Protein Dossier — CD109 (CD109 antigen)
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 |
| Heel bone mineral density (BMD) T-score automated |
-0.0553 |
0.00752 |
1.80e-13 |
Wald ratio |
1 |
cis |
NA |
| Forced vital capacity (FVC) |
-0.0172 |
0.00477 |
3.01e-04 |
Wald ratio |
1 |
cis |
NA |
| Diagnoses - main ICD10: I84 Haemorrhoids |
-0.146 |
0.0433 |
7.49e-04 |
Wald ratio |
1 |
cis |
NA |
| Forced expiratory volume in 1-second (FEV1) |
-0.0141 |
0.00503 |
0.0051 |
Wald ratio |
1 |
cis |
NA |
| Urinary albumin-to-creatinine ratio |
0.041 |
0.0147 |
0.00532 |
Wald ratio |
1 |
cis |
NA |
| Neuroticism |
-0.0193 |
0.00724 |
0.00766 |
Wald ratio |
1 |
cis |
NA |
| Breast cancer (Combined Oncoarray; iCOGS; GWAS meta analysis) |
-0.0398 |
0.015 |
0.00778 |
Wald ratio |
1 |
cis |
NA |
| Non-cancer illness code self-reported: hayfever or allergic rhinitis |
0.0592 |
0.0225 |
0.00854 |
Wald ratio |
1 |
cis |
NA |
| Age at menopause |
0.121 |
0.0482 |
0.0124 |
Wald ratio |
1 |
cis |
NA |
| Diagnoses - main ICD10: N20 Calculus of kidney and ureter |
-0.216 |
0.0865 |
0.0127 |
Wald ratio |
1 |
cis |
NA |
| Microalbuminuria |
0.118 |
0.0507 |
0.0196 |
Wald ratio |
1 |
cis |
NA |
| Diagnoses - main ICD10: K44 Diaphragmatic hernia |
-0.12 |
0.0526 |
0.0222 |
Wald ratio |
1 |
cis |
NA |
| …and 106 more outcomes (see JSON) |
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2. pQTL instrument availability (Tier-B probe)
| Dataset |
Trait |
Author |
Year |
prot-c-3290_50_2 |
CD109 |
Suhre K |
2019 |
3. GWAS Catalog results — traits with signal at this locus
144 association rows across 52 traits (135 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 CD109 levels |
4e-3715 |
rs4708083 |
8 |
GCST90860630 |
no MR -> candidate analysis |
| CD109/CNTN4 protein level ratio |
1e-2191 |
rs9442951 |
1 |
GCST90313727 |
no MR -> candidate analysis |
| CD109 antigen levels |
1e-823 |
rs57799429 |
10 |
GCST90246928 |
no MR -> candidate analysis |
| Serum levels of protein CD109 |
5e-202 |
rs1973483 |
2 |
GCST90088292 |
no MR -> candidate analysis |
| Blood protein levels |
1e-115 |
rs6909201 |
1 |
GCST006585 |
no MR -> candidate analysis |
| CD109 protein levels |
2e-111 |
rs555278092 |
51 |
GCST90468597 |
no MR -> candidate analysis |
| CD109 antigen levels (CD109.3290.50.2) |
7e-69 |
rs6903575 |
1 |
GCST90240635 |
no MR -> candidate analysis |
| Calcium levels (UKB data field 30680) |
4e-66 |
rs6909201 |
1 |
GCST90468065 |
no MR -> candidate analysis |
| Calcium levels |
5e-63 |
rs7769064 |
4 |
GCST90018951 |
no MR -> candidate analysis |
| Cerebrospinal fluid protein CD109 levels |
6e-63 |
rs1973483 |
1 |
GCST90944695 |
no MR -> candidate analysis |
| Estimated bone mineral density |
1e-42 |
rs9447004 |
2 |
GCST90726625 |
no MR -> candidate analysis |
| Heel bone mineral density |
1e-40 |
rs10943130 |
8 |
GCST006433 |
MR: beta=-0.0553, p=1.80e-13 (cis) |
| …and 40 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 1105 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 |
| uterine corpus leiomyoma |
0.806 |
— |
common-variant locus |
no MR -> candidate analysis |
| endometriosis |
0.559 |
— |
common-variant locus |
no MR -> candidate analysis |
| myocardial infarction |
0.466 |
— |
common-variant locus |
no MR -> candidate analysis |
| coronary artery disorder |
0.466 |
— |
common-variant locus |
no MR -> candidate analysis |
| basal cell carcinoma |
0.464 |
— |
common-variant locus |
MR: beta=-0.15, p=0.0341 (cis) |
| color vision disorder |
0.456 |
— |
common-variant locus |
no MR -> candidate analysis |
| open-angle glaucoma |
0.441 |
— |
common-variant locus |
no MR -> candidate analysis |
| Nasal polyposis |
0.435 |
— |
common-variant locus |
no MR -> candidate analysis |
| eye disorder |
0.431 |
— |
common-variant locus |
no MR -> candidate analysis |
| ocular hypotension |
0.431 |
— |
common-variant locus |
no MR -> candidate analysis |
| Uterine leiomyoma |
0.431 |
— |
common-variant locus |
no MR -> candidate analysis |
| response to xenobiotic stimulus |
0.431 |
— |
common-variant locus |
no MR -> candidate analysis |
| multiple sclerosis |
0.426 |
— |
established (curated) |
no MR -> candidate analysis |
| dislocation |
0.384 |
— |
common-variant locus |
no MR -> candidate analysis |
| autoimmune thyroid disease |
0.272 |
— |
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 |
not available — no ChEMBL target (undrugged) |
| gnomAD constraint |
pLI=2.5e-45, LOEUF=1.03 — LoF-tolerant |
| GWAS Catalog |
104 unique SNPs / 231 rows |
| ClinVar |
298 records; 0 pathogenic in sample of 30 |
| PharmGKB/ClinPGx |
no annotations |
phenome — Top 30 of 1105 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 ‘CD109’.clinvar — Pathogenic count is over the 30 record(s) retrieved, NOT over all 298 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 52 traits by best p-value, aggregated from 144 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/Q6YHK3 — 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/ENSG00000156535/associations — Open Targets data release 26.06gnomad: https://gnomad.broadinstitute.org/gene/CD109 — gnomAD constraint via GraphQL API (reference genome GRCh38)gwas: https://www.ebi.ac.uk/gwas/genes/CD109 — GWAS Catalog REST (live; release not exposed by this endpoint)clinvar: https://www.ncbi.nlm.nih.gov/clinvar/?term=CD109%5Bgene%5D — ClinVar build Build260809-1055.1gwas_traits: https://www.ebi.ac.uk/gwas/genes/CD109 — GWAS Catalog search API (live; release not exposed)
Provenance
- Generated: 2026-08-14T01:40:07 · 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