ClinVar Genomic variation as it relates to human health

The F8 c.6089G>A variant is classified as Likely Pathogenic (PS4, PM1, PP3, PP4, PP5)

Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as pathogenic. The following criteria are met: 0102 - Loss of function is a known mechanism of disease in this gene and is associated with haemophilia A (MIM#306700). (I) 0109 - This gene is associated with X-linked recessive disease. (I) 0200 - Variant is predicted to result in a missense amino acid change from serine to asparagine. (I) 0251 - This variant is heterozygous. (I) 0304 - Variant is present in gnomAD (v2) <0.01 for a recessive condition (2 heterozygotes, 0 homozygotes, 3 hemizygotes). (SP) 0502 - Missense variant with conflicting in silico predictions and uninformative conservation. (I) 0600 - Variant is located in the annotated multicopper oxidase domain (DECIPHER). (I) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. This is a well reported pathogenic variant associated with mild haemophilia A (ClinVar, PMID: 29296726; 32166871; 18691168). (SP) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign

The F8 c.6089G>A; p.Ser2030Asn variant (rs369414658), also known as Ser2011Asn, is reported in the literature in multiple individuals affected with mild hemophilia A (see F8 database and references therein, Lannoy 2015, Liu 1998, Markoff 2009, Repesse 2007) and is considered a pathogenic founder variant in the Belgian population (Lannoy 2015). This variant is reported in ClinVar (Variation ID: 439683). It is found in the non-Finnish European population with an allele frequency of 0.006% (5/81740 alleles, including 3 hemizygotes) in the Genome Aggregation Database. The serine at codon 2030 is highly conserved, but computational analyses are uncertain whether this variant is neutral or deleterious (REVEL: 0.573). Based on available information, this variant is considered to be pathogenic. References: European Association of Haemophilia and Allied Disorders (EAHAD)-Factor VIII Variant Database: https://f8-db.eahad.org/ Lannoy N et al. Overrepresentation of missense mutations in mild hemophilia A patients from Belgium: founder effect or independent occurrence? Thromb Res. 2015 135:1057-1063. PMID: 25824987. Liu M et al. A domain mutations in 65 haemophilia A families and molecular modelling of dysfunctional factor VIII proteins. Br J Haematol. 1998 103:1051-1060. PMID: 9886318. 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 15:932-941. PMID: 19473423. Repesse Y et al. Factor VIII (FVIII) gene mutations in 120 patients with hemophilia A: detection of 26 novel mutations and correlation with FVIII inhibitor development. J Thromb Haemost. 2007 5:1469-1476. PMID: 17445092.

Variant summary: F8 c.6089G>A (p.Ser2030Asn) results in a conservative amino acid change located in the Multicopper oxidase, C-terminal domain (IPR011706) of the encoded protein sequence. Three of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 2.7e-05 in 183248 control chromosomes in the gnomAD database to include 3 hemizygous males and two females. The presence of low frequency treatable pediatric disease alleles in gnomAD has been acknolwedged (Gold_2022). c.6089G>A has been widely reported in the literature in multiple individuals affected with Factor VIII Deficiency (Hemophilia A) (example, Nance_2013, Lannoy_2015, Downes_2019). Some studies report this variant as a mild Hemophilia A variant. These data indicate that the variant is very likely to be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Seven submitters have cited clinical-significance assessments for this variant to ClinVar after 2014. The following publications have been ascertained in the context of this evaluation (PMID: 31064749, 18691168, 25824987, 23711294). All submitters classified the variant as pathogenic/likely pathogenic. Based on the evidence outlined above, the variant was classified as likely pathogenic.

The c.6089G>A (p.S2030N) alteration is located in coding exon 19 of the F8 gene. This alteration results from a G to A substitution at nucleotide position 6089, causing the serine (S) at amino acid position 2030 to be replaced by an asparagine (N). Based on data from gnomAD, the A allele has an overall frequency of 0.003% (5/183248) total alleles studied, with 3 hemizygote(s) observed. The highest observed frequency was 0.006% (5/81740) of European (non-Finnish) alleles. This variant has been reported in multiple individuals meeting diagnostic criteria, including typically mild hemophilia and abnormal factor VIII clotting activity (Liu, 1998; Markoff, 2009; Lannoy, 2012; Lannoy, 2015; Johnsen, 2017; Karch, 2020). In one study, this variant was present in 10 unrelated Belgian families and haplotype analysis was suggestive of a founder effect (Lannoy, 2015). This amino acid position is not well conserved in available vertebrate species. This alteration is predicted to be tolerated by in silico analysis. Based on the available evidence, this alteration is classified as likely pathogenic.

The F8 c.6089G>A variant is predicted to result in the amino acid substitution p.Ser2030Asn. This variant is also described using legacy nomenclature as p.Ser2011Asn, has been reported in several studies of patients with bleeding disorders and mild forms of Hemophilia A (Liu et al. 1998. PubMed ID: 9886318; Lannoy et al. 2015. PubMed ID: 25824987; Downes et al. 2019. PubMed ID: 31064749. Suppl3_SNV+INDEL; Factor VIII Gene (F8) Variant Database, http://www.factorviii-db.org/). This variant is reported in 0.0061% of alleles in individuals of European (Non-Finnish) descent in gnomAD. This variant is interpreted as pathogenic.