FOXP2 p.Pro96=
c.288C>T · rs75306477 · VCV1797272
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.426%, eas)
Conditions
1
Inborn genetic diseases
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 1.4 | GERP -0.73, phastCons 1 |
| Overall | ||
| CADD | 10.48 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.426%
East Asian · 191/44,878 alleles
Filtering AF
0.376%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.357%
Overall
0.0131%
212/1,614,068 alleles · rare
exomes 190/1,461,836 · genomes 22/152,232 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.426% | 235 |
| Remaining individualsnot grpmax-eligible | 0.0096% | 10,418 |
| European (non-Finnish) | 0.00119% | 84,284 |
| South Asian | 0.0011% | 91,080 |
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
- FOXP2
- Protein
- p.Pro96=
- Coding
- c.288C>T
- MANE Select
- NM_014491
- dbSNP
- rs75306477
- Type
- single nucleotide variant
- Location
- chr7:114628569 (GRCh38)
- Gene constraint
- LOEUF 0.157 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 60.82 · 2 PDB
Similar variants
- FOXP2 p.Arg328Ter Pathogenic ★★ same condition
- FOXP2 p.Gln168Ter Pathogenic/Likely pathogenic ★★ same condition
- FOXP2 p.Glu712Ala Uncertain significance ★★ same condition
- FOXP2 p.Pro310Ser Uncertain significance ★★ ⚠ same condition
- FOXP2 p.Ser619Asn Uncertain significance ★★ same condition
- FOXP2 p.Val426Leu Uncertain significance ★★ ⚠ same condition
- FOXP2 p.Ala307= Likely benign ★★ same condition
- FOXP2 p.Ala615Thr Benign/Likely benign ★★ ⚠ 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/foxp2-p-pro96 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown