Is F9 p.Val419= (c.1257G>A) pathogenic?

F9 p.Val419= (c.1257G>A) is classified Likely benign in F9 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-06-14). Absent from gnomAD v4.1; Associated with thrombophilia, X-linked, due to factor 9 defect.

What condition is associated with F9 p.Val419= (c.1257G>A)?

F9 p.Val419= (c.1257G>A) is associated with thrombophilia, X-linked, due to factor 9 defect, hemophilia B (ClinVar).

How common is F9 p.Val419= (c.1257G>A) in the general population?

F9 p.Val419= (c.1257G>A) is absent from gnomAD v4.1 (gnomAD).

F9 p.Val419=

c.1257G>A · rs61731481 · VCV2935855

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

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 -0.84, phastCons 1
Overall
CADD	5.143	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.Val419=
Coding: c.1257G>A
MANE Select: NM_000133
dbSNP: rs61731481
Type: single nucleotide variant
Location: chrX:139561942 (GRCh38)
Structure: AlphaFold pLDDT 80.45 · 57 PDB
Residue 419: a UniProt-annotated variant site (in hemb; moderately severe); a β-strand; 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.Val419Met Uncertain significance ★ ⚠ same residue
F9 p.Val419Glu Pathogenic ⚠ same residue
F9 p.Val419Gly Likely 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-val419 (accessed [today's date]).

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