FOXI1 p.Phe207=
c.621C>T · rs532647880 · VCV1957958
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0165%, sas)
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 -7.3 | GERP -3.6 |
| Overall | ||
| CADD | 8.459 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0165%
South Asian · 15/91,072 alleles
Filtering AF
0.0101%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00811%
Overall
0.00254%
41/1,613,976 alleles · ultra-rare
exomes 40/1,461,830 · genomes 1/152,146 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0165% | 6,071 |
| Middle Eastern | 0.0164% | 6,084 |
| Admixed American | 0.00333% | 29,998 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,243 |
| Finnishnot grpmax-eligible | 0.00313% | 31,997 |
| African / African-American | 0.00267% | 37,455 |
| East Asian | 0.00223% | 44,890 |
| European (non-Finnish) | 0.00136% | 73,752 |
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
- FOXI1
- Protein
- p.Phe207=
- Coding
- c.621C>T
- MANE Select
- NM_012188
- dbSNP
- rs532647880
- Type
- single nucleotide variant
- Location
- chr5:170108095 (GRCh38)
- Gene constraint
- LOEUF 1.061 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 60.03
- Residue 207
- a DNA-binding region
Similar variants
- FOXI1 c.-18G>A Uncertain significance ★★ same type
- FOXI1 p.Ala255Thr Uncertain significance ★★ ⚠ same type
- FOXI1 p.Ala338Val Uncertain significance ★★ ⚠ same type
- FOXI1 p.Arg213Cys Uncertain significance ★★ ⚠ same type
- FOXI1 p.Arg213His Uncertain significance ★★ ⚠ same type
- FOXI1 p.Arg267Gln Uncertain significance ★★ ⚠ same type
- FOXI1 p.Arg267Trp Uncertain significance ★★ ⚠ same type
- FOXI1 p.Asn344Asp 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/foxi1-p-phe207 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown