F7 p.Ala282=
c.846G>C · rs200316840 · VCV3043321
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0401%, eas)
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 -4.2 | GERP -3.4 |
| Overall | ||
| CADD | 0.432 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0401%
East Asian · 18/44,874 alleles
Filtering AF
0.0259%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0214%
Overall
0.0013%
21/1,611,650 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0401% | 2,493 |
| European (non-Finnish) | 0.000254% | 393,298 |
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.Ala282=
- Coding
- c.846G>C
- MANE Select
- NM_019616
- dbSNP
- rs200316840
- Type
- single nucleotide variant
- Location
- chr13:113118519 (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 282
- a β-strand; a disulfide bond; the peptidase s1 domain
Similar variants
- F7 p.Ala282Val Pathogenic/Likely pathogenic ★★ ⚠ same residue
- F7 p.Ala282Thr Conflicting classifications of pathogenicity ★ ⚠ same residue
- 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
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-ala282 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown