TOR1A p.Val242=
c.726G>A · rs530037930 · VCV1148238
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0356%, eas)
Conditions
1
dystonic disorder
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 0.23 | GERP 0.43, phastCons 0.008 |
| Overall | ||
| CADD | 7.26 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0356%
East Asian · 16/44,888 alleles
Filtering AF
0.0223%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0182%
Overall
0.00105%
17/1,614,204 alleles · ultra-rare
exomes 13/1,461,874 · genomes 4/152,330 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0356% | 2,805 |
| Admixed American | 0.00167% | 60,022 |
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
- TOR1A
- Protein
- p.Val242=
- Coding
- c.726G>A
- MANE Select
- NM_000113
- dbSNP
- rs530037930
- Type
- single nucleotide variant
- Location
- chr9:129818542 (GRCh38)
- Gene constraint
- LOEUF 0.84 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 85.82 · 3 PDB
- Residue 242
- the 'interaction with snapin' region; a turn
Similar variants
- TOR1A p.Arg288Ter Pathogenic/Likely pathogenic ★★ same condition
- TOR1A p.Ala239Thr Uncertain significance ★★ ⚠ same condition
- TOR1A p.Ala239Val Uncertain significance ★★ ⚠ same condition
- TOR1A p.Arg213Gly Uncertain significance ★★ ⚠ same condition
- TOR1A p.Arg260Trp Uncertain significance ★★ ⚠ same condition
- TOR1A p.Asp331Asn Uncertain significance ★★ ⚠ same condition
- TOR1A p.Cys44Gly Uncertain significance ★★ ⚠ same condition
- TOR1A p.Leu179Phe 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/tor1a-p-val242 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown