Is F9 p.Trp431Cys (c.1293G>T) pathogenic?

F9 p.Trp431Cys (c.1293G>T) is classified Pathogenic in F9 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-04-12). AlphaMissense: likely pathogenic (0.9892); Absent from gnomAD v4.1; Associated with thrombophilia, X-linked, due to factor 9 defect.

What condition is associated with F9 p.Trp431Cys (c.1293G>T)?

F9 p.Trp431Cys (c.1293G>T) is associated with thrombophilia, X-linked, due to factor 9 defect, hemophilia B (ClinVar).

How common is F9 p.Trp431Cys (c.1293G>T) in the general population?

F9 p.Trp431Cys (c.1293G>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about F9 p.Trp431Cys (c.1293G>T)?

AlphaMissense predicts likely pathogenic (score 0.9892) — an in-silico prediction, not a clinical call.

F9 p.Trp431Cys

c.1293G>T · rs1371750567 · VCV2925701

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9892 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

thrombophilia, X-linked, due to factor 9 defect

Computational evidence

Protein change
AlphaMissense	0.9892	likely pathogenic ✓ concordant with ClinVar · top 2% in F9
REVEL	0.914	moderately pathogenic-leaning
SaProt	LLR -14.09	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 5.3, phastCons 1
Regional constraint	o/e 0.57	unconstrained · MANE · 25 kb · p 2.3e-14 · regional, not allelic
Overall
CADD	27.4	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

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.Trp431Cys
Coding: c.1293G>T
MANE Select: NM_000133
dbSNP: rs1371750567
Type: single nucleotide variant
Location: chrX:139561978 (GRCh38)
Structure: AlphaFold pLDDT 80.45 · 57 PDB
Residue 431: a UniProt-annotated variant site (in hemb); a UniProt-annotated variant site (in hemb; moderate); a β-strand; a disulfide bond; 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 p.Trp431Leu Uncertain significance ★ ⚠ same residue
F9 p.Trp431Ser Uncertain significance ★ ⚠ same residue
F9 p.Trp431Ter Pathogenic same residue
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-trp431cys (accessed [today's date]).

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