FOXP2 p.Asp701=
c.2103C>T · rs559347815 · VCV358612
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.016%, afr)
Conditions
2
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 -5.3 | |
| Overall | ||
| CADD | 3.129 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.016%
African / African-American · 12/74,952 alleles
Filtering AF
0.00921%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00842%
Overall
0.00917%
148/1,613,346 alleles · ultra-rare
exomes 140/1,461,210 · genomes 8/152,136 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.016% | 6,246 |
| Remaining individualsnot grpmax-eligible | 0.0144% | 6,942 |
| European (non-Finnish) | 0.0105% | 9,512 |
| Admixed American | 0.00334% | 29,974 |
| East Asian | 0.00223% | 44,840 |
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.Asp701=
- Coding
- c.2103C>T
- MANE Select
- NM_014491
- dbSNP
- rs559347815
- Type
- single nucleotide variant
- Location
- chr7:114689881 (GRCh38)
- Gene constraint
- LOEUF 0.157 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 60.82 · 2 PDB
- Residue 701
- the 'disordered' region
Similar variants
- FOXP2 p.Arg328Ter Pathogenic ★★ same condition
- FOXP2 p.Arg376Ter Pathogenic ★★ same condition
- FOXP2 p.Arg476Ter Pathogenic/Likely pathogenic ★★ same condition
- FOXP2 p.Arg478Ter Pathogenic ★★ same condition
- FOXP2 p.Arg553His Pathogenic/Likely pathogenic ★★ same condition
- FOXP2 p.Arg564Ter Pathogenic ★★ same condition
- FOXP2 p.Gln168Ter Pathogenic/Likely pathogenic ★★ same condition
- FOXP2 p.Gln187Ter 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/foxp2-p-asp701 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown