X-139560852-G-A

Position:

• chrX-139560852-G-A

Variant summary

Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PP4_Moderate PM1 PP3 PM2_Supporting PS4

This summary comes from the ClinGen Evidence Repository: The NM_000133.3:c.835G>A variant that results in the Ala279Thr missense change is absent from gnomAD v2.1.1 and v3, meeting PM2_Supporting. It is located within the peptidase S2 domain, which is deemed critical to protein function, meeting PM1. More than 59 male patients with mild hemophilia B are reported hemizygous for this variant in the literature, meeting PS4_Very strong and PP4_Moderate criteria (PMID:29296726, 29656491). It is noted as a founder variant but may also have arisen de novo as a recurrent variant and is found in multiple ethnicities. The variant has a REVEL score of 0.765 (>0.6) and CADD score of 23 (>21) which meet the thresholds recommended for PP3. In summary, the 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: PS4_Very Strong, PM1, PP3, PP4_Moderate, PM2_Supporting. LINK:https://erepo.genome.network/evrepo/ui/classification/CA277507/MONDO:0010604/080

• Frequency:
  • Genomes: not found (cov: 23)
  • Exomes 𝑓: 0.0000019 (0 hom. 0 hem.)
• Consequence: F9 NM_000133.4 missense
• Clinical Significance: Pathogenic reviewed by expert panel P:10
• Conservation: PhyloP100: 8.12

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 10 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
F9	NM_000133.4	c.835G>A	p.Ala279Thr	missense_variant	7/8	ENST00000218099.7
F9	NM_001313913.2	c.721G>A	p.Ala241Thr	missense_variant	6/7
F9	XM_005262397.5	c.706G>A	p.Ala236Thr	missense_variant	6/7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
F9	ENST00000218099.7	c.835G>A	p.Ala279Thr	missense_variant	7/8	1	NM_000133.4	P1
F9	ENST00000394090.2	c.721G>A	p.Ala241Thr	missense_variant	6/7	1
F9	ENST00000643157.1	n.1502G>A		non_coding_transcript_exon_variant	5/7

Frequencies

GnomAD3 genomes Cov.: 23

GnomAD4 exome AF: 0.00000190 AC: 2 AN: 1050721 Hom.: 0 Cov.: 25 AF XY: 0.00 AC XY: 0 AN XY: 321079

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000250

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 23

Bravo AF: 0.0000642

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:10

Revision: reviewed by expert panel

Submissions by phenotype

Hereditary factor IX deficiency disease Pathogenic:5

Likely pathogenic, criteria provided, single submitter	clinical testing	Genetics and Molecular Pathology, SA Pathology	Nov 25, 2020	PS4, PP3, PP2, PP5, PP4. -
Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Apr 24, 2024	Variant summary: F9 c.835G>A (p.Ala279Thr), also reported as p.Ala233Thr, results in a non-conservative amino acid change located in the Serine proteases, trypsin domain (IPR001254) of the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 183314 control chromosomes. c.835G>A has been reported in the literature in multiple individuals affected with Factor IX Deficiency (Hemophilia B) ranging from mild to severe (Green_1990, Hallden_2013, Saad_1994, https://f9-db.eahad.org/). These data indicate that the variant is very likely to be associated with disease. In at least 1 study, FIX:C coagulation activities in samples from affected individuals ranged between 5-22% of controls (Green_1990). The following publications have been ascertained in the context of this evaluation (PMID: 1972560, 24219067, 8091381). ClinVar contains an entry for this variant (Variation ID: 216926). Based on the evidence outlined above, the variant was classified as pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	UCLA Clinical Genomics Center, UCLA	Jul 15, 2014	- -
Pathogenic, criteria provided, single submitter	clinical testing	ISTH-SSC Genomics in Thrombosis and Hemostasis, KU Leuven, Center for Molecular and Vascular Biology	-	- -
Pathogenic, reviewed by expert panel	curation	ClinGen Coagulation Factor Deficiency Variant Curation Expert Panel, Clingen	Feb 09, 2024	The NM_000133.3:c.835G>A variant that results in the Ala279Thr missense change is absent from gnomAD v2.1.1 and v3, meeting PM2_Supporting. It is located within the peptidase S2 domain, which is deemed critical to protein function, meeting PM1. More than 59 male patients with mild hemophilia B are reported hemizygous for this variant in the literature, meeting PS4_Very strong and PP4_Moderate criteria (PMID: 29296726, 29656491). It is noted as a founder variant but may also have arisen de novo as a recurrent variant and is found in multiple ethnicities. The variant has a REVEL score of 0.765 (>0.6) and CADD score of 23 (>21) which meet the thresholds recommended for PP3. In summary, the 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: PS4_Very Strong, PM1, PP3, PP4_Moderate, PM2_Supporting. -

