X-154957060-C-T

Position:

• chrX-154957060-C-T

Variant summary

Our verdict is Pathogenic. Variant got 8 ACMG points: 8P and 0B. PP4_Moderate PM2_Supporting PP3 PS4

This summary comes from the ClinGen Evidence Repository: The c.1649G>A (p.Arg550His) variant is absent from males in gnomAD v2.1.1. It is reported in heterozygotes at a frequency of 0.00002442 (2/81904 alleles) in the non-Finnish European population. At least 35 male individuals with mild hemophilia A are found in the literature and internal laboratory data with the Arg550His variant. More cases are available in the literature (EAHAD reports 64 patients), however >8 probands have been counted towards PS4_VeryStrong and one for PP4_moderate. This variant is associated with discrepant factor VIII activity levels with some individuals having normal levels on one-stage assays and levels in the mild hemophilia range on a chromogenic, or two-stage, assay (CDC Champs/EAHAD databases). Some individuals have been reported to have a history of inhibitor formation to factor replacement products (CDC Champs/EAHAD databases). The c.1649G>A (p.Arg550His) missense variant has a REVEL score of 0.78 (>0.6). Other variants at the same residue, Arg550Cys, Arg550Gly, Arg550Leu and Arg550Pro have been reported, but evidence from these variant curations has not been used in classifying the Arg550His variant. 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_VeryStrong, PP3, PM2_Supporting. LINK:https://erepo.genome.network/evrepo/ui/classification/CA255115/MONDO:0010602/071

• Frequency:
  • Genomes: not found (cov: 22)
  • Exomes 𝑓: 0.0000018 (0 hom. 1 hem.)
• Consequence: F8 NM_000132.4 missense
• Clinical Significance: Pathogenic reviewed by expert panel P:5
• Conservation: PhyloP100: 3.24

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 8 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
F8	NM_000132.4	c.1649G>A	p.Arg550His	missense_variant	11/26	ENST00000360256.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
F8	ENST00000360256.9	c.1649G>A	p.Arg550His	missense_variant	11/26	1	NM_000132.4	P1
F8	ENST00000647125.1	c.*1525G>A		3_prime_UTR_variant, NMD_transcript_variant	12/14

Frequencies

GnomAD3 genomes Cov.: 22

GnomAD3 exomes AF: 0.0000109 AC: 2 AN: 183443 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 67891

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000244

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00000183 AC: 2 AN: 1095586 Hom.: 0 Cov.: 30 AF XY: 0.00000277 AC XY: 1 AN XY: 361004

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: 0.00000238

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 22

ExAC AF: 0.00000824 AC: 1

EpiCase AF: 0.0000545

EpiControl AF: 0.00

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:5

Revision: reviewed by expert panel

Submissions by phenotype

Hereditary factor VIII deficiency disease Pathogenic:4

Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Apr 30, 2024	Variant summary: F8 c.1649G>A (p.Arg550His) results in a non-conservative amino acid change located in the Multicopper oxidase-like, N-terminal domain (IPR011707) 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 1.1e-05 in 183443 control chromosomes (gnomAD). c.1649G>A has been reported in the literature in multiple individuals affected with Factor VIII Deficiency (Hemophilia A; e.g. Gilmore_2010). These data indicate that the variant is very likely to be associated with disease. At least one publication reports experimental evidence evaluating an impact on protein function, finding that the variant results in substantially reduced F8 activity (Pipe_2001). The following publications have been ascertained in the context of this evaluation (PMID: 20148980, 11157485). ClinVar contains an entry for this variant (Variation ID: 10225). Based on the evidence outlined above, the variant was classified as pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Genetics and Molecular Pathology, SA Pathology	Mar 05, 2021	- -
Pathogenic, no assertion criteria provided	literature only	OMIM	Jan 01, 1995	- -
Pathogenic, reviewed by expert panel	curation	ClinGen Coagulation Factor Deficiency Variant Curation Expert Panel, Clingen	Feb 02, 2024	The c.1649G>A (p.Arg550His) variant is absent from males in gnomAD v2.1.1. It is reported in heterozygotes at a frequency of 0.00002442 (2/81904 alleles) in the non-Finnish European population. At least 35 male individuals with mild hemophilia A are found in the literature and internal laboratory data with the Arg550His variant. More cases are available in the literature (EAHAD reports 64 patients), however >8 probands have been counted towards PS4_VeryStrong and one for PP4_moderate. This variant is associated with discrepant factor VIII activity levels with some individuals having normal levels on one-stage assays and levels in the mild hemophilia range on a chromogenic, or two-stage, assay (CDC Champs/EAHAD databases). Some individuals have been reported to have a history of inhibitor formation to factor replacement products (CDC Champs/EAHAD databases). The c.1649G>A (p.Arg550His) missense variant has a REVEL score of 0.78 (>0.6). Other variants at the same residue, Arg550Cys, Arg550Gly, Arg550Leu and Arg550Pro have been reported, but evidence from these variant curations has not been used in classifying the Arg550His variant. 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_VeryStrong, PP3, PM2_Supporting. -

