Protein Dossier — PTN (Pleiotrophin)
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 |
| Alcohol intake frequency |
-0.0571 |
0.0164 |
5.09e-04 |
Wald ratio |
1 |
cis |
NA |
| Body mass index (BMI) |
-0.037 |
0.0111 |
8.57e-04 |
Wald ratio |
1 |
cis |
NA |
| Schizophrenia |
0.156 |
0.0483 |
0.00121 |
Wald ratio |
1 |
cis |
NA |
| Neuroticism |
-0.041 |
0.0137 |
0.0027 |
Wald ratio |
1 |
cis |
NA |
| Non-cancer illness code self-reported: hypertension |
-0.0594 |
0.0201 |
0.00312 |
Wald ratio |
1 |
cis |
NA |
| Cardioembolic stroke |
-0.418 |
0.146 |
0.00408 |
Wald ratio |
1 |
cis |
NA |
| Non-cancer illness code self-reported: pernicious anaemia |
0.389 |
0.142 |
0.0062 |
Wald ratio |
1 |
cis |
NA |
| Diagnoses - main ICD10: R07 Pain in throat and chest |
-0.156 |
0.0581 |
0.00712 |
Wald ratio |
1 |
cis |
NA |
| Age at menarche |
0.0683 |
0.0269 |
0.011 |
Wald ratio |
1 |
cis |
NA |
| Non-cancer illness code self-reported: hyperthyroidism or thyrotoxicosis |
0.245 |
0.102 |
0.0165 |
Wald ratio |
1 |
cis |
NA |
| Non-cancer illness code self-reported: anxiety or panic attacks |
-0.301 |
0.132 |
0.0225 |
Wald ratio |
1 |
cis |
NA |
| Years of schooling |
0.041 |
0.0182 |
0.0244 |
Wald ratio |
1 |
cis |
NA |
| …and 111 more outcomes (see JSON) |
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2. pQTL instrument availability (Tier-B probe)
| Dataset |
Trait |
Author |
Year |
prot-c-3045_72_2 |
PTN |
Suhre K |
2019 |
3. GWAS Catalog results — traits with signal at this locus
43 association rows across 33 traits (25 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 |
| Circulating PTN levels (id: OID00823_OID20083) |
6e-120 |
rs1431092 |
1 |
GCST90860152 |
no MR -> candidate analysis |
| Circulating PTN levels (id: OID01099_OID20083) |
5e-119 |
rs1431092 |
1 |
GCST90860311 |
no MR -> candidate analysis |
| PTN protein levels |
4e-118 |
rs10271620 |
1 |
GCST90470374 |
no MR -> candidate analysis |
| Pleiotrophin levels |
4e-50 |
rs10255150 |
2 |
GCST90249177 |
no MR -> candidate analysis |
| Height |
7e-19 |
rs10256915 |
1 |
GCST90245848 |
MR: beta=0.0191, p=0.148 (cis) |
| Pleiotrophin levels (PTN.3045.72.2) |
8e-19 |
rs1431093 |
1 |
GCST90242297 |
no MR -> candidate analysis |
| Cognitive ability, years of educational attainment or schizo |
1e-17 |
rs320700 |
1 |
GCST008595 |
no MR -> candidate analysis |
| Serum levels of protein PTN |
4e-17 |
rs161095 |
1 |
GCST90088204 |
no MR -> candidate analysis |
| Blood protein levels |
3e-11 |
rs322329 |
1 |
GCST006585 |
no MR -> candidate analysis |
| Waist-hip ratio |
2e-10 |
rs13229637 |
1 |
GCST008996 |
no MR -> candidate analysis |
| ISEI occupational score (MTAG) |
5e-10 |
rs320692 |
1 |
GCST90492677 |
no MR -> candidate analysis |
| SIOPS occupational score (MTAG) |
5e-10 |
rs161344 |
1 |
GCST90492679 |
no MR -> candidate analysis |
| …and 21 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 402 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 |
| alcohol drinking |
0.709 |
— |
common-variant locus |
no MR -> candidate analysis |
| schizophrenia |
0.546 |
— |
common-variant locus |
MR: beta=0.156, p=0.00121 (cis) |
| glomerulonephritis |
0.548 |
— |
common-variant locus |
no MR -> candidate analysis |
| facial nerve disorder |
0.482 |
— |
common-variant locus |
no MR -> candidate analysis |
| myeloid leukemia |
0.479 |
— |
common-variant locus |
no MR -> candidate analysis |
| risk-taking behaviour |
0.432 |
— |
common-variant locus |
no MR -> candidate analysis |
| insomnia |
0.398 |
— |
common-variant locus |
no MR -> candidate analysis |
| intelligence |
0.392 |
— |
common-variant locus |
MR: beta=0.107, p=0.0695 (cis) |
| glaucoma |
0.384 |
— |
common-variant locus |
no MR -> candidate analysis |
| vitiligo |
0.328 |
— |
common-variant locus |
no MR -> candidate analysis |
| osteoarthritis, hip |
0.212 |
— |
common-variant locus |
MR: beta=-0.092, p=0.332 (cis) |
| osteoarthritis, knee |
0.212 |
— |
common-variant locus |
MR: beta=-0.139, p=0.247 (cis) |
| dermatophytosis |
0.209 |
— |
common-variant locus |
no MR -> candidate analysis |
| urolithiasis |
0.203 |
— |
common-variant locus |
no MR -> candidate analysis |
| Abnormality of the gastrointestinal tract |
0.203 |
— |
common-variant locus |
no MR -> candidate analysis |
Of the 15 rows above, 11 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 (Pleiotrophin) |
| gnomAD constraint |
pLI=2e-05, LOEUF=1.11 — LoF-tolerant |
| GWAS Catalog |
95 unique SNPs / 173 rows |
| ClinVar |
60 records; 10 pathogenic in sample of 30 |
| PharmGKB/ClinPGx |
no annotations |
phenome — Top 30 of 402 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 ‘PTN’ and resolved to ‘Pleiotrophin’ — confirm this is the intended target.clinvar — Pathogenic count is over the 30 record(s) retrieved, NOT over all 60 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 33 traits by best p-value, aggregated from 43 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/P21246 — 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/ENSG00000105894/associations — Open Targets data release 26.06chembl: https://www.ebi.ac.uk/chembl/target_report_card/CHEMBL4523199/ — ChEMBL_37 (released 2026-05-01)gnomad: https://gnomad.broadinstitute.org/gene/PTN — gnomAD constraint via GraphQL API (reference genome GRCh38)gwas: https://www.ebi.ac.uk/gwas/genes/PTN — GWAS Catalog REST (live; release not exposed by this endpoint)clinvar: https://www.ncbi.nlm.nih.gov/clinvar/?term=PTN%5Bgene%5D — ClinVar build Build260809-1055.1gwas_traits: https://www.ebi.ac.uk/gwas/genes/PTN — GWAS Catalog search API (live; release not exposed)
Provenance
- Generated: 2026-08-14T04:42:02 · 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