Is F9 p.Cys435Ser (c.1303T>A) pathogenic?

F9 p.Cys435Ser (c.1303T>A) is classified Uncertain significance in F9 (ClinVar, Expert panel, 1 submitter; last evaluated 2024-05-09). AlphaMissense: likely pathogenic (0.9944); Absent from gnomAD v4.1; Associated with hemophilia B.

What condition is associated with F9 p.Cys435Ser (c.1303T>A)?

F9 p.Cys435Ser (c.1303T>A) is associated with hemophilia B (ClinVar).

How common is F9 p.Cys435Ser (c.1303T>A) in the general population?

F9 p.Cys435Ser (c.1303T>A) is absent from gnomAD v4.1 (gnomAD).

How is Hemophilia B inherited?

Typically X-linked recessive (Orphanet). A genetic counselor can assess individual risk for a family.

What do computational predictors say about F9 p.Cys435Ser (c.1303T>A)?

AlphaMissense predicts likely pathogenic (score 0.9944) — an in-silico prediction, not a clinical call.

F9 p.Cys435Ser

c.1303T>A · rs2520848336 · VCV3242388

Uncertain significance Expert panel

Classification

Uncertain significance

ClinVar

Review

Expert panel ★★★☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9944 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

hemophilia B

Computational evidence

Protein change
AlphaMissense	0.9944	likely pathogenic · top 1% in F9
REVEL	0.962	strongly pathogenic-leaning
SaProt	LLR -12.47	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 7.9	GERP 5.3, phastCons 1
Regional constraint	o/e 0.57	unconstrained · MANE · 25 kb · p 2.3e-14 · regional, not allelic
Overall
CADD	26.1	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — a triage signal, not a reclassification

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.Cys435Ser
Coding: c.1303T>A
MANE Select: NM_000133
dbSNP: rs2520848336
Type: single nucleotide variant
Location: chrX:139561988 (GRCh38)
Structure: AlphaFold pLDDT 80.45 · 57 PDB
Residue 435: a UniProt-annotated variant site (in hemb); 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

hemophilia B — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Hemophilia B (Orphanet):

Inheritance: X-linked recessive
Onset: Childhood, Infancy, Neonatal
Prevalence: 1-9 / 100 000 (Europe)

Similar variants

F9 p.Cys435Gly Likely pathogenic ★★★ same residue
F9 p.Cys435Tyr Pathogenic ★★★ same residue
F9 p.Cys435Arg Uncertain significance ★★★ ⚠ same residue
F9 p.Cys435Phe Uncertain significance ★★★ ⚠ same residue
F9 p.Cys435= Likely benign ★ 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

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-cys435ser (accessed [today's date]).

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