F11 p.Gln533=
c.1599G>A · rs4253861 · VCV1169452
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.322%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.429 | indeterminate |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.42 | GERP -2.5, phastCons 0.98 |
| Overall | ||
| CADD | 6.008 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.322%
African / African-American · 241/74,874 alleles
Filtering AF
0.289%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.276%
Overall
0.0179%
289/1,612,934 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.322% | 311 |
| Middle Eastern | 0.033% | 3,030 |
| Remaining individualsnot grpmax-eligible | 0.0288% | 3,469 |
| Admixed American | 0.025% | 3,995 |
| South Asian | 0.00988% | 10,117 |
| European (non-Finnish) | 0.000339% | 294,869 |
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.Gln533=
- Coding
- c.1599G>A
- MANE Select
- NM_000128
- dbSNP
- rs4253861
- Type
- single nucleotide variant
- Location
- chr4:186287706 (GRCh38)
- Gene constraint
- LOEUF 1.145 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 86.94 · 117 PDB
- Residue 533
- a β-strand; a disulfide bond; the peptidase s1 domain
Similar variants
- 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
- F11 c.755+2T>C 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-gln533 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown