Protein Dossier — PDCD1LG2 (Programmed cell death 1 ligand 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: asthma |
0.0417 |
0.0161 |
0.00978 |
Inverse variance weighted |
2 |
trans |
NA |
| Non-cancer illness code self-reported: asthma |
0.0417 |
0.0161 |
0.00978 |
Inverse variance weighted |
2 |
cis |
NA |
| Mean cell haemoglobin concentration |
-0.0232 |
0.00922 |
0.0119 |
Inverse variance weighted |
2 |
trans |
NA |
| Mean cell haemoglobin concentration |
-0.0232 |
0.00922 |
0.0119 |
Inverse variance weighted |
2 |
cis |
NA |
| Non-cancer illness code self-reported: bone disorder |
0.252 |
0.101 |
0.0123 |
Inverse variance weighted |
2 |
trans |
NA |
| Non-cancer illness code self-reported: bone disorder |
0.252 |
0.101 |
0.0123 |
Inverse variance weighted |
2 |
cis |
NA |
| Age at menarche |
0.0313 |
0.0142 |
0.0275 |
Inverse variance weighted |
2 |
trans |
NA |
| Age at menarche |
0.0313 |
0.0142 |
0.0275 |
Inverse variance weighted |
2 |
cis |
NA |
| Chronic kidney disease |
-0.083 |
0.0383 |
0.0301 |
Inverse variance weighted |
2 |
trans |
NA |
| Chronic kidney disease |
-0.083 |
0.0383 |
0.0301 |
Inverse variance weighted |
2 |
cis |
NA |
| Heel bone mineral density (BMD) T-score automated |
-0.0168 |
0.00777 |
0.0308 |
Inverse variance weighted |
2 |
trans |
NA |
| Heel bone mineral density (BMD) T-score automated |
-0.0168 |
0.00777 |
0.0308 |
Inverse variance weighted |
2 |
cis |
NA |
| …and 166 more outcomes (see JSON) |
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2. pQTL instrument availability (Tier-B probe)
| Dataset |
Trait |
Author |
Year |
prot-c-3004_67_2 |
PD-L2 |
Suhre K |
2019 |
3. GWAS Catalog results — traits with signal at this locus
78 association rows across 27 traits (71 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 PDCD1LG2 levels (id: OID00458_OID21273) |
5e-2776 |
rs62556120 |
5 |
GCST90859819 |
no MR -> candidate analysis |
| Circulating PDCD1LG2 levels (id: OID00831_OID21273) |
6e-1968 |
rs62556120 |
4 |
GCST90860159 |
no MR -> candidate analysis |
| ICOSLG/PDCD1LG2 protein level ratio |
3e-1870 |
rs62556118 |
1 |
GCST90315125 |
no MR -> candidate analysis |
| Programmed cell death 1 ligand 2 levels |
3e-258 |
rs16923189 |
16 |
GCST90248874 |
no MR -> candidate analysis |
| PDCD1LG2 protein levels |
9e-200 |
rs56299437 |
19 |
GCST90470180 |
no MR -> candidate analysis |
| Circulating CD274 levels (id: OID00518_OID20966) |
5e-140 |
rs7875928 |
2 |
GCST90859874 |
no MR -> candidate analysis |
| CD274 protein levels |
3e-135 |
rs7875928 |
5 |
GCST90468613 |
no MR -> candidate analysis |
| Serum levels of protein PDCD1LG2 |
6e-127 |
rs16923189 |
3 |
GCST90088180 |
no MR -> candidate analysis |
| Circulating CD274 levels (id: OID00799_OID20966) |
5e-125 |
rs7875928 |
2 |
GCST90860130 |
no MR -> candidate analysis |
| Blood protein levels |
3e-70 |
rs16923189 |
1 |
GCST006585 |
no MR -> candidate analysis |
| Programmed cell death 1 ligand 2 levels (PDCD1LG2.3004.67.2) |
8e-51 |
rs16923189 |
3 |
GCST90242384 |
no MR -> candidate analysis |
| Eosinophill percentage (UKB data field 30210) |
1e-19 |
rs1333192 |
1 |
GCST90468069 |
no MR -> candidate analysis |
| …and 15 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 603 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 |
| myxedema |
0.557 |
— |
common-variant locus |
no MR -> candidate analysis |
| hypothyroidism |
0.557 |
— |
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 (Programmed cell death 1 ligand 2) |
| gnomAD constraint |
pLI=1.1e-12, LOEUF=1.52 — LoF-tolerant |
| GWAS Catalog |
108 unique SNPs / 217 rows |
| ClinVar |
222 records; 8 pathogenic in sample of 30 |
| PharmGKB/ClinPGx |
no annotations |
phenome — Top 30 of 603 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 ‘PDCD1LG2’ and resolved to ‘Programmed cell death 1 ligand 2’ — confirm this is the intended target.clinvar — Pathogenic count is over the 30 record(s) retrieved, NOT over all 222 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 27 traits by best p-value, aggregated from 78 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/Q9BQ51 — 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/ENSG00000197646/associations — Open Targets data release 26.06chembl: https://www.ebi.ac.uk/chembl/target_report_card/CHEMBL3713006/ — ChEMBL_37 (released 2026-05-01)gnomad: https://gnomad.broadinstitute.org/gene/PDCD1LG2 — gnomAD constraint via GraphQL API (reference genome GRCh38)gwas: https://www.ebi.ac.uk/gwas/genes/PDCD1LG2 — GWAS Catalog REST (live; release not exposed by this endpoint)clinvar: https://www.ncbi.nlm.nih.gov/clinvar/?term=PDCD1LG2%5Bgene%5D — ClinVar build Build260809-1055.1gwas_traits: https://www.ebi.ac.uk/gwas/genes/PDCD1LG2 — GWAS Catalog search API (live; release not exposed)
Provenance
- Generated: 2026-08-14T04:14:09 · 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