TOR1A p.Asp331=
c.993T>C · rs767839320 · VCV1603924
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.174%, 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 -2.4 | GERP -4.6 |
| Overall | ||
| CADD | 2.058 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.174%
East Asian · 78/44,898 alleles
Filtering AF
0.143%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.131%
Overall
0.00496%
80/1,613,964 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.174% | 576 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,243 |
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.Asp331=
- Coding
- c.993T>C
- MANE Select
- NM_000113
- dbSNP
- rs767839320
- Type
- single nucleotide variant
- Location
- chr9:129813978 (GRCh38)
- Gene constraint
- LOEUF 0.84 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 85.82 · 3 PDB
- Residue 331
- a UniProt-annotated variant site (in amc5); the 'interaction with klc1' region; the 'interaction with syne3' region
Similar variants
- TOR1A p.Asp331Asn Uncertain significance ★★ ⚠ same residue
- 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.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-asp331 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown