SETX p.Asp1385=
c.4155C>T · rs759387462 · VCV3045139
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00439%, sas)
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 -0.17 | GERP -2.4 |
| Overall | ||
| CADD | 0.501 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00439%
South Asian · 4/91,086 alleles
Filtering AF
0.00164%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00142%
Overall
0.00204%
33/1,613,950 alleles · very rare
exomes 30/1,461,800 · genomes 3/152,150 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00439% | 22,772 |
| European (non-Finnish) | 0.00237% | 42,143 |
| African / African-American | 0.00133% | 74,916 |
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.Asp1385=
- Coding
- c.4155C>T
- MANE Select
- NM_015046
- dbSNP
- rs759387462
- Type
- single nucleotide variant
- Location
- chr9:132327443 (GRCh38)
- Gene constraint
- LOEUF 0.442 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 52.93
- Residue 1385
- the 'disordered' region
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-asp1385 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown