FOXP1 p.Pro382=
c.1146C>T · rs372765119 · VCV1732632
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0824%, sas)
Conditions
1
Inborn genetic diseases
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 0.72 | GERP -3.1, phastCons 1 |
| Overall | ||
| CADD | 12.8 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0824%
South Asian · 75/91,068 alleles
Filtering AF
0.0673%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0618%
Overall
0.00644%
104/1,613,734 alleles · ultra-rare
exomes 92/1,461,620 · genomes 12/152,114 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0824% | 1,214 |
| Admixed American | 0.0117% | 8,570 |
| African / African-American | 0.00935% | 10,696 |
| East Asian | 0.00891% | 11,223 |
| Remaining individualsnot grpmax-eligible | 0.008% | 12,494 |
| Finnishnot grpmax-eligible | 0.00156% | 64,024 |
| European (non-Finnish) | 0.000424% | 235,964 |
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.Pro382=
- Coding
- c.1146C>T
- MANE Select
- NM_001349338
- dbSNP
- rs372765119
- Type
- single nucleotide variant
- Location
- chr3:70987994 (GRCh38)
- Gene constraint
- LOEUF 0.279 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 59.27 · 1 PDB
- Residue 382
- the 'ctbp1-binding' region
Similar variants
- FOXP1 p.Pro382Thr Uncertain significance ★ same residue
- FOXP1 c.1146+1G>A Pathogenic/Likely pathogenic ★★ same condition
- FOXP1 c.1652+5G>C Pathogenic/Likely pathogenic ★★ same condition
- FOXP1 p.Arg544Gln Likely pathogenic ★★ same condition
- FOXP1 p.Gln177Ter Pathogenic ★★ same condition
- FOXP1 p.Leu517Phe Pathogenic ★★ same condition
- FOXP1 p.Lys393Ter Pathogenic ★★ same condition
- FOXP1 p.Phe502Leu Pathogenic/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/foxp1-p-pro382 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown