THAP1 p.Arg29Ter
c.85C>T · rs2128918641 · VCV1070763
Pathogenic/Likely pathogenic
Multiple submitters
Classification
Pathogenic/Likely pathogenic
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
Consequence
nonsense (stop-gain)
predicted LoF
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
2
THAP1-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | nonsense (stop-gain) | predicted loss-of-function in a LoF-intolerant gene |
|---|---|---|
| NMD | predicted | premature termination codon in exon 2 of 3 |
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 7.4 | GERP 0.55, phastCons 1 |
| Overall | ||
| CADD | 38.0 | PHRED · no single calibrated threshold — expert panels disagree |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
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.Arg29Ter
- Coding
- c.85C>T
- MANE Select
- NM_018105
- dbSNP
- rs2128918641
- Type
- single nucleotide variant
- Location
- chr8:42839368 (GRCh38)
- Gene constraint
- LOEUF 0.571 · pLI 0.90 (gnomAD)
- Structure
- AlphaFold pLDDT 71.61 · 3 PDB
- Residue 29
- a UniProt-annotated variant site (in dyt6)
Similar variants
- THAP1 p.Arg29Pro Pathogenic/Likely pathogenic ★★ same residue
- THAP1 p.Arg29Gly Likely pathogenic ★ same residue
- THAP1 p.Arg29Gln Likely pathogenic ★ ⚠ same residue
- THAP1 p.Arg169Ter 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-arg29ter (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown