FOXF1 p.Pro329=
c.987G>A · rs750734017 · VCV2897378
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0423%, eas)
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 -3 | GERP -4 |
| Overall | ||
| CADD | 4.963 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0423%
East Asian · 19/44,888 alleles
Filtering AF
0.0277%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.023%
Overall
0.0018%
29/1,614,048 alleles · ultra-rare
exomes 26/1,461,692 · genomes 3/152,356 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0423% | 2,363 |
| African / African-American | 0.00533% | 18,767 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,250 |
| European (non-Finnish) | 0.000339% | 295,010 |
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
- FOXF1
- Protein
- p.Pro329=
- Coding
- c.987G>A
- MANE Select
- NM_001451
- dbSNP
- rs750734017
- Type
- single nucleotide variant
- Location
- chr16:86512932 (GRCh38)
- Gene constraint
- LOEUF 0.685 · pLI 0.43 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 59.41
Similar variants
- FOXF1 p.Gln90Ter Pathogenic ★★ same type
- FOXF1 p.Glu104Ter Pathogenic ★★ same type
- FOXF1 p.Leu56Val Likely pathogenic ★★ same type
- FOXF1 p.Ser223Ter Pathogenic ★★ same type
- FOXF1 p.His357Leu Uncertain significance ★★ ⚠ same type
- FOXF1 p.Met257Ile Uncertain significance ★★ ⚠ same type
- FOXF1 p.Pro110Ala Uncertain significance ★★ ⚠ same type
- FOXF1 p.Pro11Gln Uncertain significance ★★ ⚠ 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/foxf1-p-pro329 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown