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F8 p.Arg550His

c.1649G>A · rs137852418 · VCV10225

Pathogenic Expert panel
Classification
Pathogenic
ClinVar
Review
Expert panel ★★★☆
ClinVar · 10 submitters
AlphaMissense
likely benign
0.2437 · ACMG-weighted
gnomAD v4.1
Rare
very rare (popmax 0.000224%, nfe)
Missense predictors
1/3 damaging
AlphaMissense, REVEL, SaProt
Conditions
2
hemophilia A

ClinGen expert panel — Coagulation Factor Deficiency VCEP

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

PP4_Moderate PM2_Supporting PS4_VeryStrong PP3

Curation rationale (ClinGen, verbatim)

The c.1649G>A (p.Arg550His) variant is absent from males in gnomAD v2.1.1. It is reported in heterozygotes at a frequency of 0.00002442 (2/81904 alleles) in the non-Finnish European population. At least 35 male individuals with mild hemophilia A are found in the literature and internal laboratory data with the Arg550His variant. More cases are available in the literature (EAHAD reports 64 patients), however >8 probands have been counted towards PS4_VeryStrong and one for PP4_moderate. This variant is associated with discrepant factor VIII activity levels with some individuals having normal levels on one-stage assays and levels in the mild hemophilia range on a chromogenic, or two-stage, assay (CDC Champs/EAHAD databases). Some individuals have been reported to have a history of inhibitor formation to factor replacement products (CDC Champs/EAHAD databases). The c.1649G>A (p.Arg550His) missense variant has a REVEL score of 0.78 (>0.6). Other variants at the same residue, Arg550Cys, Arg550Gly, Arg550Leu and Arg550Pro have been reported, but evidence from these variant curations has not been used in classifying the Arg550His variant. In summary, this variant meets criteria to be classified as pathogenic. ACMG/AMP criteria applied, as specified by the Coagulation Factor Deficiency Variant Curation Expert Panel for F8: PS4_VeryStrong, PP3, PM2_Supporting.

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

Computational evidence

Protein change
AlphaMissense0.2437likely benign ⚠ discordant with ClinVar
REVEL0.738pathogenic-leaning
SaProtLLR -6.69tolerated
⇒ REVEL calls this damaging; AlphaMissense and SaProt do not.
Splicing
SpliceAI<0.2no splice effect predicted · four deltas, not one · how we know
Constraint at this position
ConservationphyloP 7.5GERP 1.7, phastCons 1
Regional constrainto/e 0.74unconstrained · MANE · 38 kb · p 2.6e-06 · regional, not allelic
Overall
CADD23.2PHRED · 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
Grpmax group 0.000224% European (non-Finnish) · 2/893,107 alleles
Filtering AF 3.7e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.4e-05%
Overall 0.000165% 2/1,208,700 alleles · very rare exomes 2/1,095,586 · genomes 0/113,114 · joint denominator

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene
F8
Protein
p.Arg550His
Coding
c.1649G>A
MANE Select
NM_000132
dbSNP
rs137852418
Type
single nucleotide variant
Location
chrX:154957060 (GRCh38)
Structure
AlphaFold pLDDT 61.20 · 29 PDB
Residue 550
the plastocyanin-like 3 domain; a UniProt-annotated variant site (in hema; mild/moderate); a UniProt-annotated variant site (in hema; mild); 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

Also linked: thrombophilia, X-linked, due to factor 8 defect

For Hemophilia A (Orphanet):

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

Similar variants

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-arg550his (accessed [today's date]).

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