FOXI3 p.Phe234fs
c.701del · VCV3774268
Likely pathogenic
Single submitter
Classification
Likely pathogenic
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 (2 of 2) — the truncated protein is likely expressed. PVS1 input, not an applied code |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 2.1 | GERP -1.9, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- FOXI3
- Protein
- p.Phe234fs
- Coding
- c.701del
- MANE Select
- NM_001135649
- Type
- Deletion
- Location
- chr2:88448769 (GRCh38)
- Gene constraint
- LOEUF 0.73 · pLI 0.65 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 59.00
- Residue 234
- a DNA-binding region; a UniProt-annotated variant site (in cfm2; decreased transcription factor activity; does not affect localization to the nucleus); a UniProt-annotated variant site (in cfm2; decreased transcription factor activity; localization to the nucleus but aggregating into granular foci); the 'disordered' region
Similar variants
- FOXI3 p.Phe234Leu Uncertain significance ★ ⚠ same residue
- FOXI3 p.Phe234Val Pathogenic/Likely pathogenic same residue
- FOXI3 p.Tyr75fs Uncertain significance ★★ same type
- FOXI3 p.Gly103fs Likely pathogenic ★ same type
- FOXI3 p.Ala113fs Uncertain significance ★ same type
- FOXI3 p.Ala116_Ala124del Uncertain significance ★ same type
- FOXI3 p.Ala122_Ala124del Uncertain significance ★ same type
- FOXI3 p.Ala70_Ala74del 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/foxi3-p-phe234fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown