TUSC3 p.Val239=
c.717C>T · rs759321925 · VCV2658441
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000848%, nfe)
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 1.2 | GERP -0.53, phastCons 1 |
| Overall | ||
| CADD | 10.68 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000848%
European (non-Finnish) · 10/1,178,954 alleles
Filtering AF
0.000429%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000313%
Overall
0.00062%
10/1,612,384 alleles · very rare
exomes 9/1,460,410 · genomes 1/151,974 · joint denominator
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
- TUSC3
- Protein
- p.Val239=
- Coding
- c.717C>T
- MANE Select
- NM_006765
- dbSNP
- rs759321925
- Type
- single nucleotide variant
- Location
- chr8:15673755 (GRCh38)
- Gene constraint
- LOEUF 1.31 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 84.78 · 4 PDB
Similar variants
- TUSC3 p.Arg74Ter Likely pathogenic ★★ same type
- TUSC3 p.Gln177Ter Pathogenic ★★ same type
- TUSC3 p.Ser331Ter Pathogenic/Likely pathogenic ★★ same type
- TUSC3 c.*1197G>A Uncertain significance ★★ same type
- TUSC3 c.*1957A>G Uncertain significance ★★ same type
- TUSC3 c.*46+1G>A Uncertain significance ★★ same type
- TUSC3 p.Ala13Val Uncertain significance ★★ ⚠ same type
- TUSC3 p.Arg159Lys Uncertain significance ★★ ⚠ same type
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/tusc3-p-val239 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown