Protein Dossier — PDGFB (Platelet-derived growth factor subunit B)
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: deep venous thrombosis (dvt) |
0.328 |
0.0651 |
4.57e-07 |
Wald ratio |
1 |
trans |
NA |
| Diagnoses - main ICD10: I80 Phlebitis and thrombophlebitis |
0.498 |
0.115 |
1.42e-05 |
Wald ratio |
1 |
trans |
NA |
| Sodium in urine |
-0.0241 |
0.0125 |
0.0536 |
Wald ratio |
1 |
trans |
NA |
| Nucleus accumbens volume |
-13.7 |
7.13 |
0.0552 |
Wald ratio |
1 |
trans |
NA |
| Non-cancer illness code self-reported: gastro-oesophageal reflux (gord) or gastric reflux |
0.106 |
0.0552 |
0.0558 |
Wald ratio |
1 |
trans |
NA |
| Diagnoses - main ICD10: M54 Dorsalgia |
0.153 |
0.0853 |
0.0737 |
Wald ratio |
1 |
trans |
NA |
| Non-cancer illness code self-reported: pulmonary embolism (with or without) dvt |
0.208 |
0.116 |
0.0739 |
Wald ratio |
1 |
trans |
NA |
| Diagnoses - main ICD10: N81 Female genital prolapse |
0.162 |
0.0911 |
0.0762 |
Wald ratio |
1 |
trans |
NA |
| Thalamus volume |
-69.8 |
40.3 |
0.0837 |
Wald ratio |
1 |
trans |
NA |
| Non-cancer illness code self-reported: gout |
0.158 |
0.0917 |
0.0841 |
Wald ratio |
1 |
trans |
NA |
| Diagnoses - main ICD10: I30 Acute pericarditis |
0.723 |
0.429 |
0.092 |
Wald ratio |
1 |
trans |
NA |
| Non-cancer illness code self-reported: hyperthyroidism or thyrotoxicosis |
0.199 |
0.123 |
0.106 |
Wald ratio |
1 |
trans |
NA |
| …and 68 more outcomes (see JSON) |
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2. pQTL instrument availability (Tier-B probe)
| Dataset |
Trait |
Author |
Year |
prot-c-4149_8_2 |
PDGF-BB |
Suhre K |
2019 |
3. GWAS Catalog results — traits with signal at this locus
76 association rows across 48 traits (67 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 |
| Height |
1e-49 |
rs139426 |
4 |
GCST90245848 |
no MR -> candidate analysis |
| Inflammatory bowel disease |
5e-38 |
rs2143178 |
5 |
GCST003043 |
no MR -> candidate analysis |
| Crohn’s disease |
8e-34 |
rs2413583 |
4 |
GCST003044 |
no MR -> candidate analysis |
| Chronic inflammatory diseases (ankylosing spondylitis, Crohn |
2e-33 |
rs2143178 |
2 |
GCST005537 |
no MR -> candidate analysis |
| Lymphocyte count |
2e-28 |
rs139413 |
2 |
GCST90018962 |
no MR -> candidate analysis |
| White blood cell count |
1e-27 |
rs139407 |
2 |
GCST007070 |
no MR -> candidate analysis |
| Retinal arteriolar tortuosity |
7e-26 |
rs2267406 |
1 |
GCST90270397 |
no MR -> candidate analysis |
| Ulcerative colitis |
5e-21 |
rs9611131 |
3 |
GCST90446794 |
no MR -> candidate analysis |
| Standing height (UKB data field 50) |
2e-17 |
rs139420 |
1 |
GCST90468178 |
no MR -> candidate analysis |
| FEV1/FVC ratio |
2e-16 |
rs77516118 |
1 |
GCST90705072 |
no MR -> candidate analysis |
| Lung function (FEV1/FVC) |
4e-16 |
rs77516118 |
2 |
GCST007080 |
no MR -> candidate analysis |
| Platelet crit (UKB data field 30090) |
8e-16 |
rs11089938 |
1 |
GCST90468096 |
no MR -> candidate analysis |
| …and 36 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 1765 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 |
| bilateral striopallidodentate calcinosis |
0.83 |
— |
established (curated) |
no MR -> candidate analysis |
| Basal ganglia calcification |
0.849 |
— |
established (curated) |
no MR -> candidate analysis |
| meningioma |
0.596 |
— |
established (curated) |
no MR -> candidate analysis |
| inflammatory bowel disease |
0.74 |
— |
common-variant locus |
no MR -> candidate analysis |
| ulcerative colitis |
0.722 |
— |
common-variant locus |
no MR -> candidate analysis |
| dermatofibrosarcoma protuberans |
0.187 |
— |
established (curated) |
no MR -> candidate analysis |
| Crohn disease |
0.698 |
— |
common-variant locus |
no MR -> candidate analysis |
| retinal disorder |
0.633 |
— |
common-variant locus |
no MR -> candidate analysis |
| macular degeneration |
0.546 |
— |
common-variant locus |
no MR -> candidate analysis |
| hair color |
0.521 |
— |
common-variant locus |
no MR -> candidate analysis |
| sclerosing cholangitis |
0.475 |
— |
common-variant locus |
no MR -> candidate analysis |
| Varicose veins |
0.485 |
— |
common-variant locus |
no MR -> candidate analysis |
| degeneration of macula and posterior pole |
0.484 |
— |
common-variant locus |
no MR -> candidate analysis |
| ankylosing spondylitis |
0.475 |
— |
common-variant locus |
MR: beta=-0.558, p=0.346 (trans) |
| psoriasis |
0.475 |
— |
common-variant locus |
no MR -> candidate analysis |
Of the 15 rows above, 14 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 |
1 known modulators (Platelet-derived growth factor subunit B) |
| gnomAD constraint |
pLI=1, LOEUF=0.408 — LoF-INTOLERANT |
| GWAS Catalog |
68 unique SNPs / 136 rows |
| ClinVar |
231 records; 5 pathogenic in sample of 30 |
| PharmGKB/ClinPGx |
no annotations |
phenome — Top 30 of 1765 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 ‘PDGFB’ and resolved to ‘Platelet-derived growth factor subunit B’ — confirm this is the intended target.clinvar — Pathogenic count is over the 30 record(s) retrieved, NOT over all 231 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 48 traits by best p-value, aggregated from 76 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/P01127 — 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/ENSG00000100311/associations — Open Targets data release 26.06chembl: https://www.ebi.ac.uk/chembl/target_report_card/CHEMBL3108633/ — ChEMBL_37 (released 2026-05-01)gnomad: https://gnomad.broadinstitute.org/gene/PDGFB — gnomAD constraint via GraphQL API (reference genome GRCh38)gwas: https://www.ebi.ac.uk/gwas/genes/PDGFB — GWAS Catalog REST (live; release not exposed by this endpoint)clinvar: https://www.ncbi.nlm.nih.gov/clinvar/?term=PDGFB%5Bgene%5D — ClinVar build Build260809-1055.1gwas_traits: https://www.ebi.ac.uk/gwas/genes/PDGFB — GWAS Catalog search API (live; release not exposed)
Provenance
- Generated: 2026-08-14T04:15:06 · 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