Is F8 p.Ile405Ser (c.1214T>G) pathogenic?

F8 p.Ile405Ser (c.1214T>G) is classified Likely pathogenic in F8 (ClinVar, Expert panel, 2 submitters; last evaluated 2024-05-09). AlphaMissense: likely pathogenic (0.9227); Absent from gnomAD v4.1; Associated with hemophilia A.

What condition is associated with F8 p.Ile405Ser (c.1214T>G)?

F8 p.Ile405Ser (c.1214T>G) is associated with hemophilia A (ClinVar).

How common is F8 p.Ile405Ser (c.1214T>G) in the general population?

F8 p.Ile405Ser (c.1214T>G) 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.Ile405Ser (c.1214T>G)?

AlphaMissense predicts likely pathogenic (score 0.9227) — an in-silico prediction, not a clinical call.

F8 p.Ile405Ser

c.1214T>G · rs28933670 · VCV10208

Likely pathogenic Expert panel

Classification

Likely pathogenic

ClinVar

Review

Expert panel ★★★☆

ClinVar · 2 submitters

AlphaMissense

likely pathogenic

0.9227 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

hemophilia A

ClinGen expert panel — Coagulation Factor Deficiency VCEP

Likely Pathogenic for hemophilia A. Applied ACMG criteria (verbatim):

PP4_Moderate PM2_Supporting PM5_Supporting PS4_Moderate PP3

Curation rationale (ClinGen, verbatim)

The variant, NM_000132.3(F8):c.1214T>G causes a missense change, Ile405Ser, which is not reported in gnomAD v2.1.1 or v3 or v4. This variant has been reported in at least three patients with Hemophilia A in the literature (PS4_Moderate, PP4_Moderate, PMIDs: 8307558). The variant has a REVEL score of 0.985 (PP3 threshold >0.6). Another variant at the same codon, Ile405Thr, is curated by the Coagulation Factor Deficiency Variant Curation Expert Panel as likely pathogenic (PM5_Supporting). In summary, the clinical significance of this variant is likely pathogenic. ACMG/AMP criteria applied, as specified by the Coagulation Factor Deficiency Variant Curation Expert Panel for F8: PS4_Moderate, PP4_Moderate, PP3, PM2_Supporting, PM5_Supporting.

ClinGen Evidence Repository → · reported verbatim, not re-tallied by Sugi Variant.

Computational evidence

Protein change
AlphaMissense	0.9227	likely pathogenic ✓ concordant with ClinVar · top 4% in F8
REVEL	0.985	strongly pathogenic-leaning
SaProt	LLR -17.27	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 11	GERP 1.5, phastCons 1
Regional constraint	o/e 0.74	unconstrained · MANE · 38 kb · p 2.6e-06 · regional, not allelic
Overall
CADD	25.8	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.Ile405Ser
Coding: c.1214T>G
MANE Select: NM_000132
dbSNP: rs28933670
Type: single nucleotide variant
Location: chrX:154966483 (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.Ile405Thr Pathogenic ★★★ same residue
F8 p.Ile405Phe Uncertain significance ★★★ ⚠ 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-ile405ser (accessed [today's date]).

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