TOE1 p.Phe239=
c.717C>T · rs201403165 · VCV739598
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0423%, eas)
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 -1.4 | GERP -3.7, phastCons 0.001 |
| Overall | ||
| CADD | 6.792 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0423%
East Asian · 19/44,876 alleles
Filtering AF
0.0277%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.023%
Overall
0.00248%
40/1,614,064 alleles · ultra-rare
exomes 37/1,461,824 · genomes 3/152,240 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0423% | 2,362 |
| South Asian | 0.00878% | 11,385 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00676% | 14,802 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,835 |
| Admixed American | 0.00167% | 60,016 |
| African / African-American | 0.00133% | 75,016 |
| European (non-Finnish) | 0.000508% | 196,671 |
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
- TOE1
- Protein
- p.Phe239=
- Coding
- c.717C>T
- MANE Select
- NM_025077
- dbSNP
- rs201403165
- Type
- single nucleotide variant
- Location
- chr1:45342608 (GRCh38)
- Gene constraint
- LOEUF 1.225 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 79.16 · 1 PDB
- Residue 239
- a UniProt-annotated variant site (in pch7)
Similar variants
- TOE1 p.Phe239Ser Likely pathogenic ⚠ same residue
- MUTYH p.Trp12Ter Pathogenic/Likely pathogenic ★★ same type
- TOE1 p.Glu245Ter Pathogenic ★★ same type
- MUTYH c.36+5G>A Uncertain significance ★★ same type
- MUTYH p.Arg10His Uncertain significance ★★ ⚠ same type
- MUTYH p.Arg7Leu Uncertain significance ★★ ⚠ same type
- MUTYH p.Pro3Leu Uncertain significance ★★ ⚠ same type
- TOE1 p.Arg184Cys 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/toe1-p-phe239 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown