MR feasibility tier: A — Published pQTL-MR estimates exist for this protein (retrieved below - not computed here).
| Outcome | beta | se | p | method | nSNP | cis/trans | coloc |
|---|---|---|---|---|---|---|---|
| HDL cholesterol | 0.23 | 0.0272 | 3.10e-17 | Wald ratio | 1 | trans | 0.991 |
| Triglycerides | -0.179 | 0.0264 | 1.07e-11 | Wald ratio | 1 | trans | 0.995 |
| Mean cell volume | -0.579 | 0.146 | 6.93e-05 | Wald ratio | 1 | trans | NA |
| Heel bone mineral density (BMD) T-score automated | -0.0656 | 0.0169 | 1.04e-04 | Wald ratio | 1 | trans | NA |
| Red blood cell count | 0.0433 | 0.0125 | 5.32e-04 | Wald ratio | 1 | trans | NA |
| Mean cell haemoglobin | -0.181 | 0.0576 | 0.00165 | Wald ratio | 1 | trans | NA |
| Thyroid cancer | 1.32 | 0.47 | 0.00486 | Wald ratio | 1 | trans | NA |
| PGC cross-disorder traits | 0.189 | 0.0674 | 0.00511 | Wald ratio | 1 | trans | NA |
| Depressive symptoms | -0.0447 | 0.0179 | 0.0124 | Wald ratio | 1 | trans | NA |
| Non-cancer illness code self-reported: hypertension | -0.0585 | 0.0236 | 0.0133 | Wald ratio | 1 | trans | NA |
| Non-cancer illness code self-reported: kidney stone or ureter stone or bladder stone | 0.277 | 0.114 | 0.0146 | Wald ratio | 1 | trans | NA |
| Forced vital capacity (FVC) | 0.0244 | 0.0107 | 0.0229 | Wald ratio | 1 | trans | NA |
| …and 113 more outcomes (see JSON) |
No prot-* pQTL GWAS dataset found for this protein (matched by UniProt accession and symbol).
17 association rows across 10 traits (9 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 |
|---|---|---|---|---|---|
| Type 2 diabetes | 2e-27 | rs1043246 | 8 | GCST90492734 | MR: beta=0.132, p=0.0468 (trans) |
| Eosinophil count | 4e-12 | rs887387 | 1 | GCST007065 | no MR -> candidate analysis |
| Eosinophill percentage (UKB data field 30210) | 1e-11 | rs887387 | 1 | GCST90468069 | no MR -> candidate analysis |
| Educational attainment | 4e-8 | rs8068875 | 1 | GCST90105038 | no MR -> candidate analysis |
| Atrial fibrillation | 4e-8 | rs9904017 | 1 | GCST90559230 | MR: beta=-0.126, p=0.383 (trans) |
| Glucose homeostasis traits | 3e-6 | rs1006703 | 1 | GCST002726 | no MR -> candidate analysis |
| Oropharynx cancer and human papilloma virus 16 negative orop | 5e-6 | rs35334668 | 1 | GCST90085701 | no MR -> candidate analysis |
| Mild age-related type 2 diabetes | 5e-6 | rs55858476 | 1 | GCST90026416 | no MR -> candidate analysis |
| Stuttering | 5e-6 | rs114821226 | 1 | GCST90707227 | no MR -> candidate analysis |
| Coronary artery calcified atherosclerotic plaque (130 HU thr | 9e-6 | rs7501731 | 1 | GCST005173 | no MR -> candidate analysis |
Top diseases by Open Targets association (of 215 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 |
|---|---|---|---|---|
| diabetes mellitus | 0.698 | — | common-variant locus | no MR -> candidate analysis |
| type 2 diabetes mellitus | 0.605 | — | common-variant locus | no MR -> candidate analysis |
| gastroesophageal reflux disease | 0.555 | — | common-variant locus | no MR -> candidate analysis |
| esophageal disorder | 0.496 | — | common-variant locus | no MR -> candidate analysis |
| alcohol drinking | 0.468 | — | common-variant locus | no MR -> candidate analysis |
| stroke disorder | 0.468 | — | common-variant locus | no MR -> candidate analysis |
| alopecia areata | 0.463 | — | common-variant locus | no MR -> candidate analysis |
| diaphragmatic hernia | 0.404 | — | common-variant locus | MR: beta=-0.103, p=0.383 (trans) |
| ovarian dysfunction | 0.25 | — | common-variant locus | no MR -> candidate analysis |
| hypertensive disorder | 0.083 | — | common-variant locus | no MR -> candidate analysis |
| schizophrenia | 0.07 | — | common-variant locus | MR: beta=-0.0487, p=0.391 (trans) |
| hypothyroidism | 0.068 | — | common-variant locus | MR: beta=0.0531, p=0.337 (trans) |
| response to statin | 0.061 | — | common-variant locus | no MR -> candidate analysis |
| diverticular disease | 0.06 | — | common-variant locus | MR: beta=-0.109, p=0.293 (trans) |
| diabetic retinopathy | 0.054 | — | 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.
| Layer | Result |
|---|---|
| ChEMBL druggability | 0 known modulators (Sarcoplasmic/endoplasmic reticulum calcium ATPase 3) |
| gnomAD constraint | pLI=2.3e-10, LOEUF=0.707 — LoF-tolerant |
| GWAS Catalog | 67 unique SNPs / 134 rows |
| ClinVar | 247 records; 1 pathogenic in sample of 30 |
| PharmGKB/ClinPGx | no annotations |
phenome — Top 30 of 215 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 ‘ATP2A3’ and resolved to ‘Sarcoplasmic/endoplasmic reticulum calcium ATPase 3’ — confirm this is the intended target.clinvar — Pathogenic count is over the 30 record(s) retrieved, NOT over all 247 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 10 of 10 traits by best p-value, aggregated from 17 association rows. These are GWAS ASSOCIATIONS (loci), not causal claims; mapped genes at a locus are not necessarily the effector gene.uniprot: https://www.uniprot.org/uniprotkb/Q93084 — 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/ENSG00000074370/associations — Open Targets data release 26.06chembl: https://www.ebi.ac.uk/chembl/target_report_card/CHEMBL2401/ — ChEMBL_37 (released 2026-05-01)gnomad: https://gnomad.broadinstitute.org/gene/ATP2A3 — gnomAD constraint via GraphQL API (reference genome GRCh38)gwas: https://www.ebi.ac.uk/gwas/genes/ATP2A3 — GWAS Catalog REST (live; release not exposed by this endpoint)clinvar: https://www.ncbi.nlm.nih.gov/clinvar/?term=ATP2A3%5Bgene%5D — ClinVar build Build260809-1055.1gwas_traits: https://www.ebi.ac.uk/gwas/genes/ATP2A3 — GWAS Catalog search API (live; release not exposed)