CausalSentinel

Protein Dossier — HAVCR1 (Hepatitis A virus cellular receptor 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
Diagnoses - main ICD10: L03 Cellulitis	0.18	0.0489	2.31e-04	Wald ratio	1	cis	NA
Non-cancer illness code self-reported: high cholesterol	0.0379	0.0137	0.00556	Wald ratio	1	cis	NA
Thyroid cancer	0.448	0.184	0.0148	Wald ratio	1	cis	NA
Total cholesterol	0.0265	0.0111	0.0167	Wald ratio	1	cis	NA
Non-cancer illness code self-reported: psoriasis	0.103	0.0447	0.0217	Wald ratio	1	cis	NA
Endometrioid ovarian cancer	-0.145	0.0636	0.0224	Wald ratio	1	cis	NA
Triglycerides	0.0233	0.0102	0.0228	Wald ratio	1	cis	NA
Non-cancer illness code self-reported: enlarged prostate	-0.113	0.0504	0.0244	Wald ratio	1	cis	NA
Parkinson’s disease	0.195	0.0889	0.0283	Wald ratio	1	cis	NA
Non-cancer illness code self-reported: depression	0.0453	0.0207	0.0285	Wald ratio	1	cis	NA
Knee osteoarthritis	0.127	0.0579	0.0286	Wald ratio	1	cis	NA
Diagnoses - main ICD10: K43 Ventral hernia	-0.202	0.0974	0.0379	Wald ratio	1	cis	NA
…and 104 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

973 association rows across 522 traits (953 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 HAVCR1 levels (id: OID00426_OID21422)	2e-2307	rs6555821	5	GCST90859787	no MR -> candidate analysis
Circulating HAVCR1 levels (id: OID01075_OID21422)	2e-1545	rs6555821	4	GCST90860291	no MR -> candidate analysis
AMBP/HAVCR1 protein level ratio	2e-1335	rs6863148	1	GCST90313254	no MR -> candidate analysis
Kidney injury molecule 1 levels	4e-817	rs6555820	3	GCST90012041	no MR -> candidate analysis
T-cell immunoglobulin and mucin domain-containing protein 4	1e-363	rs6882076	3	GCST90422671	no MR -> candidate analysis
Circulating TIMD4 levels	2e-323	rs4704826	3	GCST90860495	no MR -> candidate analysis
Total cholesterol levels	5e-247	rs6874202	31	GCST90239673	no MR -> candidate analysis
LDL cholesterol levels x alcohol consumption (regular vs non	5e-226	rs10066168	2	GCST008078	no MR -> candidate analysis
Non-HDL cholesterol levels	7e-184	rs6874202	3	GCST90239667	no MR -> candidate analysis
Hepatitis A virus cellular receptor 1 levels	4e-175	rs6878069	3	GCST90247868	no MR -> candidate analysis
Low density lipoprotein cholesterol levels	8e-156	rs6874202	21	GCST90239655	no MR -> candidate analysis
Low-density lipoprotein levels	4e-147	rs6882076	2	GCST90662892	no MR -> candidate analysis
…and 510 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 556 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
metabolic disease	0.75	—	common-variant locus	no MR -> candidate analysis
familial hyperlipidemia	0.477	—	common-variant locus	no MR -> candidate analysis
alcohol drinking	0.415	—	common-variant locus	no MR -> candidate analysis
self-injurious ideation	0.295	—	common-variant locus	no MR -> candidate analysis
hypothyroidism	0.142	—	common-variant locus	MR: beta=0.0181, p=0.43 (cis)

Of the 5 rows above, 4 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=8.1e-13, LOEUF=1.42 — LoF-tolerant
GWAS Catalog	109 unique SNPs / 256 rows
ClinVar	103 records; 1 pathogenic in sample of 30
PharmGKB/ClinPGx	no annotations

Caveats declared by the tools

• phenome — Top 30 of 556 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 ‘HAVCR1’.
• clinvar — Pathogenic count is over the 30 record(s) retrieved, NOT over all 103 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 522 traits by best p-value, aggregated from 973 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/Q96D42 — 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/ENSG00000113249/associations — Open Targets data release 26.06
• gnomad: https://gnomad.broadinstitute.org/gene/HAVCR1 — gnomAD constraint via GraphQL API (reference genome GRCh38)
• gwas: https://www.ebi.ac.uk/gwas/genes/HAVCR1 — GWAS Catalog REST (live; release not exposed by this endpoint)
• clinvar: https://www.ncbi.nlm.nih.gov/clinvar/?term=HAVCR1%5Bgene%5D — ClinVar build Build260809-1055.1
• gwas_traits: https://www.ebi.ac.uk/gwas/genes/HAVCR1 — GWAS Catalog search API (live; release not exposed)

Provenance

• Generated: 2026-08-14T02:57:57 · 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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