Is F9 p.Cys382fs (c.1143_1144del) pathogenic?

F9 p.Cys382fs (c.11431144del) is classified Pathogenic in F9 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-05-14). Associated with hemophilia B.

What condition is associated with F9 p.Cys382fs (c.1143_1144del)?

F9 p.Cys382fs (c.1143_1144del) is associated with hemophilia B (ClinVar).

How is Hemophilia B inherited?

Typically X-linked recessive (Orphanet). A genetic counselor can assess individual risk for a family.

F9 p.Cys382fs

c.1143_1144del · VCV3902210

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

Conditions

hemophilia B

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 3.4	GERP 3.3, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Variant & gene context

Gene: F9
Protein: p.Cys382fs
Coding: c.1143_1144del
MANE Select: NM_000133
Type: Deletion
Location: chrX:139561828 (GRCh38)
Structure: AlphaFold pLDDT 80.45 · 57 PDB
Residue 382: a UniProt-annotated variant site (in hemb); an α-helix; a disulfide bond; the peptidase s1 domain

Full F9 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

hemophilia B — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Hemophilia B (Orphanet):

Inheritance: X-linked recessive
Onset: Childhood, Infancy, Neonatal
Prevalence: 1-9 / 100 000 (Europe)

Similar variants

F9 p.Cys382Arg Pathogenic ★ same residue
F9 p.Pro324fs Pathogenic ★★★ same condition
F9 c.838+1_838+16del Pathogenic/Likely pathogenic ★★ same condition
F9 p.Ser182fs Pathogenic ★★ same condition
F9 c.392-7_392-4del Uncertain significance ★★ same condition
F9 p.Arg364fs Pathogenic ★ same condition
F9 p.Asn245fs Pathogenic ★ same condition
F9 p.Cys382Ser Likely pathogenic ★ same residue

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-cys382fs (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown