rs137852240

chrX-139551217-C-T

Variant summary

Our verdict is Pathogenic. Variant got 16 ACMG points: 16P and 0B. PM2 PM5 PP3_Strong PP5_Very_Strong

The NM_000133.4(F9):c.676C>T(p.Arg226Trp) variant causes a missense 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 Likely pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R226Q) has been classified as Pathogenic.

• Frequency: Genomes: not found (cov: 23)
• Consequence: F9 NM_000133.4 missense
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:8
• Conservation: PhyloP100: 2.42

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 16 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chrX-139551218-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 10591.Status of the report is criteria_provided_single_submitter, 1 stars.
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.992
• PP5: Variant X-139551217-C-T is Pathogenic according to our data. Variant chrX-139551217-C-T is described in ClinVar as [Likely_pathogenic]. Clinvar id is 10590.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
F9	NM_000133.4	c.676C>T	p.Arg226Trp	missense_variant	6/8	ENST00000218099.7
F9	NM_001313913.2	c.562C>T	p.Arg188Trp	missense_variant	5/7
F9	XM_005262397.5	c.547C>T	p.Arg183Trp	missense_variant	5/7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
F9	ENST00000218099.7	c.676C>T	p.Arg226Trp	missense_variant	6/8	1	NM_000133.4	P1
F9	ENST00000394090.2	c.562C>T	p.Arg188Trp	missense_variant	5/7	1
F9	ENST00000643157.1	n.1343C>T		non_coding_transcript_exon_variant	4/7

Frequencies

GnomAD3 genomes Cov.: 23

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 23

Bravo AF: 0.0000264

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:8

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Hereditary factor IX deficiency disease Pathogenic:4

Pathogenic, criteria provided, single submitter	clinical testing	Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center	Apr 04, 2024	- -
Pathogenic, no assertion criteria provided	literature only	OMIM	Dec 15, 1989	- -
Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Nov 22, 2022	Variant summary: F9 c.676C>T (p.Arg226Trp) results in a non-conservative amino acid change located in the Serine proteases, trypsin domain (IPR001254) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 183448 control chromosomes (gnomAD). c.676C>T has been reported in the literature in multiple individuals affected with Factor IX Deficiency (Hemophilia B) (examples: Ludwig_1992, Hamasaki-Katagiri_2012, Branchini_2021). These data indicate that the variant is very likely to be associated with disease. At least one publication reports experimental evidence evaluating an impact on protein function. The most pronounced variant effect results in <10% of normal activity (example: Branchini_2021). Other variants affecting the same amino acid (e.g R226Q, R226G) has been reported in patients with severe form of Hemophila B (Hamasaki-Katagiri_2012, Branchini_2021 and HGMD). Two clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 and classified the variant as pathogenic/likely pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Genetics and Molecular Pathology, SA Pathology	Apr 22, 2021	- -

not provided Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital	Aug 15, 2023	- -
Pathogenic, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Apr 04, 2020	The F9 c.676C>T; p.Arg226Trp variant (rs137852240), also known as 20518C>T, is reported in the literature in multiple individuals affected with moderate to severe hemophilia B (see link to Factor IX database and references therein, Chavali 2009, Hamasaki-Katagiri 2012). This variant is reported in ClinVar (Variation ID: 10590), and is absent from general population databases (Exome Variant Server, Genome Aggregation Database), indicating it is not a common polymorphism. The arginine at codon 226 lies at the cleavage site in the activation peptide and is highly conserved. Computational analyses (SIFT, PolyPhen-2) predict that this variant is deleterious. Additionally, other amino acid substitutions at this codon (Gly, Gln, Pro, Leu) have been reported in individuals with hemophilia B and are considered pathogenic (see link to Factor IX database and references therein). Based on available information, the p.Arg226Trp variant is considered to be pathogenic. References: Link to Factor IX 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. Hamasaki-Katagiri N et al. Analysis of F9 point mutations and their correlation to severity of haemophilia B disease. Haemophilia. 2012 Nov;18(6):933-40. -

F9-related disorder Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Jun 21, 2023

The F9 c.676C>T variant is predicted to result in the amino acid substitution p.Arg226Trp. This variant also described using legacy nomenclature as p.Arg180Trp; has been reported in multiple individuals with moderate to severe hemophilia B (Giannelli et al. 1994. PubMed ID: 7937052; Hamasaki-Katagiri et al. 2012. PubMed ID: 22639855; Huang et al. 2020. PubMed ID: 32875744; F9 database: http://www.factorix.org/). Different missense variants in the same codon (p.Arg226Gly, p.Arg226Gln, p.Arg226Pro and p.Arg226Leu) have also been reported in individuals with hemophilia B (Giannelli et al. 1994. PubMed ID: 7937052; Hamasaki-Katagiri et al. 2012. PubMed ID: 22639855; Huang et al. 2020. PubMed ID: 32875744; F9 database: http://www.factorix.org/) suggesting that substitution of amino acid residue p.Arg226 is not tolerated. This variant has not been reported in a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare. This variant is interpreted as pathogenic. -

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

Pathogenic, criteria provided, single submitter

clinical testing

Invitae

Apr 23, 2022

This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 226 of the F9 protein (p.Arg226Trp). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with hemophilia B (PMID: 1346077, 18624698, 19699296, 32875744). This variant is also known as C20518T (180 R>W).. ClinVar contains an entry for this variant (Variation ID: 10590). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive. This variant disrupts the p.Arg226 amino acid residue in F9. Other variant(s) that disrupt this residue have been observed in individuals with F9-related conditions (PMID: 32875744), which suggests that this may be a clinically significant amino acid residue. For these reasons, this variant has been classified as Pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.50
BayesDel_addAF	Pathogenic	0.59	D
BayesDel_noAF	Pathogenic	0.61
Cadd	Uncertain	24
Dann	Uncertain	1.0
DEOGEN2	Pathogenic	0.90	D;.
FATHMM_MKL	Uncertain	0.77	D
LIST_S2	Uncertain	0.90	D;D
M_CAP	Pathogenic	0.85	D
MetaRNN	Pathogenic	0.99	D;D
MetaSVM	Uncertain	0.71	D
MutationAssessor	Uncertain	2.2	M;.
MutationTaster	Benign	0.99	A;A
PrimateAI	Uncertain	0.49	T
PROVEAN	Pathogenic	-6.6	D;D
REVEL	Pathogenic	0.79
Sift	Pathogenic	0.0	D;D
Sift4G	Pathogenic	0.0	D;D
Polyphen		1.0	D;.
Vest4		0.89
MutPred		0.93		Loss of disorder (P = 0.0377);.;
MVP		1.0
MPC		1.7
ClinPred		1.0	D
GERP RS		3.5
Varity_R		0.93
gMVP		1.0

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs137852240; hg19: chrX-138633376; COSMIC: COSV54379802; COSMIC: COSV54379802;