rs28933682

Positions:

• chrX-154904082-T-C

Variant summary

Our verdict is Pathogenic. Variant got 13 ACMG points: 13P and 0B. PM2_Supporting PS3 PS4 PP4_Moderate PP3 PP1

This summary comes from the ClinGen Evidence Repository: The c.5822A>G (p.Asn1941Ser) variant is completely absent from gnomAD v2.1.1 and v3.1.1, which meets PM2_Supporting. This missense variant has a REVEL score of 0.943 (>0.6) and meets criteria for PP3. At least 80 probands have been reported in the literature and from internal laboratory data who meet the F8 phenotype criteria meeting thresholds for PS4_Very strong (>8 probands) and PP4_Moderate. Two brothers have been reported with severe hemophilia A, which meets the PP1 criteria (PMID:15996930). Functional evidence from PMID:21217077 shows that the variant results in a secretory defect based on barely detectable levels of antigen and activity when expressed in BHK cells, which meets PS3 criteria. In summary, this variant meets criteria to be classified as pathogenic. ACMG/AMP criteria applied, as specified by the Coagulation Factor Deficiency Variant Curation Expert Panel for F8: PS4_Very strong, PS3, PM2_Supporting, PP1, PP3. LINK:https://erepo.genome.network/evrepo/ui/classification/CA255184/MONDO:0010602/071

• Frequency: Genomes: not found (cov: 22)
• Consequence: F8 NM_000132.4 missense
• Clinical Significance: Pathogenic reviewed by expert panel P:5
• Conservation: PhyloP100: 7.59

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 13 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
F8	NM_000132.4	c.5822A>G	p.Asn1941Ser	missense_variant	18/26	ENST00000360256.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
F8	ENST00000360256.9	c.5822A>G	p.Asn1941Ser	missense_variant	18/26	1	NM_000132.4	P1

Frequencies

GnomAD3 genomes Cov.: 22

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 22

Alfa AF: 0.0000810 Hom.: 0

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:5

Revision: reviewed by expert panel

Submissions by phenotype

Hereditary factor VIII deficiency disease Pathogenic:5

Pathogenic, criteria provided, single submitter	clinical testing	Johns Hopkins Genomics, Johns Hopkins University	Aug 04, 2022	- -
Pathogenic, reviewed by expert panel	curation	ClinGen Coagulation Factor Deficiency Variant Curation Expert Panel, Clingen	Feb 02, 2024	The c.5822A>G (p.Asn1941Ser) variant is completely absent from gnomAD v2.1.1 and v3.1.1, which meets PM2_Supporting. This missense variant has a REVEL score of 0.943 (>0.6) and meets criteria for PP3. At least 80 probands have been reported in the literature and from internal laboratory data who meet the F8 phenotype criteria meeting thresholds for PS4_Very strong (>8 probands) and PP4_Moderate. Two brothers have been reported with severe hemophilia A, which meets the PP1 criteria (PMID: 15996930). Functional evidence from PMID: 21217077 shows that the variant results in a secretory defect based on barely detectable levels of antigen and activity when expressed in BHK cells, which meets PS3 criteria. In summary, this variant meets criteria to be classified as pathogenic. ACMG/AMP criteria applied, as specified by the Coagulation Factor Deficiency Variant Curation Expert Panel for F8: PS4_Very strong, PS3, PM2_Supporting, PP1, PP3. -
Pathogenic, no assertion criteria provided	literature only	OMIM	Mar 17, 2011	- -
Pathogenic, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Jan 14, 2021	The F8 c.5822A>G, p.Asn1941Ser variant (rs28933682), also known as Asn1922Ser, has been reported in patients diagnosed with moderate to severe hemophilia A (Astermark 2005, Diamond 2005, Higuchi 1991, Summers 2011, Factor VIII Variant Database and references therein). Functional testing in patients with this variant suggest below 5% of normal activity (Factor VIII Variant Database), and characterization of the variant protein in heterologous cells indicates defective processing, accumulation in the endoplasmic reticulum, decreased F8 secretion (Summers 2011). This variant is absent from general population databases (Exome Variant Server, Genome Aggregation Database), indicating it is not a common polymorphism. The asparagine at residue 1941 is highly conserved, other amino acid substitutions at this codon (Asp, Ile, Lys, Thr) have been reported in individuals with hemophilia A and are considered disease-causing (Factor VIII Variant Database and references therein). Based on available information, the p.Asn1941Ser variant is considered to be pathogenic. References: Factor VIII Variant Database: http://f8-db.eahad.org/ Astermark J et al. The Malmo International Brother Study (MIBS). Genetic defects and inhibitor development in siblings with severe hemophilia A. Haematologica. 2005; 90(7):924-31. Diamond C et al. Amino acid substitutions in conserved domains of factor VIII and related proteins: study of patients with mild and moderately severe hemophilia A. Hum Mutat. 1992; 1(3):248-57. Higuchi M et al. Molecular characterization of severe hemophilia A suggests that about half the mutations are not within the coding regions and splice junctions of the factor VIII gene. Proc Natl Acad Sci U S A. 1991; 88(16):7405-9. Summers R et al. Factor VIII A3 domain substitution N1922S results in hemophilia A due to domain-specific misfolding and hyposecretion of functional protein. Blood. 2011; 117(11):3190-8. -
Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Nov 14, 2023	Variant summary: F8 c.5822A>G (p.Asn1941Ser) results in a conservative amino acid change located in the Multicopper oxidase, C-terminal domain (IPR011706) 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 183127 control chromosomes (gnomAD). c.5822A>G has been reported in the literature in multiple individuals affected with Factor VIII Deficiency (Hemophilia A) (examples: Miller_2012 and Chen_2021). These data indicate that the variant is very likely to be associated with disease. The following publications have been ascertained in the context of this evaluation (PMID: 22103590, 33706050). Two submitters have cited clinical-significance assessments for this variant to ClinVar after 2014. All submitters classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.27
BayesDel_addAF	Pathogenic	0.32	D
BayesDel_noAF	Pathogenic	0.22
CADD	Uncertain	24
DANN	Uncertain	1.0
DEOGEN2	Pathogenic	0.99	D
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Uncertain	0.91	D
M_CAP	Pathogenic	0.93	D
MetaRNN	Pathogenic	0.99	D
MetaSVM	Pathogenic	0.95	D
MutationAssessor	Pathogenic	3.8	H
MutationTaster	Benign	1.0	A
PrimateAI	Uncertain	0.52	T
PROVEAN	Pathogenic	-4.7	D
REVEL	Pathogenic	0.94
Sift	Pathogenic	0.0	D
Sift4G	Uncertain	0.012	D
Polyphen		0.99	D
Vest4		0.96
MutPred		0.92		Loss of catalytic residue at N1941 (P = 0.0772);
MVP		1.0
MPC		1.7
ClinPred		1.0	D
GERP RS		5.2
Varity_R		0.98
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: rs28933682; hg19: chrX-154132357;