Is F9 p.Glu142fs (c.423_424insAGGCCGGGCG…[116 bp]) pathogenic?

F9 p.Glu142fs (c.423424insAGGCCGGGCG…[116 bp]) is classified Pathogenic in F9 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-08-10). Absent from gnomAD; Associated with hemophilia B.

What condition is associated with F9 p.Glu142fs (c.423_424insAGGCCGGGCG…[116 bp])?

F9 p.Glu142fs (c.423_424insAGGCCGGGCG…[116 bp]) is associated with hemophilia B, thrombophilia, X-linked, due to factor 9 defect (ClinVar).

How common is F9 p.Glu142fs (c.423_424insAGGCCGGGCG…[116 bp]) in the general population?

F9 p.Glu142fs (c.423_424insAGGCCGGGCG…[116 bp]) 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.Glu142fs

c.423_424insAGGCCGGGCG…[116 bp] · rs2520790212 · VCV2010000

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 5 of 8
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 0.66	GERP 1.2, phastCons 1

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.Glu142fs
Coding: c.423_424insAGGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGTGGATCATGAGGTCNNNNNNNNNNAAAAAAAAAAAAAAAAAAAAAAGAATGGCAGATGC
MANE Select: NM_000133
dbSNP: rs2520790212
Type: Insertion
Location: chrX:139548379 (GRCh38)
Structure: AlphaFold pLDDT 80.45 · 57 PDB
Residue 142: a β-strand; a disulfide bond; the egf-like 2 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.Glu142= Likely benign ★ same residue
F9 p.Glu142Gln Uncertain significance ★ ⚠ same residue
F9 c.(391+1_392-1 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
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-glu142fs (accessed [today's date]).

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