THAP1 p.Val20=
c.60T>C · VCV3721805
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
torsion dystonia 6
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · A>T here scores Δ0.49 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.39 | GERP -3.8, phastCons 0.77 |
| Overall | ||
| CADD | 14.38 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- THAP1
- Protein
- p.Val20=
- Coding
- c.60T>C
- MANE Select
- NM_018105
- Type
- single nucleotide variant
- Location
- chr8:42843035 (GRCh38)
- Gene constraint
- LOEUF 0.571 · pLI 0.90 (gnomAD)
- Structure
- AlphaFold pLDDT 71.61 · 3 PDB
Disease context
torsion dystonia 6 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Primary dystonia, DYT6 type (Orphanet):
- Inheritance
- Autosomal dominant
- Onset
- Adolescent, Adult, Childhood
- Prevalence
- <1 / 1 000 000 (Worldwide)
Similar variants
- THAP1 p.Val20Leu Uncertain significance ★ ⚠ same residue
- THAP1 p.Arg169Ter Pathogenic/Likely pathogenic ★★ same condition
- THAP1 p.Arg29Pro Pathogenic/Likely pathogenic ★★ same condition
- THAP1 p.Arg29Ter Pathogenic/Likely pathogenic ★★ same condition
- THAP1 p.Gly9Ser Likely pathogenic ★★ same condition
- THAP1 p.Pro26Leu Pathogenic/Likely pathogenic ★★ same condition
- THAP1 p.Ser130Ter Pathogenic/Likely pathogenic ★★ same condition
- THAP1 p.Ser21Phe Likely pathogenic ★★ 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/thap1-p-val20 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown