Is F8 p.Ile405Phe (c.1213A>T) pathogenic?

F8 p.Ile405Phe (c.1213A>T) is classified Uncertain significance in F8 (ClinVar, Expert panel, 1 submitter; last evaluated 2024-05-09). AlphaMissense: ambiguous (0.4655); Absent from gnomAD v4.1; Associated with hemophilia A.

What condition is associated with F8 p.Ile405Phe (c.1213A>T)?

F8 p.Ile405Phe (c.1213A>T) is associated with hemophilia A (ClinVar).

How common is F8 p.Ile405Phe (c.1213A>T) in the general population?

F8 p.Ile405Phe (c.1213A>T) is absent from gnomAD v4.1 (gnomAD).

How is Hemophilia A inherited?

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

What do computational predictors say about F8 p.Ile405Phe (c.1213A>T)?

AlphaMissense predicts ambiguous (score 0.4655) — an in-silico prediction, not a clinical call.

F8 p.Ile405Phe

c.1213A>T · rs2523951164 · VCV3242379

Uncertain significance Expert panel

Classification

Uncertain significance

ClinVar

Review

Expert panel ★★★☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.4655 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

2/2 damaging

REVEL, SaProt · AlphaMissense no call

Conditions

hemophilia A

Computational evidence

Protein change
AlphaMissense	0.4655	ambiguous
REVEL	0.927	moderately pathogenic-leaning
SaProt	LLR -12.18	damaging
⇒ REVEL and SaProt both call this damaging; AlphaMissense makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 4.1	GERP 0.23, phastCons 1
Regional constraint	o/e 0.74	unconstrained · MANE · 38 kb · p 2.6e-06 · regional, not allelic
Overall
CADD	23.4	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: F8
Protein: p.Ile405Phe
Coding: c.1213A>T
MANE Select: NM_000132
dbSNP: rs2523951164
Type: single nucleotide variant
Location: chrX:154966484 (GRCh38)
Structure: AlphaFold pLDDT 61.20 · 29 PDB
Residue 405: the plastocyanin-like 3 domain; a UniProt-annotated variant site (in hema; uncertain significance); a UniProt-annotated variant site (in hema; severe); a β-strand; the f5/8 type a 2 domain

Full F8 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

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

For Hemophilia A (Orphanet):

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

Similar variants

F8 p.Ile405Ser Likely pathogenic ★★★ same residue
F8 p.Ile405Thr Pathogenic ★★★ same residue
F8 c.6429+2T>A Pathogenic ★★★ same condition
F8 p.Ala111Thr Likely pathogenic ★★★ same condition
F8 p.Ala2220Pro Pathogenic ★★★ same condition
F8 p.Ala415Asp Likely pathogenic ★★★ same condition
F8 p.Ala415Val Pathogenic ★★★ ⚠ same condition
F8 p.Arg1768His 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/f8-p-ile405phe (accessed [today's date]).

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