FOXA2 p.Pro362=
c.1086G>A · VCV3695936
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00958%, 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 -20 | GERP -4.6 |
| Overall | ||
| CADD | 0.119 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00958%
East Asian · 4/41,732 alleles
Filtering AF
0.00323%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0019%
Overall
0.000511%
8/1,565,648 alleles · very rare
exomes 8/1,413,378 · genomes 0/152,270 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00958% | 10,433 |
| Remaining individualsnot grpmax-eligible | 0.00165% | 60,668 |
| South Asian | 0.00116% | 86,212 |
| European (non-Finnish) | 0.000173% | 577,291 |
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
- FOXA2
- Protein
- p.Pro362=
- Coding
- c.1086G>A
- MANE Select
- NM_021784
- Type
- single nucleotide variant
- Location
- chr20:22582156 (GRCh38)
- Gene constraint
- LOEUF 0.518 · pLI 0.97 (gnomAD)
- Structure
- AlphaFold pLDDT 58.29 · 3 PDB
- Residue 362
- the 'disordered' region; the 'transactivation domain 2' region
Similar variants
- FOXA2 p.Ala92Val Uncertain significance ★★ ⚠ same type
- FOXA2 p.Glu373Asp Uncertain significance ★★ ⚠ same type
- FOXA2 p.Met108Ile Uncertain significance ★★ ⚠ same type
- FOXA2 p.Met52Thr Uncertain significance ★★ same type
- FOXA2 p.Pro358Gln Uncertain significance ★★ ⚠ same type
- FOXA2 p.Ser99Leu Uncertain significance ★★ ⚠ same type
- FOXA2 c.*6C>T Likely benign ★★ same type
- FOXA2 p.Ala100Pro Benign/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/foxa2-p-pro362 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown