FOXF1 p.Ser30=
c.90G>T · VCV4931660
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00168%, amr)
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 2.2 | GERP -0.12, phastCons 1 |
| Overall | ||
| CADD | 12.95 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00168%
Admixed American · 1/59,490 alleles
Overall
0.000125%
2/1,605,562 alleles · very rare
exomes 2/1,453,760 · genomes 0/151,802 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00168% | 59,490 |
| African / African-American | 0.00134% | 74,614 |
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.Ser30=
- Coding
- c.90G>T
- MANE Select
- NM_001451
- Type
- single nucleotide variant
- Location
- chr16:86510659 (GRCh38)
- Gene constraint
- LOEUF 0.685 · pLI 0.43 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 59.41
- Residue 30
- the 'disordered' region
Similar variants
- FOXF1 p.Ser30Leu Uncertain significance ★ ⚠ same residue
- FOXF1 p.Ser30Ter Pathogenic 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
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-ser30 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown