chrX-154837686-G-A

Position:

• chrX-154837686-G-A

Variant summary

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

The NM_000132.4(F8):​c.6967C>T​(p.Arg2323Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000165 in 1,209,520 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 Likely pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R2323H) has been classified as Pathogenic.

• Frequency:
  • Genomes: 𝑓 0.0000089 (0 hom., 0 hem., cov: 23)
  • Exomes 𝑓: 9.1e-7 (0 hom. 1 hem.)
• Consequence: F8 NM_000132.4 missense
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:4
• Conservation: PhyloP100: 2.47

Genes affected

F8 (HGNC:3546): (coagulation factor VIII) This gene encodes coagulation factor VIII, which participates in the intrinsic pathway of blood coagulation; factor VIII is a cofactor for factor IXa which, in the presence of Ca+2 and phospholipids, converts factor X to the activated form Xa. This gene produces two alternatively spliced transcripts. Transcript variant 1 encodes a large glycoprotein, isoform a, which circulates in plasma and associates with von Willebrand factor in a noncovalent complex. This protein undergoes multiple cleavage events. Transcript variant 2 encodes a putative small protein, isoform b, which consists primarily of the phospholipid binding domain of factor VIIIc. This binding domain is essential for coagulant activity. Defects in this gene results in hemophilia A, a common recessive X-linked coagulation disorder. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Pathogenic. Variant got 18 ACMG points.

• PM1: In a hotspot region, there are 3 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 0 benign, 2 uncertain in NM_000132.4
• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chrX-154837686-G-C is described in ClinVar as [Likely_pathogenic]. Clinvar id is 618642.Status of the report is criteria_provided_single_submitter, 1 stars.
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.993
• PP5: Variant X-154837686-G-A is Pathogenic according to our data. Variant chrX-154837686-G-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 10333.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-154837686-G-A is described in Lovd as [Likely_pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
F8	NM_000132.4	c.6967C>T	p.Arg2323Cys	missense_variant	26/26	ENST00000360256.9
F8	NM_019863.3	c.562C>T	p.Arg188Cys	missense_variant	5/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
F8	ENST00000360256.9	c.6967C>T	p.Arg2323Cys	missense_variant	26/26	1	NM_000132.4	P1
F8	ENST00000330287.10	c.562C>T	p.Arg188Cys	missense_variant	5/5	1
F8	ENST00000644698.1	c.700C>T	p.Arg234Cys	missense_variant	6/6

Frequencies

GnomAD3 genomes AF: 0.00000893 AC: 1 AN: 112002 Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0 AN XY: 34154

Gnomad AFR AF: 0.0000325

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 AF: 9.11e-7 AC: 1 AN: 1097518 Hom.: 0 Cov.: 29 AF XY: 0.00000276 AC XY: 1 AN XY: 362880

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: 0.00000119

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.00000893 AC: 1 AN: 112002 Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0 AN XY: 34154

Gnomad4 AFR AF: 0.0000325

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

Bravo AF: 0.0000982

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:4

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Hereditary factor VIII deficiency disease Pathogenic:4

Pathogenic, no assertion criteria provided	literature only	OMIM	Apr 01, 1992	- -
Pathogenic, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	May 20, 2019	The F8 c.6967C>T; p.Arg2323Cys variant (rs137852473) is reported in the literature in multiple individuals affected with moderate to severe hemophilia A (see link to FVIII database and references therein, Johnsen 2017, Lu 2018). This variant is reported in ClinVar (Variation ID: 10333), and is only observed on one allele in the Genome Aggregation Database, indicating it is not a common polymorphism. The arginine at codon 2323 is highly conserved, and/ computational analyses (SIFT, PolyPhen-2) predict that this variant is deleterious. Additionally, other amino acid substitutions at this codon (Gly, His, Leu) have been reported in individuals with mild hemophilia and are considered pathogenic (FVIII database and references therein). Based on available information, this variant is considered to be pathogenic. References: Link to FVIII database: http://www.factorviii-db.org Johnsen JM et al. Novel approach to genetic analysis and results in 3000 hemophilia patients enrolled in the My Life, Our Future initiative. Blood Adv. 2017 May 18;1(13):824-834. Lu Y et al. Spectrum and origin of mutations in sporadic cases of haemophilia A in China. Haemophilia. 2018 Mar;24(2):291-298. -
Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Aug 22, 2023	Variant summary: F8 c.6967C>T (p.Arg2323Cys) results in a non-conservative amino acid change located in the Coagulation factor 5/8 C-terminal domain (IPR000421) of the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 4.6e-05 in 21864 control chromosomes. c.6967C>T has been reported in the literature in multiple individuals affected with Factor VIII Deficiency (Hemophilia A) (e.g. Baz_2021, Eckhardt_2013, Johnsen_2022, Miller_2012). These data indicate that the variant is very likely to be associated with disease. Additionally, other missense variants in the same residue have been associated with Haemophilia A in HGMD and Clinvar (R2323G, R2323H, R2323L and R2323P). To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publications have been ascertained in the context of this evaluation (PMID: 34272389, 23926300, 29381227, 22103590). One submitter has cited clinical-significance assessments for this variant to ClinVar after 2014 and has classified the variant as 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	Jun 08, 2023	The F8 c.6967C>T missense variant has been classified as Likely Pathogenic (PM2_supporting, PS4_moderate, PM5, PP4). The c.6967C>T variant is in gnomAD at very low frequency (PM2_supporting) however, the variant is prevalent in affected individuals (PS4_moderate). This variant has been reported in PMID: 32897612 and 35014236 in a patient with severe and moderate haemophilia A, respectively. This variant is a missense change at an amino acid residue where a different missense change has been seen before; R2323G, R2323H, R2323P and R2323L as reported in ClinVar and/or HGMD (PM5). This variant is located in the functional C2 domain which is largely responsible for vWF and platelet membrane surface binding, and has also been shown to participate in binding to factor Xa and thrombin (PMID 15471879). The patient's phenotype and FVIII bioassay levels are consistent with the specific genetic aetiology (PP4). This variant has been reported in dbSNP (rs137852473), HMGD as disease causing (CM910153) and in ClinVar as pathogenic (ClinVar variant ID:10333). -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.32
BayesDel_addAF	Pathogenic	0.65	D
BayesDel_noAF	Pathogenic	0.70
CADD	Benign	23
DANN	Uncertain	1.0
DEOGEN2	Pathogenic	0.99	.;D;.
FATHMM_MKL	Benign	0.10	N
LIST_S2	Uncertain	0.96	D;D;D
M_CAP	Pathogenic	0.79	D
MetaRNN	Pathogenic	0.99	D;D;D
MetaSVM	Pathogenic	0.93	D
MutationAssessor	Pathogenic	4.2	.;H;.
MutationTaster	Benign	0.97	N;N
PrimateAI	Uncertain	0.50	T
PROVEAN	Pathogenic	-7.5	D;D;.
REVEL	Pathogenic	0.76
Sift	Pathogenic	0.0	D;D;.
Sift4G	Pathogenic	0.0010	D;D;.
Polyphen		1.0	.;D;.
Vest4		0.63
MutPred		0.99		.;Loss of methylation at R2323 (P = 0.0778);.;
MVP		1.0
MPC		2.2
ClinPred		1.0	D
GERP RS		3.8
Varity_R		0.95
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: rs137852473; hg19: chrX-154065961;