Protein Dossier — SEMA3E (Semaphorin-3E)
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 |
| Neuroticism |
-0.0161 |
0.00446 |
3.18e-04 |
Wald ratio |
1 |
cis |
NA |
| Happiness |
-0.0132 |
0.00413 |
0.00135 |
Wald ratio |
1 |
cis |
NA |
| Non-cancer illness code self-reported: anxiety or panic attacks |
0.0646 |
0.0268 |
0.0161 |
Wald ratio |
1 |
cis |
NA |
| Serum cystatin C (eGFRcys) |
0.00598 |
0.0025 |
0.0167 |
Wald ratio |
1 |
cis |
NA |
| Sleep duration |
0.00617 |
0.00259 |
0.0173 |
Wald ratio |
1 |
cis |
NA |
| Percent emphysema |
-0.0302 |
0.0139 |
0.0303 |
Wald ratio |
1 |
cis |
NA |
| Systolic blood pressure automated reading |
-0.00727 |
0.0034 |
0.0326 |
Wald ratio |
1 |
cis |
NA |
| Diagnoses - main ICD10: R11 Nausea and vomiting |
0.0982 |
0.048 |
0.0409 |
Wald ratio |
1 |
cis |
NA |
| Diagnoses - main ICD10: S66 Injury of muscle and tendon at wrist and hand level |
0.147 |
0.0722 |
0.0418 |
Wald ratio |
1 |
cis |
NA |
| 2hr glucose |
-0.05 |
0.025 |
0.0455 |
Wald ratio |
1 |
cis |
NA |
| Non-cancer illness code self-reported: hypertension |
-0.011 |
0.00573 |
0.0557 |
Wald ratio |
1 |
cis |
NA |
| Non-cancer illness code self-reported: vitiligo |
0.291 |
0.155 |
0.0598 |
Wald ratio |
1 |
cis |
NA |
| …and 74 more outcomes (see JSON) |
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2. pQTL instrument availability (Tier-B probe)
| Dataset |
Trait |
Author |
Year |
prot-c-5363_51_3 |
Semaphorin 3E |
Suhre K |
2019 |
3. GWAS Catalog results — traits with signal at this locus
92 association rows across 52 traits (61 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 |
| Semaphorin-3E levels |
2e-924 |
rs56921187 |
20 |
GCST90249486 |
no MR -> candidate analysis |
| Blood protein levels |
1e-331 |
rs60909458 |
2 |
GCST006585 |
no MR -> candidate analysis |
| Semaphorin-3E levels (SEMA3E.5363.51.3) |
5e-264 |
rs3757607 |
4 |
GCST90242745 |
no MR -> candidate analysis |
| Serum levels of protein SEMA3E |
2e-82 |
rs12668853 |
3 |
GCST90086399 |
no MR -> candidate analysis |
| Semaphorin-3E level in Chronic kidney disease with hypertens |
3e-21 |
rs61729612 |
1 |
GCST90237923 |
no MR -> candidate analysis |
| Cerebrospinal fluid biomarker levels |
1e-20 |
rs10273103 |
1 |
GCST004000 |
no MR -> candidate analysis |
| Lobe attachment (rater-scored or self-reported) |
1e-14 |
rs2723005 |
2 |
GCST005192 |
no MR -> candidate analysis |
| Height |
1e-13 |
rs10273103 |
1 |
GCST90245848 |
MR: beta=0.0033, p=0.4 (cis) |
| Eotaxin protein levels (SomaScan ID:5363-51) |
2e-12 |
rs188547 |
1 |
GCST90439098 |
no MR -> candidate analysis |
| Nephrotic syndrome without mention of glomerulonephritis (Ph |
3e-12 |
rs143538480 |
1 |
GCST90480368 |
no MR -> candidate analysis |
| Fracture of unspecified part of femur (PheCode 800.2) |
9e-12 |
rs181163111 |
1 |
GCST90480595 |
no MR -> candidate analysis |
| Depression |
1e-11 |
rs16887442 |
2 |
GCST007342 |
MR: beta=-0.018, p=0.197 (cis) |
| …and 40 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 915 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 |
| CHARGE syndrome |
0.571 |
— |
established (curated) |
no MR -> candidate analysis |
| open-angle glaucoma |
0.679 |
— |
common-variant locus |
no MR -> candidate analysis |
| hypogonadotropic hypogonadism 5 with or without anosmia |
0.669 |
— |
established (curated) |
no MR -> candidate analysis |
| alcohol drinking |
0.581 |
— |
common-variant locus |
no MR -> candidate analysis |
| Anxiety |
0.505 |
— |
common-variant locus |
MR: beta=0.0646, p=0.0161 (cis) |
| schizophrenia |
0.485 |
— |
common-variant locus |
no MR -> candidate analysis |
| Paralytic ileus |
0.492 |
— |
common-variant locus |
no MR -> candidate analysis |
| oral mucosa leukoplakia |
0.482 |
— |
common-variant locus |
no MR -> candidate analysis |
| skin disorder |
0.482 |
— |
common-variant locus |
no MR -> candidate analysis |
| premature birth |
0.479 |
— |
common-variant locus |
no MR -> candidate analysis |
| nephrotic syndrome |
0.436 |
— |
common-variant locus |
no MR -> candidate analysis |
| dilated cardiomyopathy 1A |
0.426 |
— |
established (curated) |
no MR -> candidate analysis |
| myasthenia gravis |
0.394 |
— |
common-variant locus |
no MR -> candidate analysis |
| muscular disease |
0.361 |
— |
common-variant locus |
no MR -> candidate analysis |
| central nervous system infectious disorder |
0.361 |
— |
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=7.8e-07, LOEUF=0.664 — LoF-tolerant |
| GWAS Catalog |
95 unique SNPs / 175 rows |
| ClinVar |
942 records; 1 pathogenic in sample of 30 |
| PharmGKB/ClinPGx |
no annotations |
phenome — Top 30 of 915 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 ‘SEMA3E’.clinvar — Pathogenic count is over the 30 record(s) retrieved, NOT over all 942 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 52 traits by best p-value, aggregated from 92 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/O15041 — 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/ENSG00000170381/associations — Open Targets data release 26.06gnomad: https://gnomad.broadinstitute.org/gene/SEMA3E — gnomAD constraint via GraphQL API (reference genome GRCh38)gwas: https://www.ebi.ac.uk/gwas/genes/SEMA3E — GWAS Catalog REST (live; release not exposed by this endpoint)clinvar: https://www.ncbi.nlm.nih.gov/clinvar/?term=SEMA3E%5Bgene%5D — ClinVar build Build260809-1055.1gwas_traits: https://www.ebi.ac.uk/gwas/genes/SEMA3E — GWAS Catalog search API (live; release not exposed)
Provenance
- Generated: 2026-08-14T04:58:41 · 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