CausalSentinel

Protein Dossier — LILRA4 (Leukocyte immunoglobulin-like receptor subfamily A member 4)

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
Potassium in urine	-0.0268	0.00821	0.00111	Inverse variance weighted	2	cis	NA
Potassium in urine	-0.0268	0.00821	0.00111	Inverse variance weighted	2	trans	NA
Non-cancer illness code self-reported: polio or poliomyelitis	0.525	0.191	0.00593	Inverse variance weighted	2	cis	NA
Non-cancer illness code self-reported: polio or poliomyelitis	0.525	0.191	0.00593	Inverse variance weighted	2	trans	NA
Diagnoses - main ICD10: I30 Acute pericarditis	0.643	0.263	0.0145	Inverse variance weighted	2	cis	NA
Diagnoses - main ICD10: I30 Acute pericarditis	0.643	0.263	0.0145	Inverse variance weighted	2	trans	NA
Non-cancer illness code self-reported: anxiety or panic attacks	-0.198	0.0857	0.0207	Inverse variance weighted	2	cis	NA
Non-cancer illness code self-reported: anxiety or panic attacks	-0.198	0.0857	0.0207	Inverse variance weighted	2	trans	NA
Gallbladder cancer	2.78	1.37	0.043	Wald ratio	1	cis	NA
Diagnoses - main ICD10: M72 Fibroblastic disorders	-0.311	0.155	0.044	Inverse variance weighted	2	cis	NA
Diagnoses - main ICD10: M72 Fibroblastic disorders	-0.311	0.155	0.044	Inverse variance weighted	2	trans	NA
Diagnoses - main ICD10: I80 Phlebitis and thrombophlebitis	0.195	0.0985	0.0473	Inverse variance weighted	2	cis	NA
…and 145 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

48 association rows across 28 traits (44 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
Circulating LAIR1 levels	3e-545	rs59862055	1	GCST90860669	no MR -> candidate analysis
LAIR1 protein levels	6e-202	rs73061003	5	GCST90469728	no MR -> candidate analysis
Leukocyte immunoglobulin-like receptor subfamily A member 4	3e-198	rs2241384	4	GCST90248298	no MR -> candidate analysis
LILRA3 protein levels	2e-158	rs542875167	5	GCST90469772	no MR -> candidate analysis
LILRB5 protein levels	1e-38	rs73938664	5	GCST90469779	no MR -> candidate analysis
High density lipoprotein cholesterol levels	2e-28	rs17634081	1	GCST90019510	no MR -> candidate analysis
Apolipoprotein A1 levels	4e-25	rs17634081	1	GCST90019495	no MR -> candidate analysis
LILRB2 protein levels	4e-22	rs78469793	5	GCST90469777	no MR -> candidate analysis
Leukocyte immunoglobulin-like receptor subfamily A member 4	3e-21	rs2241384	1	GCST90241789	no MR -> candidate analysis
Serum levels of protein LILRA4	1e-19	rs2241384	1	GCST90090112	no MR -> candidate analysis
LAIR2 protein levels	2e-17	rs59862055	1	GCST90469729	no MR -> candidate analysis
LILRB1 protein levels	5e-17	rs56374127	1	GCST90469776	no MR -> candidate analysis
…and 16 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 81 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
Abnormality of the gastrointestinal tract	0.21	—	common-variant locus	no MR -> candidate analysis
disease of peritoneum	0.21	—	common-variant locus	no MR -> candidate analysis

Of the 2 rows above, 2 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	1 known modulators (Leukocyte immunoglobulin-like receptor subfamily A member 4)
gnomAD constraint	pLI=2.4e-18, LOEUF=1.3 — LoF-tolerant
GWAS Catalog	196 unique SNPs / 532 rows
ClinVar	125 records; 0 pathogenic in sample of 30
PharmGKB/ClinPGx	no annotations

Caveats declared by the tools

• phenome — Top 30 of 81 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 ‘LILRA4’ and resolved to ‘Leukocyte immunoglobulin-like receptor subfamily A member 4’ — confirm this is the intended target.
• clinvar — Pathogenic count is over the 30 record(s) retrieved, NOT over all 125 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 20 of 28 traits by best p-value, aggregated from 48 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/P59901 — 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/ENSG00000239961/associations — Open Targets data release 26.06
• chembl: https://www.ebi.ac.uk/chembl/target_report_card/CHEMBL4804246/ — ChEMBL_37 (released 2026-05-01)
• gnomad: https://gnomad.broadinstitute.org/gene/LILRA4 — gnomAD constraint via GraphQL API (reference genome GRCh38)
• gwas: https://www.ebi.ac.uk/gwas/genes/LILRA4 — GWAS Catalog REST (live; release not exposed by this endpoint)
• clinvar: https://www.ncbi.nlm.nih.gov/clinvar/?term=LILRA4%5Bgene%5D — ClinVar build Build260809-1055.1
• gwas_traits: https://www.ebi.ac.uk/gwas/genes/LILRA4 — GWAS Catalog search API (live; release not exposed)

Provenance

• Generated: 2026-08-14T03:32:59 · 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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