Protein Dossier — HAVCR2 (Hepatitis A virus cellular receptor 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 |
| Non-cancer illness code self-reported: hyperthyroidism or thyrotoxicosis |
0.165 |
0.0416 |
7.44e-05 |
Wald ratio |
1 |
cis |
NA |
| Non-cancer illness code self-reported: high cholesterol |
-0.0397 |
0.0119 |
8.22e-04 |
Wald ratio |
1 |
cis |
NA |
| Non-cancer illness code self-reported: hypothyroidism or myxoedema |
0.0567 |
0.0177 |
0.00137 |
Wald ratio |
1 |
cis |
NA |
| LDL cholesterol |
-0.025 |
0.00802 |
0.00181 |
Inverse variance weighted |
2 |
trans |
NA |
| LDL cholesterol |
-0.025 |
0.00802 |
0.00181 |
Inverse variance weighted |
2 |
cis |
NA |
| Internalizing problems |
-0.15 |
0.0609 |
0.0136 |
Wald ratio |
1 |
trans |
NA |
| Total cholesterol |
-0.0242 |
0.0109 |
0.0261 |
Inverse variance weighted |
2 |
trans |
NA |
| Total cholesterol |
-0.0242 |
0.0109 |
0.0261 |
Inverse variance weighted |
2 |
cis |
NA |
| Eye problems or disorders: Glaucoma |
-0.0817 |
0.0383 |
0.0328 |
Wald ratio |
1 |
cis |
NA |
| Diagnoses - main ICD10: K35 Acute appendicitis |
0.115 |
0.0542 |
0.0346 |
Wald ratio |
1 |
cis |
NA |
| Alcohol intake frequency |
-0.0128 |
0.00624 |
0.0396 |
Wald ratio |
1 |
cis |
NA |
| Hirschsprung’s disease |
1.32 |
0.67 |
0.0489 |
Wald ratio |
1 |
cis |
NA |
| …and 112 more outcomes (see JSON) |
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|
|
|
|
2. pQTL instrument availability (Tier-B probe)
| Dataset |
Trait |
Author |
Year |
prot-c-5134_52_2 |
TIMD3 |
Suhre K |
2019 |
3. GWAS Catalog results — traits with signal at this locus
44 association rows across 29 traits (37 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 |
| Hepatitis A virus cellular receptor 2 levels |
2e-517 |
rs7442742 |
5 |
GCST90247869 |
no MR -> candidate analysis |
| Circulating HAVCR2 levels |
4e-316 |
rs190211816 |
4 |
GCST90860595 |
no MR -> candidate analysis |
| HAVCR2 protein levels |
1e-297 |
rs147827860 |
3 |
GCST90469432 |
no MR -> candidate analysis |
| Serum levels of protein HAVCR2 |
3e-176 |
rs919744 |
2 |
GCST90088950 |
no MR -> candidate analysis |
| Hepatitis A virus cellular receptor 2 levels (HAVCR2.5134.52 |
1e-145 |
rs6874178 |
1 |
GCST90241395 |
no MR -> candidate analysis |
| Hepatitis A virus cellular receptor 2 (analyte X5134.52) lev |
4e-145 |
rs6873659 |
1 |
GCST90426271 |
no MR -> candidate analysis |
| HAVCR1 protein levels |
1e-113 |
rs113319693 |
3 |
GCST90469431 |
no MR -> candidate analysis |
| Blood protein levels |
7e-104 |
rs4704737 |
1 |
GCST006585 |
no MR -> candidate analysis |
| Circulating HAVCR1 levels (id: OID00426_OID21422) |
9e-97 |
rs61159436 |
1 |
GCST90859787 |
no MR -> candidate analysis |
| HAVCR2/TNFRSF1B protein level ratio |
3e-80 |
rs115961055 |
1 |
GCST90315030 |
no MR -> candidate analysis |
| Circulating HAVCR1 levels (id: OID01075_OID21422) |
2e-74 |
rs61159436 |
1 |
GCST90860291 |
no MR -> candidate analysis |
| FOLR2/HAVCR2 protein level ratio |
2e-66 |
rs115961055 |
1 |
GCST90314865 |
no MR -> candidate analysis |
| …and 17 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 797 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 |
| subcutaneous panniculitis-like T-cell lymphoma |
0.752 |
— |
established (curated) |
no MR -> candidate analysis |
| late-onset Alzheimers disease |
0.43 |
— |
common-variant locus |
no MR -> candidate analysis |
| dementia |
0.385 |
— |
common-variant locus |
no MR -> candidate analysis |
Of the 3 rows above, 3 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 |
3 known modulators (Hepatitis A virus cellular receptor 2) |
| gnomAD constraint |
pLI=0.013, LOEUF=0.838 — LoF-tolerant |
| GWAS Catalog |
105 unique SNPs / 209 rows |
| ClinVar |
101 records; 1 pathogenic in sample of 30 |
| PharmGKB/ClinPGx |
no annotations |
phenome — Top 30 of 797 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 ‘HAVCR2’ and resolved to ‘Hepatitis A virus cellular receptor 2’ — confirm this is the intended target.clinvar — Pathogenic count is over the 30 record(s) retrieved, NOT over all 101 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 29 traits by best p-value, aggregated from 44 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/Q8TDQ0 — 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 v3.0phenome: https://platform.opentargets.org/target/ENSG00000135077/associations — Open Targets data release 26.06chembl: https://www.ebi.ac.uk/chembl/target_report_card/CHEMBL4630879/ — ChEMBL_37 (released 2026-05-01)gnomad: https://gnomad.broadinstitute.org/gene/HAVCR2 — gnomAD constraint via GraphQL API (reference genome GRCh38)gwas: https://www.ebi.ac.uk/gwas/genes/HAVCR2 — GWAS Catalog REST (live; release not exposed by this endpoint)clinvar: https://www.ncbi.nlm.nih.gov/clinvar/?term=HAVCR2%5Bgene%5D — ClinVar build Build260809-1055.1gwas_traits: https://www.ebi.ac.uk/gwas/genes/HAVCR2 — GWAS Catalog search API (live; release not exposed)
Provenance
- Generated: 2026-08-14T02:58:13 · 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