TOE1 p.Lys502fs
c.1503_1504del · VCV3645580
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function |
|---|---|---|
| NMD | escapes | premature termination codon in the last exon (8 of 8) — the truncated protein is likely expressed. PVS1 input, not an applied code |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 4.1 | GERP 1.9, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- TOE1
- Protein
- p.Lys502fs
- Coding
- c.1503_1504del
- MANE Select
- NM_025077
- Type
- Deletion
- Location
- chr1:45343671 (GRCh38)
- Gene constraint
- LOEUF 1.225 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 79.16 · 1 PDB
- Residue 502
- a UniProt-annotated variant site (in pch7); the 'disordered' region
Similar variants
- TOE1 p.Asn255fs Likely pathogenic ★ same type
- TOE1 p.Asn391fs Likely pathogenic ★ same type
- TOE1 p.Gln108fs Likely pathogenic ★ same type
- TOE1 p.Pro223fs Pathogenic ★ same type
- TOE1 p.Thr355fs Likely pathogenic ★ same type
- TOE1 c.334-5_334-3del Uncertain significance ★ same type
- TOE1 p.Glu413_Ile414insTer Uncertain significance ★ same type
- TOE1 c.753-9_753-7del Likely benign ★ 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/toe1-p-lys502fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown