F8 p.Arg550His
c.1649G>A · rs137852418 · VCV10225
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 | ||
| AlphaMissense | 0.2437 | likely benign ⚠ discordant with ClinVar |
|---|---|---|
| REVEL | 0.738 | pathogenic-leaning |
| SaProt | LLR -6.69 | tolerated |
| ⇒ REVEL calls this damaging; AlphaMissense and SaProt do not. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
| Constraint at this position | ||
| Conservation | phyloP 7.5 | GERP 1.7, phastCons 1 |
| Regional constraint | o/e 0.74 | unconstrained · MANE · 38 kb · p 2.6e-06 · regional, not allelic |
| Overall | ||
| CADD | 23.2 | PHRED · no single calibrated threshold — expert panels disagree |
AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.
Population frequency
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
Disease context
hemophilia A — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsAlso 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
- F8 p.Arg550Cys Pathogenic/Likely pathogenic ★★ ⚠ same residue
- F8 p.Arg550Gly Likely 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-arg550his (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown