Protein Dossier — APCS (Serum amyloid P-component)
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 |
| Non-cancer illness code self-reported: muscle or soft tissue injuries |
0.286 |
0.0862 |
9.18e-04 |
Wald ratio |
1 |
cis |
NA |
| Non-cancer illness code self-reported: osteoarthritis |
0.0842 |
0.0297 |
0.00451 |
Wald ratio |
1 |
cis |
NA |
| Low grade serous ovarian cancer |
0.55 |
0.224 |
0.0139 |
Wald ratio |
1 |
cis |
NA |
| Urate |
0.049 |
0.0215 |
0.0227 |
Wald ratio |
1 |
cis |
NA |
| Fasting proinsulin |
0.0633 |
0.0287 |
0.0272 |
Wald ratio |
1 |
cis |
NA |
| Red blood cell count |
-0.019 |
0.0092 |
0.0389 |
Wald ratio |
1 |
cis |
NA |
| Schizophrenia |
0.0839 |
0.0415 |
0.0431 |
Wald ratio |
1 |
cis |
NA |
| Non-cancer illness code self-reported: ankylosing spondylitis |
0.284 |
0.141 |
0.0436 |
Wald ratio |
1 |
cis |
NA |
| Ischemic stroke |
-0.129 |
0.0646 |
0.0459 |
Wald ratio |
1 |
cis |
NA |
| Fractured or broken bones in last 5 years |
0.0564 |
0.0284 |
0.047 |
Wald ratio |
1 |
cis |
NA |
| Diagnoses - main ICD10: R55 Syncope and collapse |
-0.272 |
0.137 |
0.0473 |
Wald ratio |
1 |
cis |
NA |
| Diagnoses - main ICD10: N20 Calculus of kidney and ureter |
-0.316 |
0.163 |
0.0516 |
Wald ratio |
1 |
cis |
NA |
| …and 75 more outcomes (see JSON) |
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2. pQTL instrument availability (Tier-B probe)
| Dataset |
Trait |
Author |
Year |
prot-c-2474_54_5 |
SAP |
Suhre K |
2019 |
3. GWAS Catalog results — traits with signal at this locus
24 association rows across 16 traits (23 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 |
| APCS protein levels |
7e-144 |
rs36126250 |
3 |
GCST90468328 |
no MR -> candidate analysis |
| Serum amyloid P-component levels |
1e-61 |
rs35737842 |
3 |
GCST90249426 |
no MR -> candidate analysis |
| C-reactive protein levels |
8e-57 |
rs16842320 |
3 |
GCST009777 |
no MR -> candidate analysis |
| C-reactive protein levels (MTAG) |
6e-49 |
rs61680681 |
2 |
GCST90179146 |
no MR -> candidate analysis |
| Circulating SPP1 levels |
1e-27 |
rs28383572 |
1 |
GCST90859966 |
no MR -> candidate analysis |
| Phosphate levels (UKB data field 30810) |
2e-27 |
rs28383573 |
1 |
GCST90468094 |
no MR -> candidate analysis |
| SLAMF8 protein levels |
6e-27 |
rs138112491 |
1 |
GCST90470652 |
no MR -> candidate analysis |
| Serum levels of protein APCS |
2e-25 |
rs28383573 |
1 |
GCST90087947 |
no MR -> candidate analysis |
| DNA methylation-estimated granulocyte proportions |
5e-18 |
rs2808661 |
2 |
GCST90014293 |
no MR -> candidate analysis |
| SPP1 protein levels |
1e-15 |
rs28383572 |
1 |
GCST90470733 |
no MR -> candidate analysis |
| C1QTNF5 protein levels |
4e-15 |
rs35834732 |
1 |
GCST90468489 |
no MR -> candidate analysis |
| Aortic stenosis |
9e-12 |
rs35485101 |
1 |
GCST90837551 |
no MR -> candidate analysis |
| …and 4 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 336 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 |
| splenic disorder |
0.363 |
— |
common-variant locus |
no MR -> candidate analysis |
| restless legs syndrome |
0.342 |
— |
common-variant locus |
no MR -> candidate analysis |
| acute tonsillitis |
0.342 |
— |
common-variant locus |
no MR -> candidate analysis |
| bacterial infectious disease |
0.207 |
— |
common-variant locus |
no MR -> candidate analysis |
| inherited retinal dystrophy |
0.195 |
— |
common-variant locus |
no MR -> candidate analysis |
| pneumonia |
0.107 |
— |
common-variant locus |
no MR -> candidate analysis |
Of the 6 rows above, 6 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 |
2 known modulators (Serum amyloid P-component) |
| gnomAD constraint |
pLI=0.11, LOEUF=2.53 — LoF-tolerant |
| GWAS Catalog |
101 unique SNPs / 210 rows |
| ClinVar |
46 records; 3 pathogenic in sample of 30 |
| PharmGKB/ClinPGx |
no annotations |
phenome — Top 30 of 336 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 ‘APCS’ and resolved to ‘Serum amyloid P-component’ — confirm this is the intended target.clinvar — Pathogenic count is over the 30 record(s) retrieved, NOT over all 46 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 16 of 16 traits by best p-value, aggregated from 24 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/P02743 — 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/ENSG00000132703/associations — Open Targets data release 26.06chembl: https://www.ebi.ac.uk/chembl/target_report_card/CHEMBL4929/ — ChEMBL_37 (released 2026-05-01)gnomad: https://gnomad.broadinstitute.org/gene/APCS — gnomAD constraint via GraphQL API (reference genome GRCh38)gwas: https://www.ebi.ac.uk/gwas/genes/APCS — GWAS Catalog REST (live; release not exposed by this endpoint)clinvar: https://www.ncbi.nlm.nih.gov/clinvar/?term=APCS%5Bgene%5D — ClinVar build Build260809-1055.1gwas_traits: https://www.ebi.ac.uk/gwas/genes/APCS — GWAS Catalog search API (live; release not exposed)
Provenance
- Generated: 2026-08-14T01:06:10 · 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