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 |
|---|---|---|---|---|---|---|---|
| Body mass index (BMI) | 0.0444 | 0.0137 | 0.00116 | Wald ratio | 1 | trans | NA |
| Heel bone mineral density (BMD) T-score automated | -0.0507 | 0.0177 | 0.00417 | Wald ratio | 1 | trans | NA |
| Creatinine (enzymatic) in urine | 0.0361 | 0.0131 | 0.00582 | Wald ratio | 1 | trans | NA |
| Weight | 0.0317 | 0.0121 | 0.00852 | Wald ratio | 1 | trans | NA |
| ER-positive Breast cancer (Combined Oncoarray; iCOGS; GWAS meta analysis) | -0.119 | 0.0458 | 0.00937 | Wald ratio | 1 | trans | NA |
| Non-cancer illness code self-reported: kidney stone or ureter stone or bladder stone | 0.3 | 0.116 | 0.00997 | Wald ratio | 1 | trans | NA |
| Breast cancer (Combined Oncoarray; iCOGS; GWAS meta analysis) | -0.0954 | 0.0383 | 0.0128 | Wald ratio | 1 | trans | NA |
| Diagnoses - main ICD10: G56 Mononeuropathies of upper limb | 0.207 | 0.0852 | 0.0153 | Wald ratio | 1 | trans | NA |
| Serum cystatin C (eGFRcys) | -0.024 | 0.0109 | 0.0273 | Wald ratio | 1 | trans | NA |
| Fractured bone site(s): Other bones | -0.14 | 0.0688 | 0.0419 | Wald ratio | 1 | trans | NA |
| Depressive symptoms | -0.0376 | 0.0188 | 0.0455 | Wald ratio | 1 | trans | NA |
| Diagnoses - main ICD10: K29 Gastritis and duodenitis | -0.223 | 0.112 | 0.0469 | Wald ratio | 1 | trans | NA |
| …and 87 more outcomes (see JSON) |
No prot-* pQTL GWAS dataset found for this protein (matched by UniProt accession and symbol).
27 association rows across 19 traits (21 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 |
|---|---|---|---|---|---|
| Hematological traits (multi-trait analysis) | 4e-38 | rs72836805 | 3 | GCST90838669 | no MR -> candidate analysis |
| Height | 7e-36 | rs3111728 | 3 | GCST90245848 | MR: beta=0.0255, p=0.131 (trans) |
| Lymphocyte count | 2e-18 | rs77713896 | 4 | GCST90002316 | no MR -> candidate analysis |
| C1QL2 protein levels | 3e-14 | rs143843154 | 1 | GCST90468487 | no MR -> candidate analysis |
| Lymphocyte count (UKB data field 30120) | 1e-12 | rs77713896 | 1 | GCST90468082 | no MR -> candidate analysis |
| Bone mineral density mean | 1e-11 | rs147401949 | 1 | GCST90321120 | no MR -> candidate analysis |
| Smoking initiation | 1e-10 | rs78986663 | 1 | GCST90243968 | no MR -> candidate analysis |
| Educational attainment | 1e-10 | rs6542543 | 1 | GCST90105038 | no MR -> candidate analysis |
| Dupuytren’s disease | 2e-10 | rs10174596 | 2 | GCST90301252 | no MR -> candidate analysis |
| Brain morphology (MOSTest) | 1e-9 | rs1995916 | 1 | GCST90239729 | no MR -> candidate analysis |
| Lymphocyte percentage of white cells | 1e-9 | rs17661862 | 1 | GCST90002389 | no MR -> candidate analysis |
| Severe COVID-19 infection | 2e-9 | rs13000543 | 1 | GCST90255357 | no MR -> candidate analysis |
| …and 7 more traits (see JSON) |
Top diseases by Open Targets association (of 352 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 |
|---|---|---|---|---|
| hereditary disease | 0.816 | — | established (curated) | no MR -> candidate analysis |
| Intellectual disability | 0.426 | — | established (curated) | no MR -> candidate analysis |
| neurodevelopmental disorder | 0.69 | — | established (curated) | no MR -> candidate analysis |
| Dupuytren Contracture | 0.612 | — | common-variant locus | no MR -> candidate analysis |
| placenta praevia | 0.548 | — | common-variant locus | no MR -> candidate analysis |
| smoking initiation | 0.42 | — | common-variant locus | no MR -> candidate analysis |
| palmar fibromatosis | 0.394 | — | common-variant locus | no MR -> candidate analysis |
| fasciitis | 0.387 | — | common-variant locus | no MR -> candidate analysis |
| scoliosis | 0.357 | — | common-variant locus | no MR -> candidate analysis |
| severe acute respiratory syndrome | 0.331 | — | common-variant locus | no MR -> candidate analysis |
| COVID-19 | 0.331 | — | common-variant locus | no MR -> candidate analysis |
Of the 11 rows above, 11 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 (Tyrosine-protein phosphatase non-receptor type 4) |
| gnomAD constraint | pLI=1, LOEUF=0.459 — LoF-INTOLERANT |
| GWAS Catalog | 32 unique SNPs / 64 rows |
| ClinVar | 222 records; 4 pathogenic in sample of 30 |
| PharmGKB/ClinPGx | no annotations |
phenome — Top 30 of 352 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 ‘PTPN4’ and resolved to ‘Tyrosine-protein phosphatase non-receptor type 4’ — 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 19 of 19 traits by best p-value, aggregated from 27 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/P29074 — 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/ENSG00000088179/associations — Open Targets data release 26.06chembl: https://www.ebi.ac.uk/chembl/target_report_card/CHEMBL3165/ — ChEMBL_37 (released 2026-05-01)gnomad: https://gnomad.broadinstitute.org/gene/PTPN4 — gnomAD constraint via GraphQL API (reference genome GRCh38)gwas: https://www.ebi.ac.uk/gwas/genes/PTPN4 — GWAS Catalog REST (live; release not exposed by this endpoint)clinvar: https://www.ncbi.nlm.nih.gov/clinvar/?term=PTPN4%5Bgene%5D — ClinVar build Build260809-1055.1gwas_traits: https://www.ebi.ac.uk/gwas/genes/PTPN4 — GWAS Catalog search API (live; release not exposed)