F5 p.Phe353fs
c.1059del · VCV3600215
Likely pathogenic
Single submitter
Classification
Likely pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Conditions
5
thrombophilia due to activated protein C resistance
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function |
|---|---|---|
| NMD | predicted | premature termination codon in exon 7 of 25 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 2.4 | GERP 0.71, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- F5
- Protein
- p.Phe353fs
- Coding
- c.1059del
- MANE Select
- NM_000130
- Type
- Deletion
- Location
- chr1:169555241 (GRCh38)
- Gene constraint
- LOEUF 0.704 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 62.57 · 23 PDB
- Residue 353
- a β-strand; the f5/8 type a 2 domain; the plastocyanin-like 3 domain
Similar variants
- F5 p.Phe353= Likely benign ★ same residue
- F5 c.4962_4971+3del Likely pathogenic ★★ same condition
- F5 p.Ile847fs Pathogenic/Likely pathogenic ★★ same condition
- F5 p.Leu1267fs Pathogenic/Likely pathogenic ★★ same condition
- F5 p.Leu1818fs Pathogenic/Likely pathogenic ★★ same condition
- F5 p.Lys674fs Pathogenic/Likely pathogenic ★★ same condition
- F5 p.Ser955fs Pathogenic/Likely pathogenic ★★ same condition
- F5 p.Thr397_Tyr399del Uncertain significance ★★ same condition
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/f5-p-phe353fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown