Is F9 p.Ile344= (c.1032C>T) pathogenic?

F9 p.Ile344= (c.1032C>T) is classified Likely benign in F9 (ClinVar, Single submitter, 1 submitter). Absent from gnomAD v4.1.

How common is F9 p.Ile344= (c.1032C>T) in the general population?

F9 p.Ile344= (c.1032C>T) is absent from gnomAD v4.1 (gnomAD).

F9 p.Ile344=

c.1032C>T · rs886038243 · VCV255226

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.4	GERP 2.2, phastCons 1
Overall
CADD	9.506	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: F9
Protein: p.Ile344=
Coding: c.1032C>T
MANE Select: NM_000133
dbSNP: rs886038243
Type: single nucleotide variant
Location: chrX:139561717 (GRCh38)
Structure: AlphaFold pLDDT 80.45 · 57 PDB
Residue 344: a UniProt-annotated variant site (in hemb); an α-helix; the peptidase s1 domain

Full F9 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

F9 p.Ile344Asn Uncertain significance ★ ⚠ same residue
F9 p.Ile344Phe Uncertain significance ★ ⚠ same residue
F9 p.Ile344Val Uncertain significance ★ ⚠ same residue
F9 p.Ile344Thr Pathogenic ⚠ same residue
F9 c.520+13A>G Pathogenic ★★★ same type
F9 c.88+1G>A Pathogenic ★★★ same type
F9 c.88+5G>T Likely pathogenic ★★★ same type
F9 p.Ala279Thr Pathogenic ★★★ ⚠ same type

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-ile344 (accessed [today's date]).

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