Protein Dossier — CGA (Glycoprotein hormones alpha chain)
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 |
| Creatinine (enzymatic) in urine |
-0.0127 |
0.00388 |
0.00107 |
Wald ratio |
1 |
trans |
NA |
| Alcohol intake frequency |
0.0183 |
0.00599 |
0.00223 |
Wald ratio |
1 |
trans |
NA |
| Age at menarche |
-0.0306 |
0.0101 |
0.0024 |
Wald ratio |
1 |
trans |
NA |
| Fractured or broken bones in last 5 years |
-0.0385 |
0.0131 |
0.0034 |
Wald ratio |
1 |
trans |
NA |
| Diagnoses - main ICD10: Z09 Follow-up examination after treatment for conditions other than malignant neoplasms |
0.0851 |
0.0303 |
0.00495 |
Wald ratio |
1 |
trans |
NA |
| Potassium in urine |
-0.0106 |
0.00411 |
0.00968 |
Wald ratio |
1 |
trans |
NA |
| Weight |
-0.00912 |
0.00358 |
0.0108 |
Wald ratio |
1 |
trans |
NA |
| Non-cancer illness code self-reported: kidney stone or ureter stone or bladder stone |
-0.129 |
0.0522 |
0.0132 |
Wald ratio |
1 |
trans |
NA |
| Fractured bone site(s): Other bones |
-0.0441 |
0.0184 |
0.0166 |
Wald ratio |
1 |
trans |
NA |
| Low grade serous ovarian cancer |
-0.203 |
0.0875 |
0.0201 |
Wald ratio |
1 |
trans |
NA |
| Cancer code self-reported: prostate cancer |
-0.125 |
0.0539 |
0.0205 |
Wald ratio |
1 |
trans |
NA |
| Diagnoses - main ICD10: L03 Cellulitis |
0.0922 |
0.0412 |
0.0251 |
Wald ratio |
1 |
trans |
NA |
| …and 79 more outcomes (see JSON) |
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|
2. pQTL instrument availability (Tier-B probe)
| Dataset |
Trait |
Author |
Year |
prot-c-2953_31_2 |
Luteinizing hormone |
Suhre K |
2019 |
prot-c-3032_11_2 |
FSH |
Suhre K |
2019 |
prot-c-3521_16_2 |
TSH |
Suhre K |
2019 |
prot-c-4914_10_1 |
HCG |
Suhre K |
2019 |
3. GWAS Catalog results — traits with signal at this locus
23 association rows across 16 traits (22 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 |
| Thyroid stimulating hormone levels |
5e-78 |
rs1998615 |
4 |
GCST90572789 |
no MR -> candidate analysis |
| Thyroid-stimulating hormone levels |
3e-22 |
rs2031365 |
1 |
GCST90662868 |
no MR -> candidate analysis |
| White blood cell count |
2e-20 |
rs4574603 |
2 |
GCST90002378 |
no MR -> candidate analysis |
| Circulating CGA levels |
2e-18 |
rs2031367 |
1 |
GCST90860633 |
no MR -> candidate analysis |
| Neutrophil percentage of granulocytes |
6e-18 |
rs67614146 |
1 |
GCST004623 |
no MR -> candidate analysis |
| CGA protein levels |
4e-17 |
rs2031367 |
1 |
GCST90468732 |
no MR -> candidate analysis |
| FSHB protein levels |
4e-15 |
rs779759288 |
1 |
GCST90469270 |
no MR -> candidate analysis |
| Eosinophil percentage of granulocytes |
5e-15 |
rs67614146 |
1 |
GCST004617 |
no MR -> candidate analysis |
| Free thyroxine levels within normal range in pregnancy |
1e-13 |
rs9362387 |
1 |
GCST90435196 |
no MR -> candidate analysis |
| Neutrophil-to-lymphocyte ratio |
8e-13 |
rs981087 |
3 |
GCST90866310 |
no MR -> candidate analysis |
| Eosinophil percentage of white cells |
6e-12 |
rs67614146 |
1 |
GCST004600 |
no MR -> candidate analysis |
| Educational attainment |
5e-11 |
rs9362387 |
1 |
GCST90105038 |
no MR -> candidate analysis |
| …and 4 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 877 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 |
| hypothyroidism |
0.807 |
— |
common-variant locus |
no MR -> candidate analysis |
| interstitial lung disease |
0.244 |
— |
common-variant locus |
no MR -> candidate analysis |
| placenta praevia |
0.216 |
— |
common-variant locus |
no MR -> candidate analysis |
Of the 3 rows above, 3 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 (Glycoprotein hormones alpha chain) |
| gnomAD constraint |
pLI=0.6, LOEUF=0.763 — LoF-tolerant |
| GWAS Catalog |
45 unique SNPs / 90 rows |
| ClinVar |
35 records; 12 pathogenic in sample of 30 |
| PharmGKB/ClinPGx |
no annotations |
phenome — Top 30 of 877 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 ‘CGA’ and resolved to ‘Glycoprotein hormones alpha chain’ — confirm this is the intended target.clinvar — Pathogenic count is over the 30 record(s) retrieved, NOT over all 35 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 16 of 16 traits by best p-value, aggregated from 23 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/P01215 — 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/ENSG00000135346/associations — Open Targets data release 26.06chembl: https://www.ebi.ac.uk/chembl/target_report_card/CHEMBL2146305/ — ChEMBL_37 (released 2026-05-01)gnomad: https://gnomad.broadinstitute.org/gene/CGA — gnomAD constraint via GraphQL API (reference genome GRCh38)gwas: https://www.ebi.ac.uk/gwas/genes/CGA — GWAS Catalog REST (live; release not exposed by this endpoint)clinvar: https://www.ncbi.nlm.nih.gov/clinvar/?term=CGA%5Bgene%5D — ClinVar build Build260809-1055.1gwas_traits: https://www.ebi.ac.uk/gwas/genes/CGA — GWAS Catalog search API (live; release not exposed)
Provenance
- Generated: 2026-08-14T01:49:07 · 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