rs137852227

chrX-139537144-C-T

Variant summary

Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1 PM2 PP5_Very_Strong

The NM_000133.4(F9):c.223C>T(p.Arg75Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★★). Variant results in nonsense mediated mRNA decay.

• Frequency: Genomes: not found (cov: 23)
• Consequence: F9 NM_000133.4 stop_gained
• Clinical Significance: Pathogenic reviewed by expert panel P:6 O:1
• Conservation: PhyloP100: 0.808

Genes affected

F9 (HGNC:3551): (coagulation factor IX) This gene encodes vitamin K-dependent coagulation factor IX that circulates in the blood as an inactive zymogen. This factor is converted to an active form by factor XIa, which excises the activation peptide and thus generates a heavy chain and a light chain held together by one or more disulfide bonds. The role of this activated factor IX in the blood coagulation cascade is to activate factor X to its active form through interactions with Ca+2 ions, membrane phospholipids, and factor VIII. Alterations of this gene, including point mutations, insertions and deletions, cause factor IX deficiency, which is a recessive X-linked disorder, also called hemophilia B or Christmas disease. Alternative splicing results in multiple transcript variants encoding different isoforms that may undergo similar proteolytic processing. [provided by RefSeq, Sep 2015]

ACMG classification

Verdict is Pathogenic. Variant got 18 ACMG points.

• PVS1: Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant X-139537144-C-T is Pathogenic according to our data. Variant chrX-139537144-C-T is described in ClinVar as [Pathogenic]. Clinvar id is 10572.Status of the report is reviewed_by_expert_panel, 3 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
F9	NM_000133.4	c.223C>T	p.Arg75Ter	stop_gained	2/8	ENST00000218099.7
F9	NM_001313913.2	c.223C>T	p.Arg75Ter	stop_gained	2/7
F9	XM_005262397.5	c.223C>T	p.Arg75Ter	stop_gained	2/7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
F9	ENST00000218099.7	c.223C>T	p.Arg75Ter	stop_gained	2/8	1	NM_000133.4	P1
F9	ENST00000394090.2	c.223C>T	p.Arg75Ter	stop_gained	2/7	1
F9	ENST00000479617.2	n.230C>T		non_coding_transcript_exon_variant	2/4	5

Frequencies

GnomAD3 genomes Cov.: 23

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 23

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:6 Other:1

Revision: reviewed by expert panel

Submissions by phenotype

Hereditary factor IX deficiency disease Pathogenic:3 Other:1

Pathogenic, reviewed by expert panel	curation	ClinGen Coagulation Factor Deficiency Variant Curation Expert Panel, Clingen	Feb 09, 2024	The F9 c.223C>T; p.Arg75Ter causes a protein truncation that is expected to undergo NMD, meeting PVS1. The variant is completely absent from gnomAD v2.1.1 and v3.1.1, meeting PM2_Supporting. Over 75 patients are reported in the literature with moderate-severe hemophilia B, some with a history of inhibitors to factor replacement products, meeting F9 phenotype criteria for PS4_Very strong and PP4_Moderate (EAHAD database; PMID: 29296726). 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 F9: PVS1, PS4_Very strong, PP4_Moderate, PM2_Supporting. -
not provided, no classification provided	literature only	GeneReviews	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Jun 09, 2023	Variant summary: F9 c.223C>T (p.Arg75X) results in a premature termination codon and is predicted to cause absence of the protein due to nonsense mediated decay, which is a commonly known mechanism for disease. The variant was absent in 182973 control chromosomes (gnomAD). c.223C>T has been reported in the literature in multiple individuals affected with Factor IX Deficiency (Hemophilia B) (e.g. Li_2014). These data indicate that the variant is very likely to be associated with disease. The following publication has been ascertained in the context of this evaluation (PMID: 24375831). Three clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 and all classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -
Pathogenic, no assertion criteria provided	literature only	OMIM	Aug 01, 1990	- -

not provided Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Jul 08, 2022	Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 25525159, 25929987, 18624698, 1969838, 25470321, 30648777, 32224444, 32155688, 23093250, 28193338, 24375831, 27824213, 32875744) -
Pathogenic, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Feb 18, 2020	The F9 c.223C>T; p.Arg75Ter variant (rs137852227), also known as 6460G>A or Arg29Stop, is reported in the literature in individuals and families with hemophilia B, most often in cases of severe disease (Bottema 1993, Green 1989, Koeberl 1990, Factor IX database and references therein). Clotting assays of patient samples with this variant typically exhibit activity less than 1% of wildtype (Green 1989, Factor IX database). This variant is reported in ClinVar (Variation ID: 10572) and is absent from general population databases (Exome Variant Server, Genome Aggregation Database), indicating it is not a common polymorphism. This variant induces an early termination codon and is predicted to result in a truncated protein or mRNA subject to nonsense-mediated decay. Based on available information, the p.Arg75Ter variant is considered to be pathogenic. References: Factor IX database: http://www.factorix.org Bottema CD et al. The pattern of spontaneous germ-line mutation: relative rates of mutation at or near CpG dinucleotides in the factor IX gene. Hum Genet. 1993 Jun;91(5):496-503. Green PM et al. Molecular pathology of haemophilia B. EMBO J. 1989 Apr;8(4):1067-72. Koeberl DD et al. Recurrent nonsense mutations at arginine residues cause severe hemophilia B in unrelated hemophiliacs. Hum Genet. 1990 Apr;84(5):387-90. -

Hereditary factor IX deficiency disease;C2749016:Thrombophilia, X-linked, due to factor 9 defect Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Invitae

Jun 16, 2021

For these reasons, this variant has been classified as Pathogenic. Loss-of-function variants in F9 are known to be pathogenic (PMID: 20301668). This variant has been reported in several individuals and families affected with hemophilia B (PMID: 1969838, 27824213, 25470321, 23093250, 18624698, 2198809). This variant is also known as 6460 C>T, Arg29-Stop, R248>TGA, and p.Arg29X in the literature. ClinVar contains an entry for this variant (Variation ID: 10572). This variant is not present in population databases (ExAC no frequency). This sequence change creates a premature translational stop signal (p.Arg75*) in the F9 gene. It is expected to result in an absent or disrupted protein product. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.74	D
BayesDel_noAF	Pathogenic	0.59
Cadd	Pathogenic	35
Dann	Uncertain	1.0
FATHMM_MKL	Benign	0.67	D
MutationTaster	Benign	1.0	A;A
Vest4		0.94
GERP RS		5.2

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs137852227; hg19: chrX-138619303; COSMIC: COSV54378708;