SETX p.Asp1024del
c.3057TGA[5] · rs572772837 · VCV448320
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 8 submitters
gnomAD v4.1
Rare
rare (popmax 0.544%, sas)
Conditions
4
Inborn genetic diseases
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 -1.6 | GERP -2 |
| Overall | ||
| CADD | 9.98 | PHRED · no single calibrated threshold — expert panels disagree |
| Region caveats | ||
| Repeat context | tandem | (TCA)n simple repeat · ambiguous alignment · confidence, not pathogenicity |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.544%
South Asian · 495/91,064 alleles
Filtering AF
0.504%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.488%
Overall
0.0365%
589/1,613,864 alleles · rare
exomes 558/1,461,572 · genomes 31/152,292 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.544% | 184 |
| Remaining individualsnot grpmax-eligible | 0.0432% | 2,315 |
| Middle Eastern | 0.033% | 3,031 |
| African / African-American | 0.0213% | 4,690 |
| East Asian | 0.0111% | 8,976 |
| Admixed American | 0.005% | 20,002 |
| European (non-Finnish) | 0.00339% | 29,499 |
| Finnishnot grpmax-eligible | 0.00157% | 63,856 |
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.Asp1024del
- Coding
- c.3057TGA[5]
- MANE Select
- NM_015046
- dbSNP
- rs572772837
- Type
- Microsatellite
- Location
- chr9:132328524 (GRCh38)
- Gene constraint
- LOEUF 0.442 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 52.93
Similar variants
- SETX p.Asp1024dup Benign/Likely benign ★★ 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-asp1024del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown