CausalSentinel

Protein Dossier — NPTXR (Neuronal pentraxin receptor)

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: R11 Nausea and vomiting	0.432	0.0911	2.11e-06	Wald ratio	1	cis	NA
Schizophrenia	0.12	0.0337	3.79e-04	Wald ratio	1	cis	NA
Diagnoses - main ICD10: R14 Flatulence and related conditions	0.608	0.208	0.00345	Wald ratio	1	cis	NA
Diagnoses - main ICD10: D12 Benign neoplasm of colon rectum anus and anal canal	0.158	0.0632	0.0126	Wald ratio	1	cis	NA
Cough on most days	-0.12	0.0508	0.0181	Wald ratio	1	cis	NA
Non-cancer illness code self-reported: asthma	0.0531	0.0232	0.0221	Wald ratio	1	cis	NA
Non-cancer illness code self-reported: diverticular disease or diverticulitis	0.158	0.0708	0.0256	Wald ratio	1	cis	NA
Diagnoses - main ICD10: N81 Female genital prolapse	0.134	0.0641	0.0369	Wald ratio	1	cis	NA
Forearm bone mineral density	0.109	0.0577	0.059	Wald ratio	1	cis	NA
Non-cancer illness code self-reported: osteoporosis	0.112	0.0629	0.0755	Wald ratio	1	cis	NA
Fractured bone site(s): Other bones	0.0625	0.0357	0.0799	Wald ratio	1	cis	NA
Birth weight	0.021	0.0123	0.0884	Wald ratio	1	cis	NA
…and 62 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

30 association rows across 21 traits (25 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 NPTXR levels	5e-1848	rs185853862	4	GCST90860330	no MR -> candidate analysis
NPTXR protein levels	2e-218	rs5757299	3	GCST90470080	no MR -> candidate analysis
Neuronal pentraxin receptor levels	2e-213	rs117773903	3	GCST90179374	no MR -> candidate analysis
BCAN/NPTXR protein level ratio	1e-204	rs5757299	1	GCST90313482	no MR -> candidate analysis
Serum levels of protein NPTXR	3e-32	rs74703065	1	GCST90090436	no MR -> candidate analysis
Height	5e-32	rs13053505	1	GCST90245848	no MR -> candidate analysis
Blood protein levels	5e-21	rs12628473	1	GCST006585	no MR -> candidate analysis
Neuronal pentraxin receptor level in Chronic kidney disease	2e-20	rs180925984	1	GCST90234412	no MR -> candidate analysis
Neuronal pentraxin receptor level in Chronic kidney disease	2e-15	rs111444671	1	GCST90239143	no MR -> candidate analysis
NPTX2 protein levels	1e-14	rs192164176	1	GCST90470079	no MR -> candidate analysis
Sex hormone-binding globulin levels	9e-12	rs2075915	1	GCST90012111	no MR -> candidate analysis
Insomnia	1e-11	rs9607581	3	GCST90131901	no MR -> candidate analysis
…and 9 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 175 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
insomnia	0.59	—	common-variant locus	no MR -> candidate analysis
cholelithiasis	0.263	—	common-variant locus	MR: beta=0.0531, p=0.359 (cis)
atrial fibrillation	0.054	—	common-variant locus	no MR -> candidate analysis
luminal A breast carcinoma	0.034	—	common-variant locus	no MR -> candidate analysis

Of the 4 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	not available — no ChEMBL target (undrugged)
gnomAD constraint	pLI=0.66, LOEUF=0.604 — LoF-tolerant
GWAS Catalog	66 unique SNPs / 132 rows
ClinVar	119 records; 0 pathogenic in sample of 30
PharmGKB/ClinPGx	no annotations

Caveats declared by the tools

• phenome — Top 30 of 175 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 ‘NPTXR’.
• clinvar — Pathogenic count is over the 30 record(s) retrieved, NOT over all 119 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 21 traits by best p-value, aggregated from 30 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/O95502 — 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/ENSG00000221890/associations — Open Targets data release 26.06
• gnomad: https://gnomad.broadinstitute.org/gene/NPTXR — gnomAD constraint via GraphQL API (reference genome GRCh38)
• gwas: https://www.ebi.ac.uk/gwas/genes/NPTXR — GWAS Catalog REST (live; release not exposed by this endpoint)
• clinvar: https://www.ncbi.nlm.nih.gov/clinvar/?term=NPTXR%5Bgene%5D — ClinVar build Build260809-1055.1
• gwas_traits: https://www.ebi.ac.uk/gwas/genes/NPTXR — GWAS Catalog search API (live; release not exposed)

Provenance

• Generated: 2026-08-14T04:03:02 · 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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