F7 p.Ile281=
c.843C>T · VCV4803900
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00636%, 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 -5.7 | GERP -3.4 |
| Overall | ||
| CADD | 0.861 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00636%
European (non-Finnish) · 75/1,179,902 alleles
Filtering AF
0.00519%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00474%
Overall
0.00484%
78/1,611,422 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00636% | 15,732 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,458 |
| African / African-American | 0.00133% | 74,928 |
| South Asian | 0.0011% | 91,082 |
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
- F7
- Protein
- p.Ile281=
- Coding
- c.843C>T
- MANE Select
- NM_019616
- Type
- single nucleotide variant
- Location
- chr13:113118516 (GRCh38)
- Gene constraint
- LOEUF 1.113 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 82.64 · 114 PDB
- Residue 281
- a β-strand; a disulfide bond; the peptidase s1 domain
Similar variants
- F7 c.225+1G>C Pathogenic ★★ same type
- F7 c.364+1G>A Pathogenic/Likely pathogenic ★★ same type
- F7 c.365-2A>G Likely pathogenic ★★ same type
- F7 c.505+78G>A Pathogenic/Likely pathogenic ★★ same type
- F7 c.615+1G>T Pathogenic/Likely pathogenic ★★ same type
- F7 c.64+5G>A Pathogenic/Likely pathogenic ★★ same type
- F7 c.739+1G>A Pathogenic/Likely pathogenic ★★ same type
- F7 c.-30A>C 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/f7-p-ile281 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown