ClinVar Genomic variation as it relates to human health

The c.6046C>T (p.Arg2016Trp) variant is completely absent from gnomAD v2.1.1 and gnomAD v3 meeting PM2_Supporting. This missense variant has a REVEL score of 0.822 (>0.6) meeting PP3 criteria. More than 46 probands are reported with the variant and moderate-severe hemophilia A in the literature and internal laboratory data (PMID: 29296726, 20102490, 18387975), meeting F8 phenotype criteria. This variant has been associated with discrepant factor VIII activity levels (PMID: 32232366). This variant has also been reported in individuals with a history of inhibitor development to factor replacement therapy (EAHAD database). 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_Very Strong, PP4_Moderate, PP3, PM2_Supporting.

The F8 c.6046C>T; p.Arg2016Trp variant (rs137852453), also known as p.Arg1997Trp in traditional nomenclature, is reported in the literature in multiple individuals and families affected with severe to moderate/mild hemophilia A (Fernandez-Lopez 2005, Garagiola 2015, Guo 2018, Higuchi 1991, Hill 2005, Liu 1998, Pieneman 1995, Reitter 2010, Rossetti 2007, Santagostino 2010, Theophilus 2001, Timur 2001, Vidal 2001, Waseem 1999). This variant is absent from general population databases (1000 Genomes Project, Exome Variant Server, and Genome Aggregation Database), indicating it is not a common polymorphism. Additionally, multiple other variants at this codon (p.Arg2016Gln/Leu/Pro) have been reported in individuals with hemophilia A (Markoff 2009, Vidal 2001). Functional analyses of the variant protein show a reduction in secreted protein and activity, and an impact on splicing that further reduces protein activity (Donadon 2018, Theophilus 2001). The arginine at codon 2016 is highly conserved, and computational analyses (SIFT, PolyPhen-2) predict that this variant is deleterious. Based on available information, this variant is considered to be pathogenic. References: Donadon I et al. Clustered F8 missense mutations cause hemophilia A by combined alteration of splicing and protein biosynthesis and activity. Haematologica. 2018 Feb;103(2):344-350. Fernandez-Lopez O et al. The spectrum of mutations in Southern Spanish patients with hemophilia A and identification of 28 novel mutations. Haematologica. 2005 May;90(5):707-10. Garagiola I et al. A recurrent F8 mutation (c.6046C>T) causing hemophilia A in 8% of northern Italian patients: evidence for a founder effect. Mol Genet Genomic Med. 2015 Dec 14;4(2):152-9. Guo Z et al. Spectrum of Molecular Defects in 216 Chinese Families With Hemophilia A: Identification of Noninversion Mutation Hot Spots and 42 Novel Mutations. Clin Appl Thromb Hemost. 2018 Jan;24(1):70-78. Higuchi M et al. Molecular characterization of mild-to-moderate hemophilia A: detection of the mutation in 25 of 29 patients by denaturing gradient gel electrophoresis. Proc Natl Acad Sci U S A. 1991 Oct 1;88(19):8307-11. Hill M et al. Mutation analysis in 51 patients with haemophilia A: report of 10 novel mutations and correlations between genotype and clinical phenotype. Haemophilia. 2005 Mar;11(2):133-41. Liu M et al. A domain mutations in 65 haemophilia A families and molecular modelling of dysfunctional factor VIII proteins. Br J Haematol. 1998 Dec;103(4):1051-60. Markoff A et al. Combined homology modelling and evolutionary significance evaluation of missense mutations in blood clotting factor VIII to highlight aspects of structure and function. Haemophilia. 2009 Jul;15(4):932-41. Pieneman WC et al. Screening for mutations in haemophilia A patients by multiplex PCR-SSCP, Southern blotting and RNA analysis: the detection of a genetic abnormality in the factor VIII gene in 30 out of 35 patients. Br J Haematol. 1995 Jun;90(2):442-9. Reitter S et al. Spectrum of causative mutations in patients with haemophilia A in Austria. Thromb Haemost. 2010 Jul;104(1):78-85. Rossetti LC et al. Sixteen novel hemophilia A causative mutations in the first Argentinian series of severe molecular defects. Haematologica. 2007 Jun;92(6):842-5. Santagostino E et al. Severe hemophilia with mild bleeding phenotype: molecular characterization and global coagulation profile. J Thromb Haemost. 2010 Apr;8(4):737-43. Theophilus BD et al. Site and type of mutations in the factor VIII gene in patients and carriers of haemophilia A. Haemophilia. 2001 Jul;7(4):381-91. Timur AA et al. Molecular pathology of haemophilia A in Turkish patients: identification of 36 independent mutations. Haemophilia. 2001 Sep;7(5):475-81. Vidal F et al. Rapid hemophilia A molecular diagnosis by a simple DNA sequencing procedure: identification of 14 novel mutations. Thromb Haemost. 2001 Apr;85(4):580-3. Waseem NH et al. Start of UK confidential haemophilia A database: analysis of 142 patients by solid phase fluorescent chemical cleavage of mismatch. Haemophilia Centres. Thromb Haemost. 1999 Jun;81(6):900-5.