Is F9 p.Asn343= (c.1029C>T) pathogenic?

F9 p.Asn343= (c.1029C>T) is classified Likely benign in F9 (ClinVar, Multiple submitters, 4 submitters; last evaluated 2025-12-14). Ultra-rare (popmax 0.0685%, mid); Associated with thrombophilia, X-linked, due to factor 9 defect.

What condition is associated with F9 p.Asn343= (c.1029C>T)?

F9 p.Asn343= (c.1029C>T) is associated with thrombophilia, X-linked, due to factor 9 defect, hemophilia B (ClinVar).

How common is F9 p.Asn343= (c.1029C>T) in the general population?

F9 p.Asn343= (c.1029C>T) is ultra-rare (popmax 0.0685%, mid) (gnomAD).

F9 p.Asn343=

c.1029C>T · rs145026483 · VCV700040

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0685%, mid)

Conditions

thrombophilia, X-linked, due to factor 9 defect

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 0.86	GERP 0.37, phastCons 1
Overall
CADD	6.603	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0685% Middle Eastern · 3/4,377 alleles

Filtering AF 0.0186% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.017%

Overall 0.0166% 201/1,210,304 alleles · ultra-rare

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0685%	1,459
European (non-Finnish)	0.0203%	4,919
Remaining individualsnot grpmax-eligible	0.0168%	5,949
Admixed American	0.0131%	7,631
African / African-American	0.00349%	28,653

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: F9
Protein: p.Asn343=
Coding: c.1029C>T
MANE Select: NM_000133
dbSNP: rs145026483
Type: single nucleotide variant
Location: chrX:139561714 (GRCh38)
Structure: AlphaFold pLDDT 80.45 · 57 PDB
Residue 343: an α-helix; the peptidase s1 domain

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

Disease context

thrombophilia, X-linked, due to factor 9 defect — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: hemophilia B

Similar variants

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
F9 p.Ala337Thr Pathogenic ★★★ ⚠ same condition
F9 p.Ala337Val Pathogenic ★★★ ⚠ same condition
F9 p.Arg191His 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-asn343 (accessed [today's date]).

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