ClinVar Genomic variation as it relates to human health

The c.316G>A (p.Gly106Ser) variant affects one of the functional domains (aa 93-129; EGF-like 1 domain) in the F9 protein, meeting the PM1 criteria. This missense variant has a REVEL score of 0.905(>0.6), meeting the PP3 criteria. It is reported at an MAF of 0.00002441 (5/204867 alleles) in the overall population in gnomAD v2.1.1, with 3 hemizygotes; however BS1 criteria of MAF >=0.0000278 is not met. Over 60 patients with mild and moderate hemophilia B are reported in the literature meeting PS4_Very strong and PP4_Moderate criteria (PMID: 22103590, 29296726). In summary, the clinical significance of this variant is pathogenic. ACMG/AMP criteria applied, as specified by the Coagulation Factor Deficiency Variant Curation Expert Panel for F9: PS4_Very strong, PM1, PP4_Moderate, PP3.

The F9 c.316G>A; p.Gly106Ser variant (rs1378522233), also known as Gly60Ser or FIX Durham, is reported in numerous patients diagnosed with mild hemophilia B (Chavali 2009, Chen 1989, Denton 1988, Poort 1989, Factor IX Variant Database and references therein). This variant is reported as pathogenic in ClinVar (Variation ID: 10579) and is found in the general population at a low overall allele frequency of 0.003% (5/204867 alleles, including 3 hemizygotes) in the Genome Aggregation Database. The glycine at codon 106 is highly conserved and located in the calcium-binding EGF-like domain. Structural analyses demonstrate that the variant increases the likelihood of defective folding in the EGF-like domain of the protein (Whiteman 1998). Additionally, other amino acid substitutions at this codon (Arg, Cys, and Asp) have been reported in individuals with hemophilia B and are considered disease-causing (Factor IX Variant Database and references therein). Based on available information, the p.Gly106Ser variant is considered to be pathogenic. References: Factor IX Variant Database: http://f9-db.eahad.org/ Chavali S et al. Hemophilia B is a quasi-quantitative condition with certain mutations showing phenotypic plasticity. Genomics. 2009 Dec;94(6):433-7. Chen SH et al. Three point mutations in the factor IX genes of five hemophilia B patients. Identification strategy using localization by altered epitopes in their hemophilic proteins. J Clin Invest. 1989 Jul;84(1):113-8. Denton PH et al. Hemophilia B Durham: a mutation in the first EGF-like domain of factor IX that is characterized by polymerase chain reaction. Blood. 1988 Oct;72(4):1407-11. Poort SR et al. A Dutch pedigree with mild hemophilia B with a missense mutation in the first EGF domain (factor IXOud en Nieuw Gastel). Nucleic Acids Res. 1989 Jul 25;17(14):5869. Whiteman P et al. A Gly --> Ser change causes defective folding in vitro of calcium-binding epidermal growth factor-like domains from factor IX and fibrillin-1. J Biol Chem. 1998 Apr 3;273(14):7807-13.

The F9 c.316G>A missense variant has been classified as Pathogenic (PS4_Strong, PP3, PS3_Moderate, PP1_Moderate, PP4). The c.316G>A variant is a single nucleotide change in exon 4/8 of the F9 gene, which is predicted to change the amino acid glycine at position 106 in the protein to serine. This variant is in gnomAD at very low frequency (0.003%, allele count 4/111504, 2 hemizygous) and has been reported in numerous affected individuals with mild haemophilia B (PMID:22639855, 35842956, and 2472424) (PS4_strong). Note that this variant has been previously reported in the literature as p.Gly60Ser. Computational data predicts a deleterious effect (PP3). This variant is located in the functional cbEGF domain and has been predicted to affect protein folding (PMID: 9525872) (PS3_moderate). The variant has been shown to segregate with disease in 2 patients and a proband from 2 families (PMID: 2472424, 3651597) and has been reported to have been found in at least 5 generations (PP1_Moderate). The patient's family history and FIX bioassay levels are consistent with the specific gene aetiology (PP4). This variant is a missense change at an amino acid residue where different missense changes have been seen before: p.Gly106Arg (CM940467), p.Gly106Asp (CM940465), p.Gly106Cys (CM960576). This variant has been reported in dbSNP (rs137852233), HGMD as disease causing (CM940466) and in ClinVar as pathogenic (ClinVar variant ID: 10579).

PP3, PP5, PM1_supporting, PM5, PS3, PS4_moderate

This sequence change replaces glycine, which is neutral and non-polar, with serine, which is neutral and polar, at codon 106 of the F9 protein (p.Gly106Ser). This variant is present in population databases (rs137852233, gnomAD 0.01%). This missense change has been observed in individuals with mild hemophilia B (PMID: 2472424, 19699296, 22639855). It has also been observed to segregate with disease in related individuals. This variant is also known as Gly60Ser, 10430G>A, and FIX Durham. ClinVar contains an entry for this variant (Variation ID: 10579). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt F9 protein function with a negative predictive value of 80%. Experimental studies are conflicting or provide insufficient evidence to determine the effect of this variant on F9 function (PMID: 9525872). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic.

Variant summary: F9 c.316G>A (p.Gly106Ser) results in a non-conservative amino acid change located in the EGF-like domain (IPR000742) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 1.1e-05 in 183001 control chromosomes. c.316G>A has been reported in the literature in multiple individuals affected with Factor IX Deficiency (Hemophilia B) and segregated with disease (Li_2014, Chen_1989). These data indicate that the variant is very likely to be associated with disease. At least one publication reports experimental evidencethat this variant results in defective folding of calcium-binding epidermal growth factor-like domains (Whiteman_1998). This variant is also known as Gly60Ser, 10430G>A, and FIX Durham. The following publications have been ascertained in the context of this evaluation (PMID: 2472424, 24375831, 11278305). ClinVar contains an entry for this variant (Variation ID: 10579). Based on the evidence outlined above, the variant was classified as pathogenic.

The F9 c.316G>A variant is predicted to result in the amino acid substitution p.Gly106Ser. This variant, also referred to as Hemophilia B Durham, has been reported previously in many patients to be causative for Hemophilia B (Denton et al. 1988. PubMed ID: 3262389; Tengguo et al. 2014. PubMed ID: 24375831; Factor IX Gene (F9) Variant Database: http://www.factorix.org/). Several other missense changes at this same position (p.Gly106Cys, p.Gly106Arg, and p.Gly106Asp) have also been reported to be causative for Hemophilia B (Factor IX Gene (F9) Variant Database: http://www.factorix.org/). This variant is reported in 0.011% of alleles in individuals of African descent in gnomAD. The c.316G>A (p.Gly106Ser) variant is interpreted as pathogenic.