not provided Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

Jul 19, 2023

The F8 c.1649G>A; p.Arg550His variant, also known as p.Arg531His, is reported in the literature in multiple individuals affected with mild hemophilia A (Markoff 2009, Schwaab 1995, Winter 2008, Factor VIII database and references therein). This variant is reported in ClinVar (Variation ID: 10225), and is only observed on two alleles in the Genome Aggregation Database, indicating it is not a common polymorphism. Additionally, other amino acid substitutions at this codon (Cys, Gly, Leu, Pro) have been reported in individuals with mild to moderate hemophilia A and are considered pathogenic (Factor VIII database and references therein). Functional characterization of the p.Arg550His variant protein indicates an increase in dissociation from the thrombin-activated heterodimer (Pipe 2001). Computational analyses predict that this variant is deleterious (REVEL: 0.738). Based on available information, the p.Arg550His variant is considered to be mildly pathogenic. References: Link to Factor VIII database: http://www.factorviii-db.org/ Markoff A et al. Combined homology modelling and evolutionary significance evaluation of missense mutations in blood clotting factor VIII to highlight aspects of structure and function. Haemophilia. 2009 15(4):932-41. PMID: 19473423. Pipe S et al. Hemophilia A mutations associated with 1-stage/2-stage activity discrepancy disrupt protein-protein interactions within the triplicated A domains of thrombin-activated factor VIIIa. Blood. 2001 97(3):685-91. PMID: 11157485. Schwaab R et al. Characterization of mutations within the factor VIII gene of 73 unrelated mild and moderate haemophiliacs. Br J Haematol. 1995 91(2):458-64. PMID: 8547094. Winter P et al. A recurrent F8 mutation in Irish haemophilia A patients: evidence for a founder effect. Haemophilia. 2008 14(2):394-5. PMID: 18179574. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.24
BayesDel_addAF	Pathogenic	0.52	D
BayesDel_noAF	Pathogenic	0.56
CADD	Uncertain	23
DANN	Uncertain	1.0
DEOGEN2	Pathogenic	0.98	D
FATHMM_MKL	Benign	0.74	D
LIST_S2	Uncertain	0.88	D
M_CAP	Pathogenic	0.94	D
MetaRNN	Pathogenic	0.99	D
MetaSVM	Pathogenic	0.83	D
MutationAssessor	Benign	1.7	L
MutationTaster	Benign	1.0	N
PrimateAI	Uncertain	0.52	T
PROVEAN	Uncertain	-4.2	D
REVEL	Pathogenic	0.74
Sift	Benign	0.035	D
Sift4G	Uncertain	0.0020	D
Polyphen		1.0	D
Vest4		0.81
MutPred		0.94		Loss of sheet (P = 0.0315);
MVP		1.0
MPC		1.8
ClinPred		0.93	D
GERP RS		5.2
Varity_R		0.84
gMVP		0.96

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: rs137852418; hg19: chrX-154185335; COSMIC: COSV64275004;