FOXF1 p.Pro116=
c.348C>T · rs111830706 · VCV750896
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0403%, nfe)
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 -6.7 | GERP -4.2 |
| Overall | ||
| CADD | 4.015 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0403%
European (non-Finnish) · 475/1,180,028 alleles
Filtering AF
0.0372%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0361%
Overall
0.0307%
495/1,613,714 alleles · ultra-rare
exomes 464/1,461,600 · genomes 31/152,114 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0403% | 2,484 |
| Remaining individualsnot grpmax-eligible | 0.0192% | 5,207 |
| African / African-American | 0.0107% | 9,365 |
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.Pro116=
- Coding
- c.348C>T
- MANE Select
- NM_001451
- dbSNP
- rs111830706
- Type
- single nucleotide variant
- Location
- chr16:86510917 (GRCh38)
- Gene constraint
- LOEUF 0.685 · pLI 0.43 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 59.41
- Residue 116
- a DNA-binding region; a UniProt-annotated variant site (in acdmpv)
Similar variants
- FOXF1 p.Pro116Ser Conflicting classifications of pathogenicity ★ ⚠ same residue
- 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
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-pro116 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown