Is F5 p.Lys348fs (c.1042_1049del) pathogenic?

F5 p.Lys348fs (c.10421049del) is classified Pathogenic in F5 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2001-07-15). Absent from gnomAD; Associated with factor V deficiency.

What condition is associated with F5 p.Lys348fs (c.1042_1049del)?

F5 p.Lys348fs (c.1042_1049del) is associated with factor V deficiency (ClinVar).

How common is F5 p.Lys348fs (c.1042_1049del) in the general population?

F5 p.Lys348fs (c.1042_1049del) is absent from gnomAD (gnomAD).

F5 p.Lys348fs

c.1042_1049del · rs2101829195 · VCV648

Pathogenic No assertion criteria

Classification

Pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

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 7 of 25
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.7	GERP 2.1, 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: F5
Protein: p.Lys348fs
Coding: c.1042_1049del
MANE Select: NM_000130
dbSNP: rs2101829195
Type: Deletion
Location: chr1:169555251 (GRCh38)
Gene constraint: LOEUF 0.704 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 62.57 · 23 PDB
Residue 348: the f5/8 type a 2 domain; the plastocyanin-like 3 domain

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

Disease context

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

Similar variants

F5 p.Ile847fs Pathogenic/Likely pathogenic ★★ same condition
F5 p.Ser955fs Pathogenic/Likely pathogenic ★★ same condition
F5 p.Thr397_Tyr399del Uncertain significance ★★ same condition
F5 p.Arg872fs Pathogenic ★ same condition
F5 p.Asn1057fs Likely pathogenic ★ same condition
F5 p.Gln1192_Val1193insTer Likely pathogenic ★ same condition
F5 p.Leu1366fs Pathogenic ★ same condition
F5 p.Lys1801fs 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/f5-p-lys348fs (accessed [today's date]).

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