F11 p.Arg413=
c.1239A>G · rs779310675 · VCV2973795
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00167%, 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 1.9 | GERP -4.5, phastCons 1 |
| Overall | ||
| CADD | 7.464 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00167%
Admixed American · 1/60,028 alleles
Overall
6.84e-05%
1/1,461,890 alleles · very rare
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
- F11
- Protein
- p.Arg413=
- Coding
- c.1239A>G
- MANE Select
- NM_000128
- dbSNP
- rs779310675
- Type
- single nucleotide variant
- Location
- chr4:186284195 (GRCh38)
- Gene constraint
- LOEUF 1.145 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 86.94 · 117 PDB
- Residue 413
- a β-strand; the peptidase s1 domain
Similar variants
- F11 p.Arg413fs Pathogenic ★ same residue
- F11 c.1136-1G>C Likely pathogenic ★★ same type
- F11 c.1480+1G>T Likely pathogenic ★★ same type
- F11 c.1481-1G>T Likely pathogenic ★★ same type
- F11 c.1716+1G>A Pathogenic ★★ same type
- F11 c.325+1G>A Pathogenic ★★ same type
- F11 c.326-1G>A Pathogenic ★★ same type
- F11 c.595+3A>G 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/f11-p-arg413 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown