FOXA2 p.Ala84=
c.252G>T · rs1254581121 · VCV2756634
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -1.7 | GERP -4.1 |
| Overall | ||
| CADD | 5.862 | 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
- FOXA2
- Protein
- p.Ala84=
- Coding
- c.252G>T
- MANE Select
- NM_021784
- dbSNP
- rs1254581121
- Type
- single nucleotide variant
- Location
- chr20:22582990 (GRCh38)
- Gene constraint
- LOEUF 0.518 · pLI 0.97 (gnomAD)
- Structure
- AlphaFold pLDDT 58.29 · 3 PDB
- Residue 84
- the 'transactivation domain 1' 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-ala84 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown