoint)clinvar: https://www.ncbi.nlm.nih.gov/clinvar/?term=PGLYRP1%5Bgene%5D — ClinVar build Build260809-1055.1gwas_traits: https://www.ebi.ac.uk/gwas/genes/PGLYRP1 — GWAS Catalog search API (live; release not exposed)
Provenance
- Generated: 2026-08-14T04:19:02 · 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