Protein Dossier — XCL1 (Lymphotactin)
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 |
| Cancer code self-reported: prostate cancer |
-0.263 |
0.11 |
0.0169 |
Wald ratio |
1 |
cis |
NA |
| Non-cancer illness code self-reported: hiatus hernia |
0.0984 |
0.0425 |
0.0207 |
Wald ratio |
1 |
cis |
NA |
| Urate |
-0.0349 |
0.0156 |
0.0252 |
Wald ratio |
1 |
cis |
NA |
| Happiness |
0.0192 |
0.00887 |
0.0306 |
Wald ratio |
1 |
cis |
NA |
| Thalamus volume |
38.3 |
18.7 |
0.0404 |
Wald ratio |
1 |
cis |
NA |
| Haemoglobin concentration |
0.0317 |
0.0161 |
0.0487 |
Wald ratio |
1 |
cis |
NA |
| Diagnoses - main ICD10: N20 Calculus of kidney and ureter |
-0.204 |
0.106 |
0.0535 |
Wald ratio |
1 |
cis |
NA |
| Body mass index (BMI) |
0.0136 |
0.00713 |
0.0572 |
Wald ratio |
1 |
cis |
NA |
| Diagnoses - main ICD10: R55 Syncope and collapse |
-0.172 |
0.0908 |
0.0577 |
Wald ratio |
1 |
cis |
NA |
| Sodium in urine |
0.0132 |
0.00702 |
0.0592 |
Wald ratio |
1 |
cis |
NA |
| Hip osteoarthritis |
0.158 |
0.0838 |
0.0601 |
Wald ratio |
1 |
cis |
NA |
| Weight |
0.0115 |
0.0063 |
0.0691 |
Wald ratio |
1 |
cis |
NA |
| …and 111 more outcomes (see JSON) |
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|
|
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|
2. pQTL instrument availability (Tier-B probe)
| Dataset |
Trait |
Author |
Year |
prot-c-4143_74_2 |
Lymphotactin |
Suhre K |
2019 |
3. GWAS Catalog results — traits with signal at this locus
70 association rows across 25 traits (63 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 |
| XCL1 protein levels |
1e-191 |
rs76683928 |
22 |
GCST90471081 |
no MR -> candidate analysis |
| Circulating XCL1 levels |
2e-120 |
rs61801331 |
2 |
GCST90859793 |
no MR -> candidate analysis |
| DPT protein levels |
1e-65 |
rs77143649 |
8 |
GCST90469036 |
no MR -> candidate analysis |
| neutrophil (fraction, minimum, inv-norm transformed) |
3e-21 |
rs1337742 |
1 |
GCST90479715 |
no MR -> candidate analysis |
| Autoimmune hypothyroidism |
5e-21 |
rs10753774 |
1 |
GCST90837324 |
no MR -> candidate analysis |
| neutrophil (fraction, mean, inv-norm transformed) |
1e-17 |
rs1337742 |
1 |
GCST90479714 |
no MR -> candidate analysis |
| Hypothyroidism |
1e-15 |
rs10753774 |
2 |
GCST90627750 |
MR: beta=0.0427, p=0.16 (cis) |
| Height |
2e-15 |
rs6427140 |
2 |
GCST90245848 |
MR: beta=-0.0107, p=0.214 (cis) |
| white blood cell count (WBC, maximum, inv-norm transformed) |
3e-15 |
rs1337742 |
1 |
GCST90480723 |
no MR -> candidate analysis |
| neutrophil (absolute count, maximum, inv-norm transformed) |
9e-14 |
rs1337742 |
1 |
GCST90479710 |
no MR -> candidate analysis |
| Cytokine SCM-1 beta levels |
5e-13 |
rs10753774 |
2 |
GCST90249451 |
no MR -> candidate analysis |
| Cerebrospinal fluid protein XCL1 levels |
1e-12 |
rs10753774 |
1 |
GCST90944069 |
no MR -> candidate analysis |
| …and 13 more traits (see JSON) |
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|
|
4. Phenome map — where this gene is a genetic locus, vs. where MR exists
Top diseases by Open Targets association (of 394 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 |
| adolescent idiopathic scoliosis |
0.519 |
— |
common-variant locus |
no MR -> candidate analysis |
| rhabdomyolysis |
0.482 |
— |
common-variant locus |
no MR -> candidate analysis |
| gestational diabetes |
0.48 |
— |
common-variant locus |
no MR -> candidate analysis |
| psoriasis |
0.379 |
— |
common-variant locus |
MR: beta=-0.126, p=0.0995 (cis) |
| phlebitis |
0.302 |
— |
common-variant locus |
no MR -> candidate analysis |
| Thrombophlebitis |
0.302 |
— |
common-variant locus |
no MR -> candidate analysis |
| hypothyroidism |
0.299 |
— |
common-variant locus |
MR: beta=0.0427, p=0.16 (cis) |
| streptococcal infection |
0.225 |
— |
common-variant locus |
no MR -> candidate analysis |
Of the 8 rows above, 6 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=0.01, LOEUF=1.61 — LoF-tolerant |
| GWAS Catalog |
103 unique SNPs / 178 rows |
| ClinVar |
48 records; 9 pathogenic in sample of 30 |
| PharmGKB/ClinPGx |
no annotations |
phenome — Top 30 of 394 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 ‘XCL1’.clinvar — Pathogenic count is over the 30 record(s) retrieved, NOT over all 48 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 25 traits by best p-value, aggregated from 70 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/P47992 — 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/ENSG00000143184/associations — Open Targets data release 26.06gnomad: https://gnomad.broadinstitute.org/gene/XCL1 — gnomAD constraint via GraphQL API (reference genome GRCh38)gwas: https://www.ebi.ac.uk/gwas/genes/XCL1 — GWAS Catalog REST (live; release not exposed by this endpoint)clinvar: https://www.ncbi.nlm.nih.gov/clinvar/?term=XCL1%5Bgene%5D — ClinVar build Build260809-1055.1gwas_traits: https://www.ebi.ac.uk/gwas/genes/XCL1 — GWAS Catalog search API (live; release not exposed)
Provenance
- Generated: 2026-08-14T05:38:38 · 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