Gene Validity Curation

F9 - hemophilia B

Gene: F9 (HGNC:3551)
Classification - 05/22/2019
Disease: hemophilia B (MONDO_0010604)
Mode of Inheritance: X-linked inheritance (HP:0001417)
Replication over time: YES Contradictory Evidence: NO
Expert Panel: Hemostasis Thrombosis EP
Evidence Summary: 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)
Genetic Evidence
Case-Level Data
Evidence Type Case Information Type Guidelines Points PMIDs/Notes
Default Range Max Count Total Counted
Variant Evidence
Autosomal Dominant or X-linked Disorder Variant is de novo 2 0-3 12
Proband with predicted or proven null variant 1.5 0-2 10 8 10.5 10
Mårtensson A et al. 2016 May (PMID:26612714); Zahari M et al. 2018 Sep 1 (PMID:30210749);
Proband with other variant type with some evidence of gene impact 0.5 0-1.5 7 5
2.2
2.2
Bicocchi MP et al. 2006 May (PMID:16643212); Mårtensson A et al. 2016 May (PMID:26612714); Cao DH et al. 2014 Sep 5 (PMID:25330515); Zahari M et al. 2018 Sep 1 (PMID:30210749); Reitsma PH et al. 1988 Sep (PMID:3416069);
Autosomal Recessive Disease Two variants in trans and at least one de novo or a predicted/proven null variant 2 0-3 12
Two variants (not predicted/proven null) with some evidence of gene impact in trans 1 0-1.5
Segregation Evidence   Summed LOD Family Count 0.5 0.5  
Candidate gene sequencing 2.11 1
Cao DH et al. 2014 Sep 5 (PMID:25330515);
Exome/genome or all genes sequenced in linkage region
Total Summed LOD Score 2.11    
Case-Control Data
Case-Control Study Type Case-Control Quality Criteria Guidelines Points PMIDs/Notes
Points/Study Max Count Points Counted
Single Variant Analysis 1. Variant Detection Methodology
2. Power
3. Bias and confounding
4. Statistical Significance
0-6 12
Aggregate Variant Analysis 0-6
Total Genetic Evidence Points (Maximum 12) 12
Experimental Evidence
Evidence Category Evidence Type Guidelines Points PMIDs/Notes
Default Range Max Count Total Counted
Function Biochemical Function 0.5 0 - 2 2 1
0.5
0.5
Furie B et al. 1988 May 20 (PMID:3286010);
Protein Interaction 0.5 0 - 2
Expression 0.5 0 - 2
Functional Alteration Patient cells 1 0 - 2 2
Non-patient cells 0.5 0 - 1
Models Non-human model organism 2 0 - 4 4 1 2 4
Kundu RK et al. 1998 Jul 1 (PMID:9639513);
Cell culture model 1 0 - 2
Rescue Rescue in human 2 0 - 4
Rescue in non-human model organism 2 0 - 4 1
2
Guan Y et al. 2016 May (PMID:26964564);
Rescue in cell culture model 1 0 - 2
Rescue in patient cells 1 0 - 2
Total Experimental Evidence Points (Maximum 6) 4.5

 


 

Assertion criteria Genetic Evidence (0-12 points) Experimental Evidence
(0-6 points)
Total Points
(0-18)
Replication Over Time (Y/N)
Description Case-level, family segregation, or case-control data that support the gene-disease association Gene-level experimental evidence that support the gene-disease association Sum of Genetic & Experimental
Evidence
> 2 pubs w/ convincing evidence over time (>3 yrs)
Assigned Points 12 4.5 16.5 YES
CALCULATED CLASSIFICATION LIMITED 1-6
MODERATE 7-11
STRONG 12-18
DEFINITIVE 12-18 AND replication over time
Valid contradictory evidence (Y/N)*
NO
CALCULATED CLASSIFICATION (DATE)
Definitive
05/22/2019
EXPERT CURATION (DATE)
Definitive
05/22/2019
EVIDENCE SUMMARY
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)