FOXC1 p.Pro202=
c.606G>A · VCV4973480
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00855%, afr)
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 0.082 | GERP -3.1 |
| Overall | ||
| CADD | 9.378 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00855%
African / African-American · 6/70,202 alleles
Filtering AF
0.00366%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00251%
Overall
0.00139%
21/1,509,466 alleles · very rare
exomes 17/1,359,484 · genomes 4/149,982 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00855% | 11,700 |
| Remaining individualsnot grpmax-eligible | 0.00344% | 29,033 |
| European (non-Finnish) | 0.00115% | 86,665 |
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
- FOXC1
- Protein
- p.Pro202=
- Coding
- c.606G>A
- MANE Select
- NM_001453
- Type
- single nucleotide variant
- Location
- chr6:1611051 (GRCh38)
- Gene constraint
- LOEUF 1.276 · pLI 0.05 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 56.09
- Residue 202
- the 'disordered' region
Similar variants
- FOXC1 p.Pro202Leu Uncertain significance ★★ ⚠ same residue
- FOXC1 p.Pro202Gln Uncertain significance ★ ⚠ same residue
- FOXC1 p.Pro202Ser Uncertain significance ★ ⚠ same residue
- FOXC1 p.Pro202fs Pathogenic ★ same residue
- FOXC1 p.Arg127His Pathogenic ★★ same type
- FOXC1 p.Arg127Leu Pathogenic/Likely pathogenic ★★ same type
- FOXC1 p.Arg170Trp Pathogenic ★★ same type
- FOXC1 p.Cys135Tyr 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/foxc1-p-pro202 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown