TONSL p.464DE[1]
c.1389AGATGA[1] · rs768606981 · VCV1345209
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00133%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -2.8 | GERP -3.9 |
| Region caveats | ||
| Repeat context | tandem | (CTCCGC)n simple repeat · ambiguous alignment · confidence, not pathogenicity |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00133%
African / African-American · 1/74,972 alleles
Filtering AF
0.000124%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 9e-05%
Overall
0.000372%
6/1,610,934 alleles · very rare
exomes 6/1,458,592 · genomes 0/152,342 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00133% | 74,972 |
| European (non-Finnish) | 0.000424% | 235,745 |
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
- TONSL
- Protein
- p.464DE[1]
- Coding
- c.1389AGATGA[1]
- MANE Select
- NM_013432
- dbSNP
- rs768606981
- Type
- Microsatellite
- Location
- chr8:144440101 (GRCh38)
- Gene constraint
- LOEUF 1.024 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 76.06 · 3 PDB
Similar variants
- TONSL p.469EEA[3] Uncertain significance ★★ same type
- TONSL p.Glu983fs Pathogenic ★ same type
- TONSL p.Leu1274fs Pathogenic ★ same type
- TONSL p.Val957fs Pathogenic ★ same type
- TONSL p.469EEA[1] Uncertain significance ★ same type
- TONSL p.Asp496del Uncertain significance ★ same type
- TONSL p.Glu468_Glu470dup Uncertain significance ★ same type
- TONSL p.Glu470del 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/tonsl-p-464de-1 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown