Protein Dossier — PGK1 (Phosphoglycerate kinase 1)
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 |
| Fasting glucose |
0.0485 |
0.0193 |
0.0119 |
Wald ratio |
1 |
trans |
NA |
| Underlying (primary) cause of death: ICD10: E85.4 Organ-limited amyloidosis |
1.59 |
0.671 |
0.0181 |
Inverse variance weighted |
2 |
trans |
NA |
| Underlying (primary) cause of death: ICD10: E85.4 Organ-limited amyloidosis |
1.59 |
0.671 |
0.0181 |
Inverse variance weighted |
2 |
trans |
NA |
| Large vessel disease |
0.483 |
0.213 |
0.0238 |
Wald ratio |
1 |
trans |
NA |
| Diagnoses - main ICD10: Z09 Follow-up examination after treatment for conditions other than malignant neoplasms |
-0.216 |
0.0989 |
0.0289 |
Inverse variance weighted |
2 |
trans |
NA |
| Diagnoses - main ICD10: Z09 Follow-up examination after treatment for conditions other than malignant neoplasms |
-0.216 |
0.0989 |
0.0289 |
Inverse variance weighted |
2 |
trans |
NA |
| Birth length |
0.126 |
0.0596 |
0.0348 |
Wald ratio |
1 |
trans |
NA |
| Diagnoses - main ICD10: N92 Excessive frequent and irregular menstruation |
-0.17 |
0.0805 |
0.0349 |
Inverse variance weighted |
2 |
trans |
NA |
| Diagnoses - main ICD10: N92 Excessive frequent and irregular menstruation |
-0.17 |
0.0805 |
0.0349 |
Inverse variance weighted |
2 |
trans |
NA |
| Ferritin |
-0.121 |
0.0574 |
0.0352 |
Wald ratio |
1 |
trans |
NA |
| Diagnoses - main ICD10: K57 Diverticular disease of intestine |
-0.17 |
0.0814 |
0.0367 |
Inverse variance weighted |
2 |
trans |
NA |
| Diagnoses - main ICD10: K57 Diverticular disease of intestine |
-0.17 |
0.0814 |
0.0367 |
Inverse variance weighted |
2 |
trans |
NA |
| …and 143 more outcomes (see JSON) |
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2. pQTL instrument availability (Tier-B probe)
| Dataset |
Trait |
Author |
Year |
prot-c-5020_50_1 |
phosphoglycerate kinase 1 |
Suhre K |
2019 |
3. GWAS Catalog results — traits with signal at this locus
4 association rows across 4 traits (4 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 |
3e-30 |
rs12837147 |
1 |
GCST008839 |
MR: beta=0.0336, p=0.0645 (trans) |
| Mean platelet volume |
3e-14 |
rs5913634 |
1 |
GCST90002395 |
no MR -> candidate analysis |
| Weight |
1e-13 |
rs151280158 |
1 |
GCST90018729 |
no MR -> candidate analysis |
| Red blood cell count |
1e-8 |
rs16657 |
1 |
GCST90018971 |
no MR -> candidate analysis |
4. Phenome map — where this gene is a genetic locus, vs. where MR exists
Top diseases by Open Targets association (of 435 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 |
| glycogen storage disease due to phosphoglycerate kinase 1 deficiency |
0.906 |
— |
established (curated) |
no MR -> candidate analysis |
| Menkes disease |
0.946 |
— |
established (curated) |
no MR -> candidate analysis |
| X-linked distal spinal muscular atrophy type 3 |
0.916 |
— |
established (curated) |
no MR -> candidate analysis |
| occipital horn syndrome |
0.915 |
— |
established (curated) |
no MR -> candidate analysis |
| hereditary disease |
0.838 |
— |
established (curated) |
no MR -> candidate analysis |
| Obstructive azoospermia |
0.426 |
— |
established (curated) |
no MR -> candidate analysis |
| Ehlers-Danlos syndrome |
0.304 |
— |
established (curated) |
no MR -> candidate analysis |
| Intellectual disability |
0.245 |
— |
established (curated) |
no MR -> candidate analysis |
| Charcot-Marie-Tooth disease |
0.228 |
— |
established (curated) |
no MR -> candidate analysis |
| Epileptic encephalopathy |
0.195 |
— |
established (curated) |
no MR -> candidate analysis |
| Au-Kline syndrome |
0.195 |
— |
established (curated) |
no MR -> candidate analysis |
| Profound global developmental delay |
0.195 |
— |
established (curated) |
no MR -> candidate analysis |
| Charcot-Marie-Tooth disease type 2 |
0.195 |
— |
established (curated) |
no MR -> candidate analysis |
| optic atrophy |
0.182 |
— |
established (curated) |
no MR -> candidate analysis |
Of the 14 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 |
0 known modulators (Phosphoglycerate kinase 1) |
| gnomAD constraint |
pLI=1, LOEUF=0.288 — LoF-INTOLERANT |
| GWAS Catalog |
9 unique SNPs / 15 rows |
| ClinVar |
544 records; 3 pathogenic in sample of 30 |
| PharmGKB/ClinPGx |
no annotations |
phenome — Top 30 of 435 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 ‘PGK1’ and resolved to ‘Phosphoglycerate kinase 1’ — confirm this is the intended target.clinvar — Pathogenic count is over the 30 record(s) retrieved, NOT over all 544 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 4 of 4 traits by best p-value, aggregated from 4 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/P00558 — 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/ENSG00000102144/associations — Open Targets data release 26.06chembl: https://www.ebi.ac.uk/chembl/target_report_card/CHEMBL2886/ — ChEMBL_37 (released 2026-05-01)gnomad: https://gnomad.broadinstitute.org/gene/PGK1 — gnomAD constraint via GraphQL API (reference genome GRCh38)gwas: https://www.ebi.ac.uk/gwas/genes/PGK1 — GWAS Catalog REST (live; release not exposed by this endpoint)clinvar: https://www.ncbi.nlm.nih.gov/clinvar/?term=PGK1%5Bgene%5D — ClinVar build Build260809-1055.1gwas_traits: https://www.ebi.ac.uk/gwas/genes/PGK1 — GWAS Catalog search API (live; release not exposed)
Provenance
- Generated: 2026-08-14T04:18:48 · 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