Protein Dossier — LSAMP (Limbic system-associated membrane protein)
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 |
| Non-cancer illness code self-reported: sleep apnoea |
0.551 |
0.154 |
3.40e-04 |
Wald ratio |
1 |
cis |
NA |
| Cancer code self-reported: prostate cancer |
0.356 |
0.12 |
0.00297 |
Wald ratio |
1 |
cis |
NA |
| Diagnoses - main ICD10: B37 Candidiasis |
0.886 |
0.317 |
0.00525 |
Wald ratio |
1 |
cis |
NA |
| Lumbar spine bone mineral density |
-0.144 |
0.0527 |
0.00635 |
Wald ratio |
1 |
cis |
NA |
| Mean cell haemoglobin |
0.152 |
0.0581 |
0.00879 |
Wald ratio |
1 |
cis |
NA |
| Knee osteoarthritis |
-0.388 |
0.158 |
0.0138 |
Wald ratio |
1 |
cis |
NA |
| Cough on most days |
-0.228 |
0.0939 |
0.0151 |
Wald ratio |
1 |
cis |
NA |
| Creatinine (enzymatic) in urine |
0.0314 |
0.0137 |
0.0223 |
Wald ratio |
1 |
cis |
NA |
| Microalbuminuria |
0.288 |
0.131 |
0.0273 |
Wald ratio |
1 |
cis |
NA |
| Diagnoses - main ICD10: C61 Malignant neoplasm of prostate |
0.283 |
0.136 |
0.0373 |
Wald ratio |
1 |
cis |
NA |
| Non-cancer illness code self-reported: gastro-oesophageal reflux (gord) or gastric reflux |
-0.161 |
0.0819 |
0.0493 |
Wald ratio |
1 |
cis |
NA |
| Neuroblastoma |
-0.523 |
0.268 |
0.0508 |
Wald ratio |
1 |
cis |
NA |
| …and 101 more outcomes (see JSON) |
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2. pQTL instrument availability (Tier-B probe)
| Dataset |
Trait |
Author |
Year |
prot-c-2999_6_2 |
LSAMP |
Suhre K |
2019 |
3. GWAS Catalog results — traits with signal at this locus
435 association rows across 216 traits (304 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 |
| Height |
4e-82 |
rs10804533 |
12 |
GCST90245848 |
no MR -> candidate analysis |
| Smoking initiation |
3e-43 |
rs1353910 |
12 |
GCST90243968 |
no MR -> candidate analysis |
| Menarche (age at onset) |
7e-33 |
rs7433864 |
5 |
GCST007078 |
no MR -> candidate analysis |
| Limbic system-associated membrane protein levels |
6e-27 |
rs2116308 |
2 |
GCST90248340 |
no MR -> candidate analysis |
| Adolescent idiopathic scoliosis |
2e-25 |
rs1520115 |
1 |
GCST006287 |
no MR -> candidate analysis |
| Bone mineral density mean |
2e-24 |
rs146999981 |
1 |
GCST90321120 |
no MR -> candidate analysis |
| Insomnia |
2e-23 |
rs9815484 |
58 |
GCST90131901 |
no MR -> candidate analysis |
| Educational attainment |
2e-22 |
rs7430651 |
9 |
GCST90105038 |
no MR -> candidate analysis |
| Externalizing behaviour (multivariate analysis) |
2e-22 |
rs2865303 |
2 |
GCST90061435 |
no MR -> candidate analysis |
| Serum levels of protein LSAMP |
6e-20 |
rs17646258 |
1 |
GCST90088177 |
no MR -> candidate analysis |
| GLIPR1 protein levels |
2e-18 |
rs554518807 |
4 |
GCST90469357 |
no MR -> candidate analysis |
| Smoking initiation (ever regular vs never regular) (MTAG) |
2e-17 |
rs1353910 |
2 |
GCST007468 |
no MR -> candidate analysis |
| …and 204 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 129 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 |
0.633 |
— |
common-variant locus |
no MR -> candidate analysis |
| ovarian neoplasm |
0.564 |
— |
common-variant locus |
no MR -> candidate analysis |
| liver disorder |
0.523 |
— |
common-variant locus |
no MR -> candidate analysis |
| frozen shoulder |
0.523 |
— |
common-variant locus |
no MR -> candidate analysis |
| major depressive disorder |
0.503 |
— |
common-variant locus |
MR: beta=0.112, p=0.38 (cis) |
| placental abruption |
0.499 |
— |
common-variant locus |
no MR -> candidate analysis |
| kidney disorder |
0.49 |
— |
common-variant locus |
no MR -> candidate analysis |
| male infertility |
0.419 |
— |
common-variant locus |
no MR -> candidate analysis |
| hypertrophic cardiomyopathy |
0.406 |
— |
common-variant locus |
no MR -> candidate analysis |
| musculoskeletal system disorder |
0.406 |
— |
common-variant locus |
no MR -> candidate analysis |
| ovarian dysfunction |
0.382 |
— |
common-variant locus |
no MR -> candidate analysis |
| Abnormal nasolacrimal system morphology |
0.382 |
— |
common-variant locus |
no MR -> candidate analysis |
| Epidermal thickening |
0.358 |
— |
common-variant locus |
no MR -> candidate analysis |
| Alzheimer disease |
0.351 |
— |
common-variant locus |
no MR -> candidate analysis |
| smoking initiation |
0.348 |
— |
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=1, LOEUF=0.341 — LoF-INTOLERANT |
| GWAS Catalog |
238 unique SNPs / 402 rows |
| ClinVar |
74 records; 0 pathogenic in sample of 30 |
| PharmGKB/ClinPGx |
no annotations |
phenome — Top 30 of 129 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 ‘LSAMP’.clinvar — Pathogenic count is over the 30 record(s) retrieved, NOT over all 74 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 216 traits by best p-value, aggregated from 435 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/Q13449 — 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/ENSG00000185565/associations — Open Targets data release 26.06gnomad: https://gnomad.broadinstitute.org/gene/LSAMP — gnomAD constraint via GraphQL API (reference genome GRCh38)gwas: https://www.ebi.ac.uk/gwas/genes/LSAMP — GWAS Catalog REST (live; release not exposed by this endpoint)clinvar: https://www.ncbi.nlm.nih.gov/clinvar/?term=LSAMP%5Bgene%5D — ClinVar build Build260809-1055.1gwas_traits: https://www.ebi.ac.uk/gwas/genes/LSAMP — GWAS Catalog search API (live; release not exposed)
Provenance
- Generated: 2026-08-14T03:39:05 · 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