F9 p.Arg43=
c.129G>A · rs2148356042 · VCV1114382
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
2
thrombophilia, X-linked, due to factor 9 defect
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 0.28 | GERP -1.9, phastCons 0.002 |
| Overall | ||
| CADD | 7.375 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- F9
- Protein
- p.Arg43=
- Coding
- c.129G>A
- MANE Select
- NM_000133
- dbSNP
- rs2148356042
- Type
- single nucleotide variant
- Location
- chrX:139537050 (GRCh38)
- Structure
- AlphaFold pLDDT 80.45 · 57 PDB
- Residue 43
- a UniProt-annotated variant site (in hemb; severe; bendorf, beuten, gleiwitz; impairs removal of propeptide); a UniProt-annotated variant site (in hemb; severe; san dimas, oxford-3, strasbourg-2; impairs removal of propeptide); a UniProt-annotated variant site (in hemb; severe; boxtel, heiden, lienen; impairs removal of propeptide)
Similar variants
- F9 p.Arg43Gln Pathogenic/Likely pathogenic ★★ ⚠ same residue
- F9 p.Arg43Trp Pathogenic ★★ ⚠ same residue
- F9 p.Arg43Leu Pathogenic ★★ same residue
- F9 c.520+13A>G Pathogenic ★★★ same condition
- F9 c.88+1G>A Pathogenic ★★★ same condition
- F9 c.88+5G>T Likely pathogenic ★★★ same condition
- F9 p.Ala279Thr Pathogenic ★★★ ⚠ same condition
- F9 p.Ala337Pro Likely pathogenic ★★★ 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/f9-p-arg43 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown