Protein Dossier — ACP1 (Low molecular weight phosphotyrosine protein phosphatase)
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 |
| Height |
0.0121 |
0.00251 |
1.31e-06 |
Wald ratio |
1 |
cis |
NA |
| Body mass index (BMI) |
-0.00826 |
0.00203 |
4.82e-05 |
Wald ratio |
1 |
cis |
NA |
| Serum cystatin C (eGFRcys) |
-0.00542 |
0.00154 |
4.21e-04 |
Wald ratio |
1 |
cis |
NA |
| Serum creatinine (eGFRcrea) |
-0.00259 |
0.000744 |
5.05e-04 |
Wald ratio |
1 |
cis |
NA |
| Eye problems or disorders: Cataract |
0.036 |
0.0107 |
7.88e-04 |
Wald ratio |
1 |
cis |
NA |
| Diagnoses - main ICD10: K44 Diaphragmatic hernia |
0.0502 |
0.0155 |
0.00118 |
Wald ratio |
1 |
cis |
NA |
| Alzheimer’s disease |
-0.0429 |
0.0136 |
0.00157 |
Wald ratio |
1 |
cis |
NA |
| HDL cholesterol |
0.0126 |
0.00404 |
0.00181 |
Wald ratio |
1 |
cis |
NA |
| Triglycerides |
-0.0101 |
0.00388 |
0.00921 |
Wald ratio |
1 |
cis |
NA |
| Systolic blood pressure automated reading |
0.00527 |
0.00208 |
0.0114 |
Wald ratio |
1 |
cis |
NA |
| Cough on most days |
0.0248 |
0.0101 |
0.0143 |
Wald ratio |
1 |
cis |
NA |
| Age at menarche |
-0.0121 |
0.00499 |
0.015 |
Wald ratio |
1 |
cis |
NA |
| …and 103 more outcomes (see JSON) |
|
|
|
|
|
|
|
2. pQTL instrument availability (Tier-B probe)
| Dataset |
Trait |
Author |
Year |
prot-c-3858_5_1 |
PPAC |
Suhre K |
2019 |
3. GWAS Catalog results — traits with signal at this locus
63 association rows across 56 traits (57 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 |
| Low molecular weight phosphotyrosine protein phosphatase lev |
1e-1095 |
rs79716074 |
1 |
GCST90241816 |
no MR -> candidate analysis |
| Blood protein levels |
6e-657 |
rs58461606 |
1 |
GCST006585 |
no MR -> candidate analysis |
| Low molecular weight phosphotyrosine protein phosphatase lev |
1e-451 |
rs79716074 |
5 |
GCST90425910 |
no MR -> candidate analysis |
| Low molecular weight phosphotyrosine protein phosphatase lev |
6e-148 |
rs79716074 |
1 |
GCST90237522 |
no MR -> candidate analysis |
| Protein quantitative trait loci |
3e-67 |
rs59937473 |
1 |
GCST010900 |
no MR -> candidate analysis |
| Refractive error |
1e-33 |
rs56321614 |
2 |
GCST90841196 |
no MR -> candidate analysis |
| Cerebrospinal fluid arabinose levels |
2e-31 |
rs62114544 |
1 |
GCST90318280 |
no MR -> candidate analysis |
| Height |
5e-26 |
rs114976176 |
1 |
GCST90662911 |
MR: beta=0.0121, p=1.31e-06 (cis) |
| High-density lipoprotein levels |
4e-23 |
rs79716074 |
1 |
GCST90662894 |
no MR -> candidate analysis |
| NUDT5/TXNRD1 protein level ratio |
8e-17 |
rs11553746 |
1 |
GCST90315582 |
no MR -> candidate analysis |
| Height (baseline) |
2e-16 |
rs12714401 |
2 |
GCST90565843 |
no MR -> candidate analysis |
| Cholesteryl Esters in Large HDL |
4e-15 |
rs79716074 |
1 |
GCST90501136 |
no MR -> candidate analysis |
| …and 44 more traits (see JSON) |
|
|
|
|
|
4. Phenome map — where this gene is a genetic locus, vs. where MR exists
Top diseases by Open Targets association (of 214 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 |
| myopia |
0.601 |
— |
common-variant locus |
no MR -> candidate analysis |
| Abnormality of the skeletal system |
0.581 |
— |
common-variant locus |
no MR -> candidate analysis |
| restless legs syndrome |
0.559 |
— |
common-variant locus |
no MR -> candidate analysis |
| aging |
0.533 |
— |
common-variant locus |
no MR -> candidate analysis |
| hypothyroidism |
0.368 |
— |
common-variant locus |
MR: beta=-0.0134, p=0.142 (cis) |
| Hashimoto thyroiditis |
0.361 |
— |
common-variant locus |
no MR -> candidate analysis |
| metabolic syndrome |
0.339 |
— |
common-variant locus |
no MR -> candidate analysis |
| refractive error |
0.311 |
— |
common-variant locus |
no MR -> candidate analysis |
| risk-taking behaviour |
0.298 |
— |
common-variant locus |
no MR -> candidate analysis |
| diabetes mellitus |
0.278 |
— |
common-variant locus |
no MR -> candidate analysis |
| type 2 diabetes mellitus |
0.28 |
— |
common-variant locus |
no MR -> candidate analysis |
| Abnormality of refraction |
0.216 |
— |
common-variant locus |
no MR -> candidate analysis |
| primary angle-closure glaucoma |
0.204 |
— |
common-variant locus |
no MR -> candidate analysis |
| osteoarthritis, hip |
0.164 |
— |
common-variant locus |
MR: beta=0.0471, p=0.0439 (cis) |
| hypertensive disorder |
0.153 |
— |
common-variant locus |
no MR -> candidate analysis |
Of the 15 rows above, 13 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 |
0 known modulators (Low molecular weight phosphotyrosine protein phosphatase) |
| gnomAD constraint |
pLI=1.8e-08, LOEUF=1.39 — LoF-tolerant |
| GWAS Catalog |
90 unique SNPs / 180 rows |
| ClinVar |
104 records; 2 pathogenic in sample of 30 |
| PharmGKB/ClinPGx |
no annotations |
phenome — Top 30 of 214 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 ‘ACP1’ and resolved to ‘Low molecular weight phosphotyrosine protein phosphatase’ — confirm this is the intended target.clinvar — Pathogenic count is over the 30 record(s) retrieved, NOT over all 104 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 20 of 56 traits by best p-value, aggregated from 63 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/P24666 — 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/ENSG00000143727/associations — Open Targets data release 26.06chembl: https://www.ebi.ac.uk/chembl/target_report_card/CHEMBL4903/ — ChEMBL_37 (released 2026-05-01)gnomad: https://gnomad.broadinstitute.org/gene/ACP1 — gnomAD constraint via GraphQL API (reference genome GRCh38)gwas: https://www.ebi.ac.uk/gwas/genes/ACP1 — GWAS Catalog REST (live; release not exposed by this endpoint)clinvar: https://www.ncbi.nlm.nih.gov/clinvar/?term=ACP1%5Bgene%5D — ClinVar build Build260809-1055.1gwas_traits: https://www.ebi.ac.uk/gwas/genes/ACP1 — GWAS Catalog search API (live; release not exposed)
Provenance
- Generated: 2026-08-14T00:51:28 · 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