FOXP1 p.Pro42=
c.126G>A · rs762082081 · VCV435246
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0593%, 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 -16 | GERP -5.4 |
| Overall | ||
| CADD | 2.51 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0593%
South Asian · 54/91,094 alleles
Filtering AF
0.0466%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0421%
Overall
0.00397%
64/1,614,028 alleles · ultra-rare
exomes 62/1,461,808 · genomes 2/152,220 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0593% | 1,687 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,243 |
| African / African-American | 0.00133% | 74,930 |
| European (non-Finnish) | 0.000593% | 168,578 |
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.Pro42=
- Coding
- c.126G>A
- MANE Select
- NM_001349338
- dbSNP
- rs762082081
- Type
- single nucleotide variant
- Location
- chr3:71198256 (GRCh38)
- Gene constraint
- LOEUF 0.279 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 59.27 · 1 PDB
- Residue 42
- the 'disordered' region
Similar variants
- FOXP1 p.Pro42Leu Uncertain significance ★★ ⚠ same residue
- FOXP1 p.Pro42Ser 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
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-pro42 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown