SETX p.Cys5del
c.12TTG[1] · rs774123592 · VCV448306
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 7.6 | GERP 1.6, phastCons 1 |
Population frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,504 |
| European (non-Finnish)grpmax | 8.47e-05% | 1,180,036 |
Remaining individuals shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- SETX
- Protein
- p.Cys5del
- Coding
- c.12TTG[1]
- MANE Select
- NM_015046
- dbSNP
- rs774123592
- Type
- Microsatellite
- Location
- chr9:132349412 (GRCh38)
- Gene constraint
- LOEUF 0.442 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 52.93
Disease context
amyotrophic lateral sclerosis type 4 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsAlso linked: ataxia, early-onset, with oculomotor apraxia and hypoalbuminemiaspinocerebellar ataxia, autosomal recessive, with axonal neuropathy 2
For Amyotrophic lateral sclerosis type 4 (Orphanet):
- Inheritance
- Autosomal dominant
- Onset
- Adolescent, Childhood
Similar variants
- SETX p.Cys5Ser Uncertain significance ★ ⚠ same residue
- SETX p.Glu1770fs Pathogenic/Likely pathogenic ★★ same condition
- SETX p.His2243fs Pathogenic/Likely pathogenic ★★ same condition
- SETX p.Val2374fs Pathogenic/Likely pathogenic ★★ same condition
- SETX p.Ile1016del Uncertain significance ★★ same condition
- SETX p.Ile741del Uncertain significance ★★ same condition
- SETX p.Lys909del Uncertain significance ★★ same condition
- SETX p.Pro1587del Uncertain significance ★★ same condition
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/setx-p-cys5del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown