Protein Dossier — NID2 (Nidogen-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 |
| Fractured bone site(s): Other bones |
0.0988 |
0.0242 |
4.32e-05 |
Wald ratio |
1 |
cis |
NA |
| ER-negative Breast cancer (Combined Oncoarray; iCOGS; GWAS meta analysis) |
-0.0888 |
0.0289 |
0.00214 |
Wald ratio |
1 |
cis |
NA |
| Hearing difficulty or problems: Yes |
-0.0294 |
0.0109 |
0.00694 |
Wald ratio |
1 |
cis |
NA |
| Fractured or broken bones in last 5 years |
0.0478 |
0.0182 |
0.00867 |
Wald ratio |
1 |
cis |
NA |
| Age at menarche |
-0.0381 |
0.0145 |
0.0088 |
Wald ratio |
1 |
cis |
NA |
| Diagnoses - main ICD10: K57 Diverticular disease of intestine |
0.0988 |
0.0391 |
0.0116 |
Wald ratio |
1 |
cis |
NA |
| Low grade serous ovarian cancer |
0.308 |
0.122 |
0.0119 |
Wald ratio |
1 |
cis |
NA |
| Non-cancer illness code self-reported: arthritis (nos) |
-0.213 |
0.088 |
0.0157 |
Wald ratio |
1 |
cis |
NA |
| Pulse rate |
-0.0257 |
0.0108 |
0.0175 |
Wald ratio |
1 |
cis |
NA |
| Diagnoses - main ICD10: I83 Varicose veins of lower extremities |
0.0924 |
0.0391 |
0.018 |
Wald ratio |
1 |
cis |
NA |
| Mean platelet volume |
0.0066 |
0.00279 |
0.0181 |
Wald ratio |
1 |
cis |
NA |
| Non-cancer illness code self-reported: asthma |
-0.0414 |
0.0179 |
0.0207 |
Wald ratio |
1 |
cis |
NA |
| …and 94 more outcomes (see JSON) |
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2. pQTL instrument availability (Tier-B probe)
| Dataset |
Trait |
Author |
Year |
prot-c-3633_70_1 |
NID2 |
Suhre K |
2019 |
3. GWAS Catalog results — traits with signal at this locus
109 association rows across 61 traits (99 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 |
| APP/NID2 protein level ratio |
2e-4580 |
rs1151580 |
1 |
GCST90313327 |
no MR -> candidate analysis |
| DKK1/NID2 protein level ratio |
6e-4324 |
rs1151580 |
1 |
GCST90314474 |
no MR -> candidate analysis |
| NID1/NID2 protein level ratio |
4e-2961 |
rs1151580 |
1 |
GCST90315541 |
no MR -> candidate analysis |
| Circulating NID2 levels |
5e-1859 |
rs2749870 |
5 |
GCST90860626 |
no MR -> candidate analysis |
| Nidogen-2 levels |
2e-1189 |
rs2516600 |
1 |
GCST90248679 |
no MR -> candidate analysis |
| NID2 protein levels |
7e-258 |
rs71426497 |
8 |
GCST90470048 |
no MR -> candidate analysis |
| Blood protein levels |
3e-190 |
rs2749870 |
2 |
GCST006585 |
no MR -> candidate analysis |
| Serum levels of protein NID2 |
2e-172 |
rs17831525 |
2 |
GCST90088470 |
no MR -> candidate analysis |
| Nidogen-2 (analyte X3633.70) levels |
3e-97 |
rs17831525 |
1 |
GCST90425842 |
no MR -> candidate analysis |
| Cell growth regulator with EF hand domain protein 1 levels |
5e-85 |
rs17831525 |
2 |
GCST90426614 |
no MR -> candidate analysis |
| Cerebrospinal fluid protein NID2 levels |
8e-77 |
rs74049344 |
1 |
GCST90944832 |
no MR -> candidate analysis |
| Nidogen-2 (analyte X16060.99) levels |
3e-74 |
rs61971555 |
1 |
GCST90422798 |
no MR -> candidate analysis |
| …and 49 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 238 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 |
| hearing loss disorder |
0.74 |
— |
common-variant locus |
no MR -> candidate analysis |
| presbycusis |
0.682 |
— |
common-variant locus |
no MR -> candidate analysis |
| benign colon neoplasm |
0.663 |
— |
common-variant locus |
MR: beta=0.0925, p=0.0504 (cis) |
| Sensorineural hearing impairment |
0.656 |
— |
common-variant locus |
no MR -> candidate analysis |
| Tinnitus |
0.598 |
— |
common-variant locus |
no MR -> candidate analysis |
| colorectal cancer |
0.445 |
— |
established (curated) |
no MR -> candidate analysis |
| polyp of colon |
0.535 |
— |
common-variant locus |
no MR -> candidate analysis |
| nontoxic goiter |
0.521 |
— |
common-variant locus |
no MR -> candidate analysis |
| sensorineural hearing loss disorder |
0.476 |
— |
common-variant locus |
no MR -> candidate analysis |
| urolithiasis |
0.473 |
— |
common-variant locus |
no MR -> candidate analysis |
| alcohol drinking |
0.473 |
— |
common-variant locus |
no MR -> candidate analysis |
| Retinal hemorrhage |
0.457 |
— |
common-variant locus |
no MR -> candidate analysis |
| ovarian neoplasm |
0.442 |
— |
common-variant locus |
no MR -> candidate analysis |
| ovarian dysfunction |
0.427 |
— |
common-variant locus |
no MR -> candidate analysis |
| placenta praevia |
0.389 |
— |
common-variant locus |
no MR -> candidate analysis |
Of the 15 rows above, 14 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=1e-13, LOEUF=0.685 — LoF-tolerant |
| GWAS Catalog |
75 unique SNPs / 150 rows |
| ClinVar |
327 records; 0 pathogenic in sample of 30 |
| PharmGKB/ClinPGx |
no annotations |
phenome — Top 30 of 238 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 ‘NID2’.clinvar — Pathogenic count is over the 30 record(s) retrieved, NOT over all 327 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 61 traits by best p-value, aggregated from 109 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/Q14112 — 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/ENSG00000087303/associations — Open Targets data release 26.06gnomad: https://gnomad.broadinstitute.org/gene/NID2 — gnomAD constraint via GraphQL API (reference genome GRCh38)gwas: https://www.ebi.ac.uk/gwas/genes/NID2 — GWAS Catalog REST (live; release not exposed by this endpoint)clinvar: https://www.ncbi.nlm.nih.gov/clinvar/?term=NID2%5Bgene%5D — ClinVar build Build260809-1055.1gwas_traits: https://www.ebi.ac.uk/gwas/genes/NID2 — GWAS Catalog search API (live; release not exposed)
Provenance
- Generated: 2026-08-14T03:59:02 · 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