MR feasibility tier: A — Published pQTL-MR estimates exist for this protein (retrieved below - not computed here).
| Outcome | beta | se | p | method | nSNP | cis/trans | coloc |
|---|---|---|---|---|---|---|---|
| Hearing difficulty or problems: Yes | -0.037 | 0.0135 | 0.00621 | Wald ratio | 1 | cis | NA |
| Potassium in urine | -0.0168 | 0.00765 | 0.0281 | Wald ratio | 1 | cis | NA |
| Creatinine (enzymatic) in urine | -0.015 | 0.00722 | 0.0377 | Wald ratio | 1 | cis | NA |
| Diagnoses - main ICD10: D12 Benign neoplasm of colon rectum anus and anal canal | 0.116 | 0.0569 | 0.0413 | Wald ratio | 1 | cis | NA |
| Diagnoses - main ICD10: R35 Polyuria | 0.202 | 0.0998 | 0.0434 | Wald ratio | 1 | cis | NA |
| Diagnoses - main ICD10: N20 Calculus of kidney and ureter | 0.156 | 0.0774 | 0.0444 | Wald ratio | 1 | cis | NA |
| Depressive symptoms | -0.0287 | 0.0144 | 0.0455 | Wald ratio | 1 | cis | NA |
| Diagnoses - main ICD10: N40 Hyperplasia of prostate | 0.137 | 0.0688 | 0.0473 | Wald ratio | 1 | cis | NA |
| Diagnoses - main ICD10: R07 Pain in throat and chest | -0.0675 | 0.036 | 0.061 | Wald ratio | 1 | cis | NA |
| Non-cancer illness code self-reported: hayfever or allergic rhinitis | -0.0609 | 0.033 | 0.0651 | Wald ratio | 1 | cis | NA |
| Hirschsprung’s disease | 0.563 | 0.32 | 0.0779 | Wald ratio | 1 | cis | NA |
| Neuroticism | -0.0168 | 0.00957 | 0.0801 | Wald ratio | 1 | cis | NA |
| …and 69 more outcomes (see JSON) |
No prot-* pQTL GWAS dataset found for this protein (matched by UniProt accession and symbol).
26 association rows across 21 traits (23 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 |
|---|---|---|---|---|---|
| NAGPA protein levels | 4e-104 | rs76557209 | 4 | GCST90469996 | no MR -> candidate analysis |
| N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosami | 1e-74 | rs12599777 | 2 | GCST90248588 | no MR -> candidate analysis |
| CPVL protein levels | 6e-66 | rs1045693 | 1 | GCST90468848 | no MR -> candidate analysis |
| Serum levels of protein NAGPA | 7e-50 | rs12599777 | 2 | GCST90086611 | no MR -> candidate analysis |
| N-acetylglucosamine-6-sulfatase (analyte X3616.3) levels | 1e-46 | rs12448709 | 1 | GCST90425832 | no MR -> candidate analysis |
| N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosami | 1e-39 | rs12599777 | 1 | GCST90242004 | no MR -> candidate analysis |
| Serum levels of protein HPSE | 2e-37 | rs1045693 | 1 | GCST90089086 | no MR -> candidate analysis |
| Cerebrospinal fluid protein NAGPA levels | 5e-35 | rs2340713 | 1 | GCST90944447 | no MR -> candidate analysis |
| TPP1 protein levels | 2e-33 | rs15951 | 1 | GCST90470946 | no MR -> candidate analysis |
| Circulating TPP1 levels | 2e-31 | rs15951 | 1 | GCST90860671 | no MR -> candidate analysis |
| Procollagen-lysine,2-oxoglutarate 5-dioxygenase 2 levels | 8e-27 | rs12448709 | 1 | GCST90426832 | no MR -> candidate analysis |
| Blood protein levels | 2e-18 | rs12599777 | 1 | GCST006585 | no MR -> candidate analysis |
| …and 9 more traits (see JSON) |
Top diseases by Open Targets association (of 64 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 |
|---|---|---|---|---|
| Kawasaki disease | 0.505 | — | common-variant locus | no MR -> candidate analysis |
| vasculitis | 0.505 | — | common-variant locus | no MR -> candidate analysis |
| stuttering, familial persistent, 2 | 0.228 | — | established (curated) | no MR -> candidate analysis |
| chronic laryngitis | 0.095 | — | common-variant locus | no MR -> candidate analysis |
| alcohol drinking | 0.083 | — | common-variant locus | no MR -> candidate analysis |
| acute tonsillitis | 0.054 | — | common-variant locus | no MR -> candidate analysis |
| pathological myopia | 0.042 | — | common-variant locus | no MR -> candidate analysis |
| Peyronie disease | 0.037 | — | common-variant locus | no MR -> candidate analysis |
| secondary malignant neoplasm | 0.034 | — | common-variant locus | no MR -> candidate analysis |
| liver disorder | 0.034 | — | common-variant locus | no MR -> candidate analysis |
| rhabdomyolysis | 0.034 | — | common-variant locus | no MR -> candidate analysis |
| smoking initiation | 0.032 | — | common-variant locus | no MR -> candidate analysis |
| systemic inflammatory response syndrome | 0.031 | — | common-variant locus | no MR -> candidate analysis |
Of the 13 rows above, 13 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.
| Layer | Result |
|---|---|
| ChEMBL druggability | 0 known modulators (N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase) |
| gnomAD constraint | pLI=4.9e-22, LOEUF=1.44 — LoF-tolerant |
| GWAS Catalog | 71 unique SNPs / 142 rows |
| ClinVar | 201 records; 1 pathogenic in sample of 30 |
| PharmGKB/ClinPGx | no annotations |
phenome — Top 30 of 64 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 ‘NAGPA’ and resolved to ‘N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase’ — confirm this is the intended target.clinvar — Pathogenic count is over the 30 record(s) retrieved, NOT over all 201 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 26 association rows. These are GWAS ASSOCIATIONS (loci), not causal claims; mapped genes at a locus are not necessarily the effector gene.uniprot: https://www.uniprot.org/uniprotkb/Q9UK23 — 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/ENSG00000103174/associations — Open Targets data release 26.06chembl: https://www.ebi.ac.uk/chembl/target_report_card/CHEMBL5920/ — ChEMBL_37 (released 2026-05-01)gnomad: https://gnomad.broadinstitute.org/gene/NAGPA — gnomAD constraint via GraphQL API (reference genome GRCh38)gwas: https://www.ebi.ac.uk/gwas/genes/NAGPA — GWAS Catalog REST (live; release not exposed by this endpoint)clinvar: https://www.ncbi.nlm.nih.gov/clinvar/?term=NAGPA%5Bgene%5D — ClinVar build Build260809-1055.1gwas_traits: https://www.ebi.ac.uk/gwas/genes/NAGPA — GWAS Catalog search API (live; release not exposed)