Protein Dossier — GDI2 (Rab GDP dissociation inhibitor beta)
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 |
| ER-positive Breast cancer (Combined Oncoarray; iCOGS; GWAS meta analysis) |
-0.189 |
0.0406 |
3.12e-06 |
Wald ratio |
1 |
cis |
NA |
| Breast cancer (Combined Oncoarray; iCOGS; GWAS meta analysis) |
-0.157 |
0.0338 |
3.34e-06 |
Wald ratio |
1 |
cis |
NA |
| LDL cholesterol |
0.102 |
0.0274 |
1.89e-04 |
Wald ratio |
1 |
cis |
NA |
| Cancer code self-reported: small intestine or small bowel cancer |
0.95 |
0.257 |
2.22e-04 |
Wald ratio |
1 |
cis |
NA |
| Cigarettes smoked per day |
-1.46 |
0.435 |
8.00e-04 |
Wald ratio |
1 |
cis |
NA |
| Fasting proinsulin |
0.119 |
0.0374 |
0.00152 |
Wald ratio |
1 |
cis |
NA |
| Schizophrenia |
-0.168 |
0.058 |
0.00376 |
Wald ratio |
1 |
cis |
NA |
| Non-cancer illness code self-reported: emphysema or chronic bronchitis |
0.254 |
0.0882 |
0.00397 |
Wald ratio |
1 |
cis |
NA |
| Diagnoses - main ICD10: M72 Fibroblastic disorders |
0.36 |
0.126 |
0.00422 |
Wald ratio |
1 |
cis |
NA |
| Haemoglobin concentration |
-0.084 |
0.0315 |
0.00766 |
Wald ratio |
1 |
cis |
NA |
| Non-cancer illness code self-reported: hypothyroidism or myxoedema |
0.134 |
0.0508 |
0.00854 |
Wald ratio |
1 |
cis |
NA |
| Packed cell volume |
-0.262 |
0.1 |
0.0092 |
Wald ratio |
1 |
cis |
NA |
| …and 107 more outcomes (see JSON) |
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2. pQTL instrument availability (Tier-B probe)
| Dataset |
Trait |
Author |
Year |
prot-c-2647_66_2 |
Rab GDP dissociation inhibitor beta |
Suhre K |
2019 |
3. GWAS Catalog results — traits with signal at this locus
23 association rows across 18 traits (16 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 |
| Telomere length (principal component 1) |
2e-31 |
rs762222726 |
1 |
GCST90435144 |
no MR -> candidate analysis |
| Monocyte count |
3e-25 |
rs11255548 |
3 |
GCST90002340 |
no MR -> candidate analysis |
| Rab GDP dissociation inhibitor beta levels |
6e-18 |
rs60583998 |
1 |
GCST90249227 |
no MR -> candidate analysis |
| Serum levels of protein GDI2 |
8e-17 |
rs3736461 |
1 |
GCST90088004 |
no MR -> candidate analysis |
| Leukocyte telomere length |
4e-16 |
rs10905255 |
1 |
GCST90709782 |
no MR -> candidate analysis |
| Core binding factor acute myeloid leukemia |
4e-15 |
rs2380205; rs12242149; rs12774966; rs12780246; rs2380208; rs11255590; rs907687; rs907688; rs907689; rs7904512; rs12359234; rs7071536; rs2203197 |
2 |
GCST008413 |
no MR -> candidate analysis |
| Monocyte count (UKB data field 30130) |
5e-14 |
rs907690 |
1 |
GCST90468090 |
no MR -> candidate analysis |
| Blood protein levels |
9e-14 |
rs2890364 |
1 |
GCST006585 |
no MR -> candidate analysis |
| IL2RA levels |
1e-10 |
rs142276437 |
1 |
GCST90274897 |
no MR -> candidate analysis |
| Prostate cancer |
1e-9 |
rs72772400 |
2 |
GCST90274713 |
MR: beta=-0.233, p=0.25 (cis) |
| Hypothyroidism |
2e-9 |
rs7089100 |
1 |
GCST90627749 |
MR: beta=0.134, p=0.00854 (cis) |
| Heel bone mineral density x serum urate levels interaction |
1e-8 |
rs545406654 |
1 |
GCST012489 |
no MR -> candidate analysis |
| …and 6 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 792 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 |
| Abnormality of the skeletal system |
0.504 |
— |
common-variant locus |
no MR -> candidate analysis |
| prostate carcinoma |
0.416 |
— |
common-variant locus |
no MR -> candidate analysis |
| kidney transplant |
0.416 |
— |
common-variant locus |
no MR -> candidate analysis |
| breast carcinoma |
0.288 |
— |
common-variant locus |
no MR -> candidate analysis |
| ovarian neoplasm |
0.255 |
— |
common-variant locus |
no MR -> candidate analysis |
| cutaneous melanoma |
0.171 |
— |
common-variant locus |
no MR -> candidate analysis |
| drug allergy |
0.152 |
— |
common-variant locus |
no MR -> candidate analysis |
Of the 7 rows above, 7 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 (Rab GDP dissociation inhibitor beta) |
| gnomAD constraint |
pLI=0.35, LOEUF=0.58 — LoF-tolerant |
| GWAS Catalog |
79 unique SNPs / 151 rows |
| ClinVar |
99 records; 1 pathogenic in sample of 30 |
| PharmGKB/ClinPGx |
no annotations |
phenome — Top 30 of 792 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 ‘GDI2’ and resolved to ‘Rab GDP dissociation inhibitor beta’ — confirm this is the intended target.clinvar — Pathogenic count is over the 30 record(s) retrieved, NOT over all 99 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 18 of 18 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/P50395 — 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/ENSG00000057608/associations — Open Targets data release 26.06chembl: https://www.ebi.ac.uk/chembl/target_report_card/CHEMBL6066507/ — ChEMBL_37 (released 2026-05-01)gnomad: https://gnomad.broadinstitute.org/gene/GDI2 — gnomAD constraint via GraphQL API (reference genome GRCh38)gwas: https://www.ebi.ac.uk/gwas/genes/GDI2 — GWAS Catalog REST (live; release not exposed by this endpoint)clinvar: https://www.ncbi.nlm.nih.gov/clinvar/?term=GDI2%5Bgene%5D — ClinVar build Build260809-1055.1gwas_traits: https://www.ebi.ac.uk/gwas/genes/GDI2 — GWAS Catalog search API (live; release not exposed)
Provenance
- Generated: 2026-08-14T02:47:43 · 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