SETX p.Asp2263=
c.6789C>T · rs913428653 · VCV3233569
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.47e-05%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 3.4 | GERP -0.02, phastCons 1 |
| Overall | ||
| CADD | 8.116 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.47e-05%
European (non-Finnish) · 1/1,179,994 alleles
Overall
6.2e-05%
1/1,614,008 alleles · very rare
exomes 0/1,461,816 · genomes 1/152,192 · joint denominator
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.Asp2263=
- Coding
- c.6789C>T
- MANE Select
- NM_015046
- dbSNP
- rs913428653
- Type
- single nucleotide variant
- Location
- chr9:132278123 (GRCh38)
- Gene constraint
- LOEUF 0.442 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 52.93
- Residue 2263
- the upf1-type sf1b helicase c-terminal domain
Similar variants
- SETX p.Arg111Ter Pathogenic ★★ same type
- SETX p.Arg1363Ter Pathogenic ★★ same type
- SETX p.Arg1606Ter Pathogenic ★★ same type
- SETX p.Arg1778Ter Pathogenic/Likely pathogenic ★★ same type
- SETX p.Arg2098Ter Pathogenic ★★ same type
- SETX p.Arg332Trp Pathogenic/Likely pathogenic ★★ same type
- SETX p.Arg778Ter Pathogenic/Likely pathogenic ★★ same type
- SETX p.Gln1695Ter Pathogenic/Likely pathogenic ★★ same type
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-asp2263 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown