FOXE3 p.Pro72=
c.216G>C · rs1646883620 · VCV3058833
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
FOXE3-related disorder
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 -0.89 | GERP -3.9 |
| Overall | ||
| CADD | 10.95 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- FOXE3
- Protein
- p.Pro72=
- Coding
- c.216G>C
- MANE Select
- NM_012186
- dbSNP
- rs1646883620
- Type
- single nucleotide variant
- Location
- chr1:47416531 (GRCh38)
- Gene constraint
- LOEUF 1.935 · pLI 0.12 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 66.68
- Residue 72
- a DNA-binding region
Disease context
FOXE3-related disorder
Similar variants
- FOXE3 p.Pro72Ser Uncertain significance ★★ ⚠ same residue
- FOXE3 p.Cys240Ter Pathogenic ★★ same condition
- FOXE3 p.Tyr144Cys Conflicting classifications of pathogenicity ★ ⚠ same condition
- FOXE3 p.Pro37Ala Uncertain significance ⚠ same condition
- FOXE3 c.-10G>A Likely benign same condition
- FOXE3 p.Ala12= Likely benign same condition
- FOXE3 p.Arg61fs Pathogenic/Likely pathogenic ★★ same condition
- FOXE3 p.Asp153fs Likely pathogenic same condition
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/foxe3-p-pro72 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown