Is F5 p.Pro1404fs (c.4205_4209dup) pathogenic?

F5 p.Pro1404fs (c.42054209dup) is classified Pathogenic in F5 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-02-16). Associated with congenital factor V deficiency.

What condition is associated with F5 p.Pro1404fs (c.4205_4209dup)?

F5 p.Pro1404fs (c.4205_4209dup) is associated with congenital factor V deficiency (ClinVar).

How is Congenital factor V deficiency inherited?

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

F5 p.Pro1404fs

c.4205_4209dup · VCV3641202

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

Conditions

congenital factor V deficiency

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 13 of 25
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -0.83	GERP -2.5

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

Variant & gene context

Gene: F5
Protein: p.Pro1404fs
Coding: c.4205_4209dup
MANE Select: NM_000130
Type: Duplication
Location: chr1:169540880 (GRCh38)
Gene constraint: LOEUF 0.704 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 62.57 · 23 PDB
Residue 1404: a UniProt-annotated variant site (in); the 'b' region; the '35 x 9 aa approximate tandem repeats of [tnp]-l-s-p-d-l-s-q-t' region

Full F5 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

congenital factor V deficiency — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Congenital factor V deficiency (Orphanet):

Inheritance: Autosomal recessive
Onset: All ages
Prevalence: 1-9 / 1 000 000 (Europe)

Similar variants

F5 p.Pro1404Ser Benign/Likely benign ★★ same residue
F5 p.His611fs Pathogenic/Likely pathogenic ★★ same condition
F5 p.Ser1680fs Pathogenic ★★ same condition
F5 p.Ser1802fs Pathogenic/Likely pathogenic ★★ same condition
F5 p.Lys327Ter Pathogenic ★ same condition
F5 p.Ser1362fs Pathogenic ★ same condition
F5 p.Ser158delinsLysTyrGlnTer Pathogenic ★ same condition
F5 c.1119-14dup Benign ★ 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/f5-p-pro1404fs (accessed [today's date]).

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