Bleeding in Mild Hemophilia A Due to a Splice-Site F8 Mutation May be Fully Abrogated By Prothrombotic Gene Variants

Introduction: While Factor VIII (FVIII) activity correlates with phenotype in most Hemophilia A (HA) males, the study of rare individuals with discrepant bleeding phenotypes can provide insight into F8 genotype-bleeding phenotype relationships, refine HA classification and improve clinical management. We present an adult male subject who carries a F8 missense mutation, c.5999G>C (p.Gly2000Ala), but remarkably has had no bleeding despite numerous challenges, including multiple surgeries. To resolve genotype-phenotype discrepancy, we evaluated F8 transcripts and screened for additional gene variants by exome sequencing.

Methods: We performed clinical laboratory assays including one-stage FVIII:C and chromogenic FVIII assays, FVIII antigen ELISA, VWF antigen and activity assays, and von Willebrand Disease (VWD) Type 2 Normandy binding activity assay.

The F8 c.5999G>C mutation is proposed to affect F8 splicing, and result in a transcript that deletes exon 19. To evaluate F8 splice variants, quantitative reverse transcription polymerase chain reaction (qRT-PCR) was performed using primers that distinguish FVIII isoforms. Samples were normalized relative to a housekeeping gene, GAPDH. Normalized relative fold expression for each primer pair was calculated by the 2^−ΔΔCT Livak method.

Whole exome sequencing was performed at 80X coverage. Sequencing reads were mapped to the GRCh37/hg19 reference genome with BWA-MEM, and high-quality variant calls were made using GATK4.0 with annotation based on refSeq 1.9, employing best practice recommendations.

Results: Clinical assays confirmed reduced FVIII activity levels consistent with mild HA. By qRT-PCR, the F8 mutation results in a partial splicing defect. Exon 19 deleted transcripts predominate, but are likely not secreted. Indeed, the reduced levels of full-length F8 isoform closely mirror measured FVIII protein and activity levels. These findings explain FVIII levels, but to do not explain the absent phenotype.

Exome sequencing analysis first confirmed the F8 mutation and excluded other genetic causes of FVIII deficiency. Additionally, we excluded thrombophilic mutations proposed to attenuate bleeding severity in HA, including Factor V Leiden (c.1601G>A, p. R534Q) and the c.*97G>A (p.G20210A) mutation in the F2 gene encoding prothrombin.

To identify additional variants that may modify hemostasis, we then screened for non-pathogenic variants in 96 genes that are known to be mutated in bleeding disorders or that alter FVIII clearance or half-life. Of 352 single nucleotide variants (SNVs) in these genes, we prioritized 10 non-synonymous variants with annotated effects on hemostasis. Of these, four are associated with functional effects that would potentiate bleeding phenotype in coagulation factor deficiency. In contrast, five variants are associated with prothrombotic effects and are strong candidates for ameliorating bleeding. Of these, two non-pathogenic VWF variants, rs1063856 and rs7962217, have been shown to increase FVIII. Three other variants in F5 reside within the R2 haplotype. R2 has effects in the absence of Factor V Leiden and can increase thrombin generation and FVIII levels.

Conclusion: The identification of multiple variants that are expected to attenuate bleeding suggests that a single gene variant is unlikely to ameliorate bleeding phenotype in this subject, particularly in the presence of additional variants that promote bleeding. These results suggest evaluation of non-pathogenic variants in non-F8 genes may further explain other cases of discrepant HA not resolved by clinical assays. While these new modulators of HA phenotype require functional confirmation, they provide new avenues for therapeutic development.