Is F9 p.Asn393del (c.1175ACA[1]) pathogenic?

F9 p.Asn393del (c.1175ACA[1]) is classified Likely pathogenic in F9 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-07-17). Absent from gnomAD; Associated with hemophilia B.

What condition is associated with F9 p.Asn393del (c.1175ACA[1])?

F9 p.Asn393del (c.1175ACA[1]) is associated with hemophilia B (ClinVar).

How common is F9 p.Asn393del (c.1175ACA[1]) in the general population?

F9 p.Asn393del (c.1175ACA[1]) is absent from gnomAD (gnomAD).

How is Hemophilia B inherited?

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

F9 p.Asn393del

c.1175ACA[1] · rs2520846740 · VCV2577226

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

hemophilia B

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -0.057	GERP -1, phastCons 0.011

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: F9
Protein: p.Asn393del
Coding: c.1175ACA[1]
MANE Select: NM_000133
dbSNP: rs2520846740
Type: Microsatellite
Location: chrX:139561859 (GRCh38)
Structure: AlphaFold pLDDT 80.45 · 57 PDB
Residue 393: a turn; 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.Ala436fs Pathogenic ★★ same condition
F9 c.88+5_88+8del Likely pathogenic ★ same condition
F9 c.*828GT[6] Benign ★ same condition
F9 c.391+5_391+8del Likely pathogenic same condition
F9 p.Arg180fs Pathogenic same condition
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

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-asn393del (accessed [today's date]).

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