F10 p.Lys49=
c.147G>A · rs763041305 · VCV750766
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000254%, 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 4.3 | GERP -0.43, phastCons 1 |
| Overall | ||
| CADD | 8.403 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000254%
European (non-Finnish) · 3/1,180,028 alleles
Filtering AF
6.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.9e-05%
Overall
0.000186%
3/1,614,194 alleles · very rare
exomes 3/1,461,882 · genomes 0/152,312 · joint denominator
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
- F10
- Protein
- p.Lys49=
- Coding
- c.147G>A
- MANE Select
- NM_000504
- dbSNP
- rs763041305
- Type
- single nucleotide variant
- Location
- chr13:113129528 (GRCh38)
- Gene constraint
- LOEUF 0.968 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 80.47 · 192 PDB
- Residue 49
- the gla domain; an α-helix
Similar variants
- F10 p.Glu54Gly Likely pathogenic ★★ same type
- F10 p.Gly21Arg Pathogenic ★★ ⚠ same type
- F10 p.Gly363Ser Likely pathogenic ★★ same type
- F10 p.Gly450Arg Likely pathogenic ★★ same type
- F10 p.Arg291Gln Uncertain significance ★★ ⚠ same type
- F10 p.Glu268Lys Uncertain significance ★★ ⚠ same type
- F10 p.Glu306Lys Uncertain significance ★★ ⚠ same type
- F10 p.Gly106= 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/f10-p-lys49 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown