FOXP1 p.Pro96=
c.288C>T · rs528713688 · VCV1215498
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0494%, sas)
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 5.8 | GERP 1.7, phastCons 1 |
| Overall | ||
| CADD | 16.18 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0494%
South Asian · 45/91,064 alleles
Filtering AF
0.0379%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0339%
Overall
0.00347%
56/1,613,946 alleles · ultra-rare
exomes 50/1,461,756 · genomes 6/152,190 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0494% | 2,024 |
| African / African-American | 0.00534% | 18,744 |
| Finnishnot grpmax-eligible | 0.00469% | 21,335 |
| Admixed American | 0.00167% | 60,016 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,498 |
| European (non-Finnish) | 0.000169% | 589,977 |
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.Pro96=
- Coding
- c.288C>T
- MANE Select
- NM_001349338
- dbSNP
- rs528713688
- Type
- single nucleotide variant
- Location
- chr3:71053768 (GRCh38)
- Gene constraint
- LOEUF 0.279 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 59.27 · 1 PDB
Similar variants
- 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
- FOXP1 p.Arg503Ter 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-pro96 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown