FOXP1 p.Pro209=
c.627C>T · rs557318477 · VCV1598477
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0167%, amr)
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 -9.2 | GERP -5.2 |
| Overall | ||
| CADD | 2.687 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0167%
Admixed American · 10/60,024 alleles
Filtering AF
0.00899%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00681%
Overall
0.00279%
45/1,614,076 alleles · ultra-rare
exomes 39/1,461,794 · genomes 6/152,282 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0167% | 6,002 |
| Middle Eastern | 0.0165% | 6,058 |
| East Asian | 0.00668% | 14,961 |
| South Asian | 0.00659% | 15,180 |
| European (non-Finnish) | 0.00195% | 51,303 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,500 |
| Finnishnot grpmax-eligible | 0.00156% | 64,038 |
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
- FOXP1
- Protein
- p.Pro209=
- Coding
- c.627C>T
- MANE Select
- NM_001349338
- dbSNP
- rs557318477
- Type
- single nucleotide variant
- Location
- chr3:71046979 (GRCh38)
- Gene constraint
- LOEUF 0.279 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 59.27 · 1 PDB
Similar variants
- FOXP1 p.Pro209Ser Uncertain significance ★ ⚠ same residue
- FOXP1 c.1146+1G>A Pathogenic/Likely pathogenic ★★ same type
- FOXP1 c.1429-1G>A Likely pathogenic ★★ same type
- FOXP1 c.1652+5G>C Pathogenic/Likely pathogenic ★★ same type
- FOXP1 c.1653-2A>T Pathogenic ★★ same type
- FOXP1 p.Arg465Gly Pathogenic/Likely pathogenic ★★ same type
- FOXP1 p.Arg497Pro Pathogenic/Likely pathogenic ★★ same type
- FOXP1 p.Arg497Ter Pathogenic ★★ 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/foxp1-p-pro209 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown