CausalSentinel

Protein Dossier — POMGNT2 (Protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2)

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
Bulimia nervosa	-0.082	0.0273	0.0027	Inverse variance weighted	2	trans	NA
Bulimia nervosa	-0.082	0.0273	0.0027	Inverse variance weighted	2	cis	NA
Diagnoses - main ICD10: R07 Pain in throat and chest	0.0849	0.0317	0.00736	Inverse variance weighted	2	trans	NA
Diagnoses - main ICD10: R07 Pain in throat and chest	0.0849	0.0317	0.00736	Inverse variance weighted	2	cis	NA
Diagnoses - main ICD10: N92 Excessive frequent and irregular menstruation	0.109	0.0424	0.00988	Inverse variance weighted	2	trans	NA
Diagnoses - main ICD10: N92 Excessive frequent and irregular menstruation	0.109	0.0424	0.00988	Inverse variance weighted	2	cis	NA
Diagnoses - main ICD10: M23 Internal derangement of knee	0.104	0.0411	0.0118	Inverse variance weighted	2	trans	NA
Diagnoses - main ICD10: M23 Internal derangement of knee	0.104	0.0411	0.0118	Inverse variance weighted	2	cis	NA
Non-cancer illness code self-reported: hypothyroidism or myxoedema	-0.0729	0.0324	0.0245	Inverse variance weighted	2	trans	NA
Non-cancer illness code self-reported: hypothyroidism or myxoedema	-0.0729	0.0324	0.0245	Inverse variance weighted	2	cis	NA
Primary sclerosing cholangitis	0.194	0.0866	0.0253	Inverse variance weighted	2	trans	NA
Primary sclerosing cholangitis	0.194	0.0866	0.0253	Inverse variance weighted	2	cis	NA
…and 203 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

65 association rows across 37 traits (53 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
Protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransf	2e-257	rs4683355	2	GCST90249061	no MR -> candidate analysis
GASK1A protein levels	5e-106	rs73074963	15	GCST90469306	no MR -> candidate analysis
Serum levels of protein POMGNT2	3e-50	rs2936818	1	GCST90089363	no MR -> candidate analysis
Protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransf	8e-34	rs79762832	1	GCST90238222	no MR -> candidate analysis
Blood protein levels	4e-30	rs729654	1	GCST006585	no MR -> candidate analysis
Height	8e-29	rs1320160	1	GCST90245848	no MR -> candidate analysis
Protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransf	9e-27	rs729654	1	GCST90242495	no MR -> candidate analysis
CCL17 protein levels	2e-25	rs11719635	1	GCST90468569	no MR -> candidate analysis
Hematological traits (multi-trait analysis)	1e-23	rs60671097	2	GCST90838669	no MR -> candidate analysis
Insomnia	5e-17	rs9875582	8	GCST90131901	no MR -> candidate analysis
CCL7 protein levels	1e-14	rs11719635	1	GCST90468585	no MR -> candidate analysis
Externalizing behaviour (multivariate analysis)	3e-13	rs76887862	1	GCST90061435	no MR -> candidate analysis
…and 25 more traits (see JSON)

4. Phenome map — where this gene is a genetic locus, vs. where MR exists

Top diseases by Open Targets association (of 61 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
muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 8	0.896	—	established (curated)	no MR -> candidate analysis
muscular dystrophy-dystroglycanopathy (limb-girdle), type C, 8	0.796	—	established (curated)	no MR -> candidate analysis
muscular dystrophy-dystroglycanopathy, type A	0.608	—	established (curated)	no MR -> candidate analysis
hereditary disease	0.561	—	established (curated)	no MR -> candidate analysis
ankylosing spondylitis	0.427	—	common-variant locus	no MR -> candidate analysis
Severe hydrocephalus	0.426	—	established (curated)	no MR -> candidate analysis
placenta praevia	0.324	—	common-variant locus	no MR -> candidate analysis
ovarian neoplasm	0.309	—	common-variant locus	no MR -> candidate analysis
response to antihypertensive drug	0.167	—	common-variant locus	no MR -> candidate analysis
spondylolisthesis	0.106	—	common-variant locus	no MR -> candidate analysis
ovarian dysfunction	0.088	—	common-variant locus	no MR -> candidate analysis
insomnia	0.051	—	common-variant locus	no MR -> candidate analysis
cleft palate	0.043	—	common-variant locus	no MR -> candidate analysis
Hypercholesterolemia	0.041	—	common-variant locus	MR: beta=0.0266, p=0.0635 (trans)
attention deficit-hyperactivity disorder	0.033	—	common-variant locus	no MR -> candidate analysis

Of the 15 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	not available — no ChEMBL target (undrugged)
gnomAD constraint	pLI=5.5e-10, LOEUF=1.14 — LoF-tolerant
GWAS Catalog	101 unique SNPs / 179 rows
ClinVar	508 records; 4 pathogenic in sample of 30
PharmGKB/ClinPGx	no annotations

Caveats declared by the tools

• phenome — Top 30 of 61 associated diseases by overall score. genetic_association aggregates GWAS common-variant AND rare-variant evidence. These are ASSOCIATIONS (loci), not causal claims.
• chembl — No ChEMBL target for ‘POMGNT2’.
• clinvar — Pathogenic count is over the 30 record(s) retrieved, NOT over all 508 ClinVar records for this gene; it is a sample, not a rate.
• gwas_traits — Top 20 of 37 traits by best p-value, aggregated from 65 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/Q8NAT1 — 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/ENSG00000144647/associations — Open Targets data release 26.06
• gnomad: https://gnomad.broadinstitute.org/gene/POMGNT2 — gnomAD constraint via GraphQL API (reference genome GRCh38)
• gwas: https://www.ebi.ac.uk/gwas/genes/POMGNT2 — GWAS Catalog REST (live; release not exposed by this endpoint)
• clinvar: https://www.ncbi.nlm.nih.gov/clinvar/?term=POMGNT2%5Bgene%5D — ClinVar build Build260809-1055.1
• gwas_traits: https://www.ebi.ac.uk/gwas/genes/POMGNT2 — GWAS Catalog search API (live; release not exposed)

Provenance

• Generated: 2026-08-14T04:31:22 · 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: pharmgkb

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