rs137852232

chrX-139541099-C-G

Variant summary

Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PM1 PM2 PM5 PP3_Strong PP5_Very_Strong

The NM_000133.4(F9):c.301C>G(p.Pro101Ala) variant causes a missense change. The variant allele was found at a frequency of 0.0000179 in 111,549 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P101Q) has been classified as Likely pathogenic.

• Frequency: Genomes: 𝑓 0.000018 (0 hom., 1 hem., cov: 23)
• Consequence: F9 NM_000133.4 missense
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:3
• Conservation: PhyloP100: 7.09

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.

• PM1: In a hotspot region, there are 8 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 0 benign, 0 uncertain in NM_000133.4
• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chrX-139541100-C-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 1067340.Status of the report is criteria_provided_single_submitter, 1 stars.
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.995
• PP5: Variant X-139541099-C-G is Pathogenic according to our data. Variant chrX-139541099-C-G is described in ClinVar as [Pathogenic]. Clinvar id is 10578.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.301C>G	p.Pro101Ala	missense_variant	4/8	ENST00000218099.7
F9	XM_005262397.5	c.301C>G	p.Pro101Ala	missense_variant	4/7
F9	NM_001313913.2	c.277+3713C>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
F9	ENST00000218099.7	c.301C>G	p.Pro101Ala	missense_variant	4/8	1	NM_000133.4	P1
F9	ENST00000394090.2	c.277+3713C>G		intron_variant		1
F9	ENST00000479617.2	n.254C>G		non_coding_transcript_exon_variant	3/4	5

Frequencies

GnomAD3 genomes AF: 0.0000179 AC: 2 AN: 111549 Hom.: 0 Cov.: 23 AF XY: 0.0000296 AC XY: 1 AN XY: 33755

Gnomad AFR AF: 0.0000652

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome Cov.: 28

GnomAD4 genome AF: 0.0000179 AC: 2 AN: 111549 Hom.: 0 Cov.: 23 AF XY: 0.0000296 AC XY: 1 AN XY: 33755

Gnomad4 AFR AF: 0.0000652

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:3

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

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

Pathogenic, criteria provided, single submitter

clinical testing

Invitae

Dec 24, 2023

This sequence change replaces proline, which is neutral and non-polar, with alanine, which is neutral and non-polar, at codon 101 of the F9 protein (p.Pro101Ala). This variant is present in population databases (rs137852232, gnomAD 0.02%). This missense change has been observed in individuals with hemophilia B (PMID: 2066105, 2743975, 19699296, 24375831). This variant is also known as 10415C>G (Pro55Ala). ClinVar contains an entry for this variant (Variation ID: 10578). 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) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on F9 protein function. This variant disrupts the p.Pro101 amino acid residue in F9. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 7937052; 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. -

Hereditary factor IX deficiency disease Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

Apr 01, 1989

- -

not provided Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

Dec 16, 2020

The F9 c.301C>G; p.Pro101Ala variant (rs137852232), also known as p.Pro55Ala, is reported in the literature in multiple individuals affected with mild-to-moderate hemophilia B (see F9 database and references therein, Chavali 2009, Spitzer 1990). Functional analyses demonstrate that individuals with this variant have factor IX activity between 5-12% (F9 database, Chavali 2009). This variant is reported in ClinVar (Variation ID: 0578). This variant is only observed on one allele in the Genome Aggregation Database, indicating it is not a common polymorphism. Additionally, other amino acid substitutions at this codon (p.Pro101Ser, p.Pro101Thr, p.Pro101Arg, p.Pro101Gln, p.Pro101Leu) have been reported in individuals with mild hemophilia B and are considered pathogenic (Green 1991, Miller 2012, Montejo 1999, Ketterling 1993). The proline at codon 101 is highly conserved, and computational analyses predict that this variant is deleterious (REVEL: 0.936). Based on available information, the p.Pro101Ala variant is considered to be pathogenic. References: F9 Variant Database: https://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. Green PM et al. Haemophilia B mutations in a complete Swedish population sample: a test of new strategy for the genetic counselling of diseases with high mutational heterogeneity. Br J Haematol. 1991 Jul;78(3):390-7. Ketterling RP et al. Germ-line origins of mutation in families with hemophilia B: the sex ratio varies with the type of mutation. Am J Hum Genet. 1993 Jan;52(1):152-66. Miller CH et al. Hemophilia Inhibitor Research Study Investigators. F8 and F9 mutations in US haemophilia patients: correlation with history of inhibitor and race/ethnicity. Haemophilia. 2012 May;18(3):375-82. Spitzer SG et al. Factor IXHollywood: substitution of Pro55 by Ala in the first epidermal growth factor-like domain. Blood. 1990 Oct 15;76(8):1530-7. Montejo JM et al. Identification of twenty-one new mutations in the factor IX gene by SSCP analysis. Hum Mutat. 1999;13(2):160-5. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.43
BayesDel_addAF	Pathogenic	0.65	D
BayesDel_noAF	Pathogenic	0.70
Cadd	Uncertain	25
Dann	Uncertain	1.0
DEOGEN2	Pathogenic	0.95	D
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Pathogenic	0.98	D
M_CAP	Pathogenic	0.86	D
MetaRNN	Pathogenic	1.0	D
MetaSVM	Pathogenic	1.1	D
MutationAssessor	Pathogenic	3.6	H
MutationTaster	Benign	1.0	A;A
PrimateAI	Uncertain	0.51	T
PROVEAN	Pathogenic	-6.5	D
REVEL	Pathogenic	0.94
Sift	Pathogenic	0.0	D
Sift4G	Uncertain	0.0060	D
Polyphen		1.0	D
Vest4		0.89
MutPred		0.98		Loss of disorder (P = 0.0665);
MVP		0.99
MPC		2.9
ClinPred		1.0	D
GERP RS		5.8
Varity_R		0.98
gMVP		0.99

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs137852232; hg19: chrX-138623258;