X-139561694-G-C

Variant names:

• chrX-139561694-G-C
• rs137852253
• NM_000133.4:c.1009G>C

Variant summary

Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PP3 PM2_Supporting PM5 PS4_Moderate

This summary comes from the ClinGen Evidence Repository: The c.1009G>C (NM_000133.4) variant in F9 is a missense variant predicted to cause substitution of alanine by proline at amino acid 337 (p.Ala337Pro). This variant is absent from males in population databases (gnomAD v2.1.1/gnomAD v3). This variant has been previously reported in at least one patient with mild hemophilia B (PMID:1998585), meeting phenotypic criteria for F9. An additional proband with severe hemophilia B has been reported in the EAHAD Factor IX (F9) variant database. The computational predictor REVEL gives a score of 0.617, which is above the threshold of 0.6, evidence that correlates with impact to F9 function (PP3). Different missense variants causing a change at the same residue (p.Ala337Thr and p.Ala337Val) have been established as pathogenic for F9 and SpliceAI predicts no impact on splicing meeting PM5. In summary, based on the evidence available at this time, the clinical significance of this variant is uncertain. ACMG/AMP criteria applied, as specified by the Coagulation Factor Deficiency Variant Curation Expert Panel for F9: PS4_Moderate + PM2_Supporting + PP3 + PM5. (ClinGen Coagulation Factor Deficiency Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for F9 Version 1.0.0., Released 10/5/2023). LINK:https://erepo.genome.network/evrepo/ui/classification/CA255378/MONDO:0010604/080

• Frequency: Genomes: not found (cov: 23)
• Consequence: F9 NM_000133.4 missense
• Clinical Significance: Likely pathogenic reviewed by expert panel P:3
• Conservation: PhyloP100: 7.54

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 Likely_pathogenic. Variant got 6 ACMG points.

• PS4: For more information check the summary or visit ClinGen Evidence Repository.
• PM2: For more information check the summary or visit ClinGen Evidence Repository.
• PM5: For more information check the summary or visit ClinGen Evidence Repository.
• PP3: For more information check the summary or visit ClinGen Evidence Repository.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
F9	NM_000133.4	c.1009G>C	p.Ala337Pro	missense_variant	Exon 8 of 8	ENST00000218099.7	NP_000124.1
F9	NM_001313913.2	c.895G>C	p.Ala299Pro	missense_variant	Exon 7 of 7		NP_001300842.1
F9	XM_005262397.5	c.880G>C	p.Ala294Pro	missense_variant	Exon 7 of 7		XP_005262454.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
F9	ENST00000218099.7	c.1009G>C	p.Ala337Pro	missense_variant	Exon 8 of 8	1	NM_000133.4	ENSP00000218099.2
F9	ENST00000394090.2	c.895G>C	p.Ala299Pro	missense_variant	Exon 7 of 7	1		ENSP00000377650.2
F9	ENST00000643157.1	n.1676G>C		non_coding_transcript_exon_variant	Exon 6 of 7

Frequencies

GnomAD3 genomes Cov.: 23

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 23

ClinVar

Significance: Likely pathogenic

Submissions summary: Pathogenic:3

Revision: reviewed by expert panel

Submissions by phenotype

Hereditary factor IX deficiency disease Pathogenic:3

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ISTH-SSC Genomics in Thrombosis and Hemostasis, KU Leuven, Center for Molecular and Vascular Biology

Significance: Likely pathogenic

Review Status: no assertion criteria provided

Collection Method: research

- -

Mar 11, 1990

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

- -

Sep 30, 2024

ClinGen Coagulation Factor Deficiency Variant Curation Expert Panel, Clingen

Significance: Likely pathogenic

Review Status: reviewed by expert panel

Collection Method: curation

The c.1009G>C (NM_000133.4) variant in F9 is a missense variant predicted to cause substitution of alanine by proline at amino acid 337 (p.Ala337Pro). This variant is absent from males in population databases (gnomAD v2.1.1/gnomAD v3). This variant has been previously reported in at least one patient with mild hemophilia B (PMID: 1998585), meeting phenotypic criteria for F9. An additional proband with severe hemophilia B has been reported in the EAHAD Factor IX (F9) variant database. The computational predictor REVEL gives a score of 0.617, which is above the threshold of 0.6, evidence that correlates with impact to F9 function (PP3). Different missense variants causing a change at the same residue (p.Ala337Thr and p.Ala337Val) have been established as pathogenic for F9 and SpliceAI predicts no impact on splicing meeting PM5. In summary, based on the evidence available at this time, the clinical significance of this variant is uncertain. ACMG/AMP criteria applied, as specified by the Coagulation Factor Deficiency Variant Curation Expert Panel for F9: PS4_Moderate + PM2_Supporting + PP3 + PM5. (ClinGen Coagulation Factor Deficiency Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for F9 Version 1.0.0., Released 10/5/2023). -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.37
BayesDel_addAF	Pathogenic	0.46	D
BayesDel_noAF	Pathogenic	0.43
CADD	Benign	22
DANN	Uncertain	0.98
DEOGEN2	Benign	0.38	T;.
FATHMM_MKL	Pathogenic	1.0	D
LIST_S2	Benign	0.83	T;T
M_CAP	Pathogenic	0.82	D
MetaRNN	Pathogenic	0.96	D;D
MetaSVM	Uncertain	-0.11	T
MutationAssessor	Benign	-1.7	N;.
PrimateAI	Benign	0.44	T
PROVEAN	Benign	2.4	N;N
REVEL	Uncertain	0.62
Sift	Benign	0.96	T;T
Sift4G	Benign	1.0	T;T
Polyphen		0.014	B;.
Vest4		0.58
MutPred		0.90		Gain of methylation at K339 (P = 0.0595);.;
MVP		0.99
MPC		1.9
ClinPred		0.98	D
GERP RS		5.7
Varity_R		0.82
gMVP		0.99

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: rs137852253; hg19: chrX-138643853;