not provided Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Nov 08, 2021	- -
Pathogenic, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Oct 21, 2021	The F9 c.835G>A; p.Ala279Thr variant (rs137852247), also known as p.Ala233Thr, is reported in the literature in numerous individuals affected with hemophilia B and is primarily associated with mild disease (Chavali 2009, Chen 1991, Hamasaki-Katagiri 2012, Kihlberg 2017, Factor IX database and references therein). This is a recurrent missense variant observed in many affected individuals due both to a founder effect and to its location in a CpG dinucleotide, which are prone to G-to-A or C-to-T transitions (Chen 1991, Lassalle 2018). Clotting activity assays indicate the p.Ala279Thr variant exhibits approximately 10-15% of wildtype activity, consistent with mild hemophilia (Chavali 2009, Chen 1991, Kihlberg 2017, Factor IX database). This variant is reported in ClinVar (Variation ID: 216926) and is absent from general population databases (Exome Variant Server, Genome Aggregation Database), indicating it is not a common polymorphism. The alanine at codon 279 is highly conserved and occurs in the catalytic serine protease domain, and computational analyses predict that this variant is deleterious (REVEL: 0.765). Additionally, another variant at this codon (c.835G>T, p.Ala279Ser) has reported in individuals with hemophilia B (Rydz 2013), suggesting this amino acid is functionally important. Based on available information, the p.Ala279Thr variant is considered to be pathogenic. References: Factor IX database: http://www.factorix.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. CG dinucleotide transitions in the factor IX gene account for about half of the point mutations in hemophilia B patients: a Seattle series. Hum Genet. 1991 Jun;87(2):177-82. 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. Kihlberg K et al. Discrepancies between the one-stage clotting assay and the chromogenic assay in haemophilia B. Haemophilia. 2017 Jul;23(4):620-627. Lassalle F et al. Recurrent F8 and F9 gene variants result from a founder effect in two large French haemophilia cohorts. Haemophilia. 2018 Apr 14. Rydz N et al. The Canadian "National Program for hemophilia mutation testing" database: a ten-year review. Am J Hematol. 2013 Dec;88(12):1030-4. -

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

Pathogenic, criteria provided, single submitter

clinical testing

Invitae

Jan 19, 2024

This sequence change replaces alanine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 279 of the F9 protein (p.Ala279Thr). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with hemophilia B (PMID: 2066105, 23093250, 27529981, 27865967, 29656491, 34355501, 34708896). This variant is also known as Ala233Thr. ClinVar contains an entry for this variant (Variation ID: 216926). 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%. This variant disrupts the p.Ala279 amino acid residue in F9. Other variant(s) that disrupt this residue have been determined to be pathogenic (Invitae). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic. -

Abnormality of coagulation Pathogenic:1

Likely pathogenic, criteria provided, single submitter

research

NIHR Bioresource Rare Diseases, University of Cambridge

Feb 01, 2019

- -

Hereditary factor VIII deficiency disease Pathogenic:1

Pathogenic, criteria provided, single submitter

research

NIHR Bioresource Rare Diseases, University of Cambridge

Feb 01, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.26
BayesDel_addAF	Pathogenic	0.50	D
BayesDel_noAF	Pathogenic	0.48
CADD	Uncertain	24
DANN	Uncertain	1.0
DEOGEN2	Uncertain	0.63	D;.
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Uncertain	0.88	D;D
M_CAP	Pathogenic	0.49	D
MetaRNN	Pathogenic	0.95	D;D
MetaSVM	Uncertain	0.66	D
MutationAssessor	Benign	1.9	M;.
MutationTaster	Benign	1.0	A;A
PrimateAI	Benign	0.45	T
PROVEAN	Benign	-1.2	N;N
REVEL	Pathogenic	0.77
Sift	Benign	0.038	D;D
Sift4G	Uncertain	0.049	D;T
Polyphen		0.96	D;.
Vest4		0.70
MutPred		0.86		Gain of glycosylation at A279 (P = 0.0306);.;
MVP		1.0
MPC		1.4
ClinPred		0.93	D
GERP RS		5.8
Varity_R		0.63
gMVP		0.97

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: rs137852247; hg19: chrX-138643011; COSMIC: COSV54378539;