Is F9 p.Val248fs (c.742del) pathogenic?

F9 p.Val248fs (c.742del) is classified Pathogenic in F9 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-01-13). No gnomAD frequency available for this variant; Associated with hemophilia B.

What condition is associated with F9 p.Val248fs (c.742del)?

F9 p.Val248fs (c.742del) is associated with hemophilia B, thrombophilia, X-linked, due to factor 9 defect (ClinVar).

How common is F9 p.Val248fs (c.742del) in the general population?

F9 p.Val248fs (c.742del) is no gnomAD frequency available for this variant (gnomAD).

How is Hemophilia B inherited?

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

F9 p.Val248fs

c.742del · rs2520839064 · VCV2922182

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

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.
Consequence	frameshift	predicted loss-of-function in a haploinsufficient gene (ClinGen)
NMD	predicted	premature termination codon in exon 7 of 8
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 0.65	GERP -1.7

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

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.Val248fs
Coding: c.742del
MANE Select: NM_000133
dbSNP: rs2520839064
Type: Deletion
Location: chrX:139560759 (GRCh38)
Structure: AlphaFold pLDDT 80.45 · 57 PDB
Residue 248: a β-strand; 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

Also linked: thrombophilia, X-linked, due to factor 9 defect

For Hemophilia B (Orphanet):

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

Similar variants

F9 p.Val248= Likely benign ★ 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.Cys382fs 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-val248fs (accessed [today's date]).

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