CausalSentinel

Protein Dossier — COLGALT1 (Procollagen galactosyltransferase 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
Systolic blood pressure automated reading	-0.0187	0.00661	0.00462	Inverse variance weighted	2	trans	NA
Systolic blood pressure automated reading	-0.0187	0.00661	0.00462	Inverse variance weighted	2	trans	NA
Creatinine (enzymatic) in urine	-0.0166	0.00618	0.00723	Inverse variance weighted	2	trans	NA
Creatinine (enzymatic) in urine	-0.0166	0.00618	0.00723	Inverse variance weighted	2	trans	NA
Diagnoses - main ICD10: G56 Mononeuropathies of upper limb	0.112	0.044	0.0107	Inverse variance weighted	2	trans	NA
Diagnoses - main ICD10: G56 Mononeuropathies of upper limb	0.112	0.044	0.0107	Inverse variance weighted	2	trans	NA
Cancer code self-reported: small intestine or small bowel cancer	0.489	0.196	0.0125	Inverse variance weighted	2	trans	NA
Cancer code self-reported: small intestine or small bowel cancer	0.489	0.196	0.0125	Inverse variance weighted	2	trans	NA
Diagnoses - main ICD10: N20 Calculus of kidney and ureter	-0.24	0.0988	0.0153	Inverse variance weighted	2	trans	NA
Diagnoses - main ICD10: N20 Calculus of kidney and ureter	-0.24	0.0988	0.0153	Inverse variance weighted	2	trans	NA
Inflammatory bowel disease	0.139	0.0595	0.0197	Wald ratio	1	trans	NA
Non-cancer illness code self-reported: ankylosing spondylitis	0.297	0.129	0.0213	Inverse variance weighted	2	trans	NA
…and 138 more outcomes (see JSON)

2. pQTL instrument availability (Tier-B probe)

No prot-* pQTL GWAS dataset found for this protein (matched by UniProt accession and symbol).

3. GWAS Catalog results — traits with signal at this locus

8 association rows across 5 traits (6 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
Procollagen galactosyltransferase 1 levels	8e-47	rs4808666	1	GCST90248987	no MR -> candidate analysis
Height	8e-13	rs7249148	3	GCST90245848	no MR -> candidate analysis
White blood cell count	1e-10	rs62119898	2	GCST90002407	no MR -> candidate analysis
Total antibody levels in response to SARS-CoV-2 vaccination	3e-9	rs149813122	1	GCST90244757	no MR -> candidate analysis
Blood protein levels	4e-6	rs73525772	1	GCST006585	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 1370 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
cerebral small vessel disease	0.824	—	established (curated)	no MR -> candidate analysis
hereditary disease	0.683	—	established (curated)	no MR -> candidate analysis
familial porencephaly	0.608	—	established (curated)	no MR -> candidate analysis
response to COVID-19 vaccine	0.3	—	common-variant locus	no MR -> candidate analysis
vascular dementia	0.182	—	established (curated)	no MR -> candidate analysis
Genetic visceral malformation of the liver, biliary tract, pancreas or spleen	0.153	—	common-variant locus	no MR -> candidate analysis
digestive system disorder	0.113	—	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 (Procollagen galactosyltransferase 1)
gnomAD constraint	pLI=9.7e-11, LOEUF=0.911 — LoF-tolerant
GWAS Catalog	43 unique SNPs / 86 rows
ClinVar	353 records; 0 pathogenic in sample of 30
PharmGKB/ClinPGx	no annotations

Caveats declared by the tools

• phenome — Top 30 of 1370 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 ‘COLGALT1’ and resolved to ‘Procollagen galactosyltransferase 1’ — confirm this is the intended target.
• clinvar — Pathogenic count is over the 30 record(s) retrieved, NOT over all 353 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 5 of 5 traits by best p-value, aggregated from 8 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/Q8NBJ5 — 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 v3.0
• phenome: https://platform.opentargets.org/target/ENSG00000130309/associations — Open Targets data release 26.06
• chembl: https://www.ebi.ac.uk/chembl/target_report_card/CHEMBL6067420/ — ChEMBL_37 (released 2026-05-01)
• gnomad: https://gnomad.broadinstitute.org/gene/COLGALT1 — gnomAD constraint via GraphQL API (reference genome GRCh38)
• gwas: https://www.ebi.ac.uk/gwas/genes/COLGALT1 — GWAS Catalog REST (live; release not exposed by this endpoint)
• clinvar: https://www.ncbi.nlm.nih.gov/clinvar/?term=COLGALT1%5Bgene%5D — ClinVar build Build260809-1055.1
• gwas_traits: https://www.ebi.ac.uk/gwas/genes/COLGALT1 — GWAS Catalog search API (live; release not exposed)

Provenance

• Generated: 2026-08-14T01:58:28 · 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

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