Submission Details

The F9 gene has been associated with the X-linked Recessive condition, Hemophilia B, using the ClinGen Clinical Validity Framework as of 10/17/2018. This association was made using case-level data only. More than 300 pathogenic variants in this gene are reported in humans, ranging from whole gene deletions, partial deletions and duplications, nonsense, frameshift and splicing variants, with a majority being missense variants. Hemophilia B is characterized by a bleeding diathesis diagnosed by an increased bleeding time, reduced Factor IX activity and antigen levels. Mutations in F9 were first associated with this disease in humans as early as 1985 by Chen et al., who found a deletion of exon 5 and 6, with an expected amino acid deletion of residues 85 to 195 (PMID: 3001143). This paper was not scored, however, for this curation as the variant remained undefined.

Summary of Case Level Data: 12 Points The association is seen in at least 13 probands in 5 publications (PMID: 16643212, 25330515, 26612714, 3416069, 30210749). Variants in this gene segregated with disease in 6 additional family members (PMID: 25330515). More case-level evidence is available in the literature, but the maximum score for genetic evidence (12 pts.) has been reached.

The mechanism for disease is hemizygous loss of function in males, with the majority of variants observed resulting in undetectable FIX activity. Women are heterozygous carriers with approximately 50% FIX activity; however, X-inactivation may result in non-expression of F9 in some female individuals. About 1-5% of patients develop inhibitory antibodies. Unlike F8, no intronic inversions are reported in F9 (PMID: 3286010, 16643212).

Hemophilia B Leyden is a subtype of Hemophilia B that occurs due to point mutations in the promoter region of F9 (at -20, -6, -5, +6, +8, and + 13 positions). The phenotype is characterized by developmental expression of FIX post puberty, perhaps due to the influence of testosterone. At childhood, FIX levels are <1%, but levels increase with growth and, in adults, it could be up to 70% of the normal levels (PMID: 3416069).

Summary of Experimental Data: 4.5 Points Dog and mouse models are available for the study of Hemophilia B (PMID: 9639513, 9354664,19416882, 14722728, 10544912). Dog models have also been used extensively in Hemophilia gene therapy. Model studies have also contributed to the development of recombinant FIX for treatment of Hemophilia B. In a mouse model, the F9 gene disruption results in loss of function and absence of detectable FIX activity in mice with a phenotype of severe bleeding (PMID: 9639513). FIX deficiency is shown to be rescued by CRISPR/Cas9-mediated correction to yield detectable levels of FIX protein in mice (PMID: 26964564). Similar to Hemophilia A, gene therapy in humans for Hemophilia B using recombinant adeno-associated virus (rAAV)–mediated gene transfer is at the clinical trials stage.

In summary, the F9-Hemophilia B gene-disease relationship is definitive. This has been repeatedly demonstrated in both the research and clinical diagnostic settings, and has been upheld over time. This classification was approved by the ClinGen Hemostasis/Thrombosis gene curation expert panel on May 22, 2019. (SOP Version 6)