F9 p.His415fs
c.1243del · VCV4542500
Likely pathogenic
Single submitter
Classification
Likely pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function in a haploinsufficient gene (ClinGen) |
|---|---|---|
| NMD | escapes | premature termination codon in the last exon (8 of 8) — the truncated protein is likely expressed. PVS1 input, not an applied code |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP -1.4 | GERP -3.3 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- F9
- Protein
- p.His415fs
- Coding
- c.1243del
- MANE Select
- NM_000133
- Type
- Deletion
- Location
- chrX:139561925 (GRCh38)
- Structure
- AlphaFold pLDDT 80.45 · 57 PDB
- Residue 415
- a β-strand; a disulfide bond; the peptidase s1 domain
Similar variants
- F9 p.His415Tyr Uncertain significance ★ ⚠ same residue
- F9 p.Pro324fs Pathogenic ★★★ same type
- F9 c.838+1_838+16del Pathogenic/Likely pathogenic ★★ same type
- F9 p.Ser182fs Pathogenic ★★ same type
- F9 c.392-7_392-4del Uncertain significance ★★ same type
- F9 c.521-35_723+84del Pathogenic ★ same type
- F9 c.724-5_731del Likely pathogenic ★ same type
- F9 p.Arg364fs 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/f9-p-his415fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown