Protein Dossier — SAA1 (Serum amyloid A-1 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 |
| Mean cell volume |
-0.529 |
0.159 |
8.44e-04 |
Inverse variance weighted |
2 |
trans |
NA |
| Mean cell volume |
-0.529 |
0.159 |
8.44e-04 |
Inverse variance weighted |
2 |
trans |
NA |
| Haemoglobin concentration |
-0.111 |
0.0351 |
0.00162 |
Inverse variance weighted |
2 |
trans |
NA |
| Haemoglobin concentration |
-0.111 |
0.0351 |
0.00162 |
Inverse variance weighted |
2 |
trans |
NA |
| Platelet count |
14.1 |
4.61 |
0.00228 |
Inverse variance weighted |
2 |
trans |
NA |
| Platelet count |
14.1 |
4.61 |
0.00228 |
Inverse variance weighted |
2 |
trans |
NA |
| Knee and hip osteoarthritis |
-0.401 |
0.137 |
0.00331 |
Inverse variance weighted |
2 |
trans |
NA |
| Knee and hip osteoarthritis |
-0.401 |
0.137 |
0.00331 |
Inverse variance weighted |
2 |
trans |
NA |
| Non-cancer illness code self-reported: sleep apnoea |
0.216 |
0.0817 |
0.00828 |
Inverse variance weighted |
3 |
trans |
NA |
| Non-cancer illness code self-reported: sleep apnoea |
0.216 |
0.0817 |
0.00828 |
Inverse variance weighted |
3 |
cis |
NA |
| Non-cancer illness code self-reported: sleep apnoea |
0.216 |
0.0817 |
0.00828 |
Inverse variance weighted |
3 |
trans |
NA |
| Knee osteoarthritis |
-0.443 |
0.173 |
0.0103 |
Inverse variance weighted |
2 |
trans |
NA |
| …and 278 more outcomes (see JSON) |
|
|
|
|
|
|
|
2. pQTL instrument availability (Tier-B probe)
| Dataset |
Trait |
Author |
Year |
prot-c-4336_2_1 |
SAA |
Suhre K |
2019 |
3. GWAS Catalog results — traits with signal at this locus
18 association rows across 8 traits (15 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 |
| Serum amyloid A-1 protein levels (SAA1.4336.2.1) |
1e-771 |
rs35179000 |
3 |
GCST90242795 |
no MR -> candidate analysis |
| Serum amyloid A-1 protein levels |
2e-247 |
rs10690148 |
5 |
GCST90162052 |
no MR -> candidate analysis |
| Amyloid A serum levels |
4e-145 |
rs11024600 |
2 |
GCST90244128 |
no MR -> candidate analysis |
| SAA4 protein levels |
1e-30 |
rs139240396 |
2 |
GCST90470521 |
no MR -> candidate analysis |
| ER membrane protein complex subunit 2 protein levels (SomaSc |
2e-29 |
rs1829575 |
1 |
GCST90441815 |
no MR -> candidate analysis |
| Bone mineral density mean |
3e-20 |
rs566507596 |
1 |
GCST90321120 |
no MR -> candidate analysis |
| SAA1 protein levels |
1e-19 |
rs10832916 |
1 |
GCST90453161 |
no MR -> candidate analysis |
| Lewy body disease |
3e-6 |
rs2124379 |
3 |
GCST002591 |
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 719 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 |
| Abnormality of the gastrointestinal tract |
0.384 |
— |
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 |
not available — no ChEMBL target (undrugged) |
| gnomAD constraint |
pLI=0.33, LOEUF=0.93 — LoF-tolerant |
| GWAS Catalog |
114 unique SNPs / 274 rows |
| ClinVar |
49 records; 5 pathogenic in sample of 30 |
| PharmGKB/ClinPGx |
no annotations |
phenome — Top 30 of 719 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 ‘SAA1’.clinvar — Pathogenic count is over the 30 record(s) retrieved, NOT over all 49 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 8 of 8 traits by best p-value, aggregated from 18 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/P0DJI8 — 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/ENSG00000173432/associations — Open Targets data release 26.06gnomad: https://gnomad.broadinstitute.org/gene/SAA1 — gnomAD constraint via GraphQL API (reference genome GRCh38)gwas: https://www.ebi.ac.uk/gwas/genes/SAA1 — GWAS Catalog REST (live; release not exposed by this endpoint)clinvar: https://www.ncbi.nlm.nih.gov/clinvar/?term=SAA1%5Bgene%5D — ClinVar build Build260809-1055.1gwas_traits: https://www.ebi.ac.uk/gwas/genes/SAA1 — GWAS Catalog search API (live; release not exposed)
Provenance
- Generated: 2026-08-14T04:55:37 · 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