Protein Dossier — CTSA (Lysosomal protective 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 platelet volume |
-0.0762 |
0.00644 |
3.14e-32 |
Wald ratio |
1 |
trans |
NA |
| Triglycerides |
-0.161 |
0.0193 |
1.01e-16 |
Wald ratio |
1 |
trans |
0.989 |
| Platelet count |
19.3 |
2.43 |
1.79e-15 |
Wald ratio |
1 |
trans |
0.65 |
| Diastolic blood pressure automated reading |
-0.0939 |
0.0144 |
7.83e-11 |
Wald ratio |
1 |
trans |
0.157 |
| HDL cholesterol |
0.114 |
0.0199 |
1.16e-08 |
Wald ratio |
1 |
trans |
0.967 |
| Sodium in urine |
-0.0748 |
0.0139 |
7.01e-08 |
Wald ratio |
1 |
trans |
0.899 |
| Body mass index (BMI) |
-0.0747 |
0.0141 |
1.18e-07 |
Wald ratio |
1 |
trans |
0.111 |
| Non-cancer illness code self-reported: hypertension |
-0.124 |
0.0273 |
5.28e-06 |
Wald ratio |
1 |
trans |
NA |
| Non-cancer illness code self-reported: deep venous thrombosis (dvt) |
0.33 |
0.0724 |
5.28e-06 |
Wald ratio |
1 |
trans |
NA |
| Diagnoses - main ICD10: K80 Cholelithiasis |
0.32 |
0.0718 |
8.32e-06 |
Wald ratio |
1 |
trans |
NA |
| Height |
0.0703 |
0.0176 |
6.33e-05 |
Wald ratio |
1 |
trans |
NA |
| Creatinine (enzymatic) in urine |
-0.0524 |
0.0135 |
1.03e-04 |
Wald ratio |
1 |
trans |
NA |
| …and 118 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-3179_51_2 |
Cathepsin A |
Suhre K |
2019 |
3. GWAS Catalog results — traits with signal at this locus
2 association rows across 2 traits (2 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 |
| Lysosomal protective protein levels |
1e-8 |
rs2075962 |
1 |
GCST90425637 |
no MR -> candidate analysis |
| Body shape phenotype PC2 |
3e-8 |
rs6104390 |
1 |
GCST90832990 |
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 1827 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 |
| galactosialidosis |
0.922 |
— |
established (curated) |
no MR -> candidate analysis |
| cathepsin a-related arteriopathy-strokes-leukoencephalopathy |
0.486 |
— |
established (curated) |
no MR -> candidate analysis |
| hereditary disease |
0.742 |
— |
established (curated) |
no MR -> candidate analysis |
| Lynch syndrome |
0.559 |
— |
established (curated) |
no MR -> candidate analysis |
| Non-immune hydrops fetalis |
0.438 |
— |
established (curated) |
no MR -> candidate analysis |
| Abnormality of prenatal development or birth |
0.438 |
— |
established (curated) |
no MR -> candidate analysis |
| coronary artery disorder |
0.276 |
— |
common-variant locus |
no MR -> candidate analysis |
| prostate carcinoma |
0.201 |
— |
common-variant locus |
no MR -> candidate analysis |
| breast carcinoma |
0.201 |
— |
common-variant locus |
no MR -> candidate analysis |
| ovarian dysfunction |
0.18 |
— |
common-variant locus |
no MR -> candidate analysis |
| macular degeneration |
0.148 |
— |
common-variant locus |
no MR -> candidate analysis |
| abdominal aortic aneurysm |
0.102 |
— |
common-variant locus |
no MR -> candidate analysis |
| familial hyperlipidemia |
0.103 |
— |
common-variant locus |
no MR -> candidate analysis |
Of the 13 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 (Lysosomal protective protein) |
| gnomAD constraint |
pLI=6.1e-09, LOEUF=0.815 — LoF-tolerant |
| GWAS Catalog |
122 unique SNPs / 294 rows |
| ClinVar |
635 records; 2 pathogenic in sample of 30 |
| PharmGKB/ClinPGx |
no annotations |
phenome — Top 30 of 1827 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 ‘CTSA’ and resolved to ‘Lysosomal protective protein’ — confirm this is the intended target.clinvar — Pathogenic count is over the 30 record(s) retrieved, NOT over all 635 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 2 of 2 traits by best p-value, aggregated from 2 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/P10619 — 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/ENSG00000064601/associations — Open Targets data release 26.06chembl: https://www.ebi.ac.uk/chembl/target_report_card/CHEMBL6115/ — ChEMBL_37 (released 2026-05-01)gnomad: https://gnomad.broadinstitute.org/gene/CTSA — gnomAD constraint via GraphQL API (reference genome GRCh38)gwas: https://www.ebi.ac.uk/gwas/genes/CTSA — GWAS Catalog REST (live; release not exposed by this endpoint)clinvar: https://www.ncbi.nlm.nih.gov/clinvar/?term=CTSA%5Bgene%5D — ClinVar build Build260809-1055.1gwas_traits: https://www.ebi.ac.uk/gwas/genes/CTSA — GWAS Catalog search API (live; release not exposed)
Provenance
- Generated: 2026-08-14T02:10:03 · 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