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 |
|---|---|---|---|---|---|---|---|
| Weight | -0.0242 | 0.00512 | 2.15e-06 | Wald ratio | 1 | cis | NA |
| Body mass index (BMI) | -0.0257 | 0.00579 | 8.97e-06 | Wald ratio | 1 | cis | NA |
| ER-positive Breast cancer (Combined Oncoarray; iCOGS; GWAS meta analysis) | 0.0599 | 0.0181 | 9.44e-04 | Wald ratio | 1 | cis | NA |
| Breast cancer (Combined Oncoarray; iCOGS; GWAS meta analysis) | 0.0492 | 0.0152 | 0.00124 | Wald ratio | 1 | cis | NA |
| Birth length | -0.0636 | 0.0251 | 0.0113 | Wald ratio | 1 | cis | NA |
| Heel bone mineral density (BMD) T-score automated | -0.0185 | 0.00751 | 0.0138 | Wald ratio | 1 | cis | NA |
| Non-cancer illness code self-reported: hypopituitarism | 0.479 | 0.205 | 0.0193 | Wald ratio | 1 | cis | NA |
| Diagnoses - main ICD10: S66 Injury of muscle and tendon at wrist and hand level | 0.254 | 0.114 | 0.0261 | Wald ratio | 1 | cis | NA |
| Body fat | -0.029 | 0.0132 | 0.0276 | Wald ratio | 1 | cis | NA |
| Diagnoses - main ICD10: K40 Inguinal hernia | 0.0714 | 0.033 | 0.0305 | Wald ratio | 1 | cis | NA |
| Cancer code self-reported: malignant melanoma | 0.124 | 0.0583 | 0.0338 | Wald ratio | 1 | cis | NA |
| Forced expiratory volume in 1-second (FEV1) | -0.0105 | 0.00502 | 0.0362 | Wald ratio | 1 | cis | NA |
| …and 98 more outcomes (see JSON) |
No prot-* pQTL GWAS dataset found for this protein (matched by UniProt accession and symbol).
40 association rows across 28 traits (37 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 |
|---|---|---|---|---|---|
| Secretogranin-3 levels | 1e-315 | rs1456295 | 2 | GCST90249447 | no MR -> candidate analysis |
| SCG3 protein levels | 8e-248 | rs2305710 | 5 | GCST90470539 | no MR -> candidate analysis |
| Serum levels of protein SCG3 | 2e-111 | rs1456297 | 1 | GCST90089949 | no MR -> candidate analysis |
| Neutrophil collagenase (analyte X2954.56) levels | 2e-74 | rs2606139 | 1 | GCST90425543 | no MR -> candidate analysis |
| Secretogranin-3 levels (SCG3.7957.2.3) | 1e-68 | rs1378892 | 2 | GCST90242735 | no MR -> candidate analysis |
| Blood protein levels | 4e-58 | rs1456297 | 1 | GCST006585 | no MR -> candidate analysis |
| Cerebrospinal fluid protein SCG3 levels | 3e-25 | rs9672605 | 1 | GCST90944552 | no MR -> candidate analysis |
| Body mass index | 9e-19 | rs7170980 | 2 | GCST90255621 | MR: beta=-0.0257, p=8.97e-06 (cis) |
| Whole body fat mass (UKB data field 23100) | 1e-13 | rs7167760 | 2 | GCST90428121 | no MR -> candidate analysis |
| Educational attainment | 2e-13 | rs1378893 | 2 | GCST90105038 | no MR -> candidate analysis |
| Adiposity (multivariate analysis) | 3e-13 | rs979259 | 1 | GCST90624107 | no MR -> candidate analysis |
| Gliomedin level in Chronic kidney disease with hypertension | 2e-12 | rs2607117 | 1 | GCST90235491 | no MR -> candidate analysis |
| …and 16 more traits (see JSON) |
Top diseases by Open Targets association (of 174 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 |
|---|---|---|---|---|
| intelligence | 0.507 | — | common-variant locus | no MR -> candidate analysis |
| placental abruption | 0.455 | — | common-variant locus | no MR -> candidate analysis |
| aortic atherosclerosis | 0.379 | — | common-variant locus | no MR -> candidate analysis |
| osteoarthritis, knee | 0.221 | — | common-variant locus | MR: beta=0.0807, p=0.11 (cis) |
| obesity disorder | 0.196 | — | common-variant locus | no MR -> candidate analysis |
| developmental and epileptic encephalopathy, 13 | 0.195 | — | established (curated) | no MR -> candidate analysis |
| osteoarthritis, hip | 0.189 | — | common-variant locus | MR: beta=0.0807, p=0.11 (cis) |
| schizophrenia | 0.182 | — | established (curated) | no MR -> candidate analysis |
| type 2 diabetes mellitus | 0.156 | — | common-variant locus | no MR -> candidate analysis |
| insomnia | 0.126 | — | common-variant locus | no MR -> candidate analysis |
| attention deficit-hyperactivity disorder | 0.085 | — | common-variant locus | no MR -> candidate analysis |
| autism spectrum disorder | 0.085 | — | common-variant locus | no MR -> candidate analysis |
Of the 12 rows above, 10 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 | not available — no ChEMBL target (undrugged) |
| gnomAD constraint | pLI=4.3e-09, LOEUF=0.887 — LoF-tolerant |
| GWAS Catalog | 74 unique SNPs / 124 rows |
| ClinVar | 90 records; 1 pathogenic in sample of 30 |
| PharmGKB/ClinPGx | no annotations |
phenome — Top 30 of 174 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 ‘SCG3’.clinvar — Pathogenic count is over the 30 record(s) retrieved, NOT over all 90 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 28 traits by best p-value, aggregated from 40 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/Q8WXD2 — 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/ENSG00000104112/associations — Open Targets data release 26.06gnomad: https://gnomad.broadinstitute.org/gene/SCG3 — gnomAD constraint via GraphQL API (reference genome GRCh38)gwas: https://www.ebi.ac.uk/gwas/genes/SCG3 — GWAS Catalog REST (live; release not exposed by this endpoint)clinvar: https://www.ncbi.nlm.nih.gov/clinvar/?term=SCG3%5Bgene%5D — ClinVar build Build260809-1055.1gwas_traits: https://www.ebi.ac.uk/gwas/genes/SCG3 — GWAS Catalog search API (live; release not exposed)