TOR1A p.Gln286=
c.858G>A · rs188191403 · VCV2720931
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.02%, afr)
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 1.1 | GERP 1.5 |
| Overall | ||
| CADD | 7.774 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.02%
African / African-American · 15/75,042 alleles
Filtering AF
0.0123%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00987%
Overall
0.00105%
17/1,614,216 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.02% | 5,003 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,256 |
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.Gln286=
- Coding
- c.858G>A
- MANE Select
- NM_000113
- dbSNP
- rs188191403
- Type
- single nucleotide variant
- Location
- chr9:129814113 (GRCh38)
- Gene constraint
- LOEUF 0.84 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 85.82 · 3 PDB
- Residue 286
- the 'interaction with klc1' region; an α-helix
Similar variants
- TOR1A p.Gln286Ter Likely pathogenic ★ 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.Asp331Asn Uncertain significance ★★ ⚠ same condition
- TOR1A p.Cys44Gly 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-gln286 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown