CausalSentinel

Protein Dossier — MGAT2 (Alpha-1,6-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase)

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
Forced vital capacity (FVC)	0.0345	0.0102	6.90e-04	Wald ratio	1	cis	NA
Forced expiratory volume in 1-second (FEV1)	0.033	0.0107	0.00207	Wald ratio	1	cis	NA
Height	0.0405	0.0149	0.00645	Wald ratio	1	cis	NA
Urate	-0.0718	0.0272	0.00825	Wald ratio	1	cis	NA
Transferrin	0.137	0.0523	0.00885	Wald ratio	1	cis	NA
Non-cancer illness code self-reported: anxiety or panic attacks	0.219	0.0864	0.0111	Wald ratio	1	cis	NA
Non-cancer illness code self-reported: hypothyroidism or myxoedema	0.123	0.0488	0.0119	Wald ratio	1	cis	NA
Bipolar disorder	-0.299	0.12	0.0126	Wald ratio	1	cis	NA
Cancer code self-reported: malignant melanoma	0.27	0.109	0.013	Wald ratio	1	cis	NA
Squamous cell lung cancer	0.326	0.133	0.0146	Wald ratio	1	cis	NA
Non-cancer illness code self-reported: asthma	-0.0918	0.0381	0.0159	Wald ratio	1	cis	NA
Caudate volume	-58.6	25.2	0.0199	Wald ratio	1	cis	NA
…and 105 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

No GWAS Catalog associations mapped to this gene.

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

Top diseases by Open Targets association (of 629 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
MGAT2-congenital disorder of glycosylation	0.834	—	established (curated)	no MR -> candidate analysis
Abnormal facial shape	0.426	—	established (curated)	no MR -> candidate analysis
Global developmental delay	0.426	—	established (curated)	no MR -> candidate analysis
Abnormal glycosylation	0.426	—	established (curated)	no MR -> candidate analysis
hereditary disease	0.316	—	established (curated)	no MR -> candidate analysis
autoimmune disorder of musculoskeletal system	0.104	—	common-variant locus	no MR -> candidate analysis
corneal neovascularization	0.098	—	common-variant locus	no MR -> candidate analysis
Abnormality of the gastrointestinal tract	0.095	—	common-variant locus	no MR -> candidate analysis
lagophthalmos	0.094	—	common-variant locus	no MR -> candidate analysis
liver disorder	0.094	—	common-variant locus	no MR -> candidate analysis

Of the 10 rows above, 10 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 (Alpha-1,6-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase)
gnomAD constraint	pLI=0.0093, LOEUF=0.755 — LoF-tolerant
GWAS Catalog	21 unique SNPs / 42 rows
ClinVar	185 records; 2 pathogenic in sample of 30
PharmGKB/ClinPGx	no annotations

Caveats declared by the tools

• phenome — Top 30 of 629 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 ‘MGAT2’ and resolved to ‘Alpha-1,6-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase’ — confirm this is the intended target.
• clinvar — Pathogenic count is over the 30 record(s) retrieved, NOT over all 185 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 — No GWAS Catalog associations mapped to this gene.

Sources

• uniprot: https://www.uniprot.org/uniprotkb/Q10469 — 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/ENSG00000168282/associations — Open Targets data release 26.06
• chembl: https://www.ebi.ac.uk/chembl/target_report_card/CHEMBL2321630/ — ChEMBL_37 (released 2026-05-01)
• gnomad: https://gnomad.broadinstitute.org/gene/MGAT2 — gnomAD constraint via GraphQL API (reference genome GRCh38)
• gwas: https://www.ebi.ac.uk/gwas/genes/MGAT2 — GWAS Catalog REST (live; release not exposed by this endpoint)
• clinvar: https://www.ncbi.nlm.nih.gov/clinvar/?term=MGAT2%5Bgene%5D — ClinVar build Build260809-1055.1

Provenance

• Generated: 2026-08-14T03:47:21 · 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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