rs137852428

Positions:

• chrX-154953961-G-A

Variant summary

Our verdict is Pathogenic. Variant got 15 ACMG points: 15P and 0B. PS4 PS2 PP1_Strong PP4_Moderate PP3

This summary comes from the ClinGen Evidence Repository: The c.1834C>T (p.Arg612Cys) variant is present in 3 hemizygotes in gnomAD v2.1.1, so PM2_Supporting in not met. The REVEL score of 0.88 which meets PP3 criteria (threshold >0.6). Thirty-two patients were reported with mild-moderate hemophilia A in a single publication and over 100 individuals were identified in the My Life Our Future Cohort, meeting F8 phenotype criteria for PP4_Moderate and PS4_Very strong (PMID:18691168, 29296726). This variant has been associated with mostly mild, but also moderate and severe, hemophilia A with and without inhibitors to factor replacement therapies. This may be in part because the variant has also been associated with discrepant factor VIII activity levels, with chromogenic assays (two-stage) being 2-fold lower than one stage assays (EAHAD database; PMID:32232366). The variant has been reported to segregate with hemophilia A in greater than 6 meioses across two families (PP1_Strong; PMID:9292523). This variant has also been found to have at least one de novo occurrence in the mother of a proband, where the proband was found to have the unaffected maternal grandfather's allele via haplotype analysis (PS2; PMID:9292523). Additionally, this variant has been reported in patients with and without a history of inhibitors to factor replacement products (EAHAD database). 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: PS2, PS4_Very strong, PP1_Strong, PP3 and PP4_Moderate. LINK:https://erepo.genome.network/evrepo/ui/classification/CA255129/MONDO:0010602/071

• Frequency:
  • Genomes: 𝑓 0.0000089 (0 hom., 1 hem., cov: 22)
  • Exomes 𝑓: 0.000010 (0 hom. 4 hem.)
• Consequence: F8 NM_000132.4 missense
• Clinical Significance: Pathogenic reviewed by expert panel P:11
• Conservation: PhyloP100: 2.73

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 15 ACMG points.

• PS2: For more information check the summary or visit ClinGen Evidence Repository.
• PS4: For more information check the summary or visit ClinGen Evidence Repository.
• PP1: For more information check the summary or visit ClinGen Evidence Repository.
• PP3: For more information check the summary or visit ClinGen Evidence Repository.
• PP4: For more information check the summary or visit ClinGen Evidence Repository.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
F8	NM_000132.4	c.1834C>T	p.Arg612Cys	missense_variant	12/26	ENST00000360256.9	NP_000123.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
F8	ENST00000360256.9	c.1834C>T	p.Arg612Cys	missense_variant	12/26	1	NM_000132.4	ENSP00000353393.4
F8	ENST00000647125.1	n.*1710C>T		non_coding_transcript_exon_variant	13/14			ENSP00000496062.1
F8	ENST00000647125.1	n.*1710C>T		3_prime_UTR_variant	13/14			ENSP00000496062.1

Frequencies

GnomAD3 genomes AF: 0.00000894 AC: 1 AN: 111816 Hom.: 0 Cov.: 22 AF XY: 0.0000294 AC XY: 1 AN XY: 33994

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

GnomAD3 exomes AF: 0.0000218 AC: 4 AN: 183438 Hom.: 0 AF XY: 0.0000442 AC XY: 3 AN XY: 67884

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.000146

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: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000100 AC: 11 AN: 1097783 Hom.: 0 Cov.: 30 AF XY: 0.0000110 AC XY: 4 AN XY: 363141

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.0000852

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000185

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000832

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.00000894 AC: 1 AN: 111816 Hom.: 0 Cov.: 22 AF XY: 0.0000294 AC XY: 1 AN XY: 33994

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

ExAC AF: 0.0000165 AC: 2

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:11

Revision: reviewed by expert panel

Submissions by phenotype

Hereditary factor VIII deficiency disease Pathogenic:5

Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Mar 08, 2024	Variant summary: F8 c.1834C>T (p.Arg612Cys) results in a non-conservative amino acid change in the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 2.2e-05 in 183438 control chromosomes (gnomAD). c.1834C>T (also known as Arg593Cys) has been reported in the literature in multiple individuals affected with Factor VIII Deficiency (Hemophilia A) (examples: Eckhardt_2009, and Rosset_2013). 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: 23711237, 19548904). ClinVar contains an entry for this variant (Variation ID: 10236). Based on the evidence outlined above, the variant was classified as pathogenic. -
Pathogenic, reviewed by expert panel	curation	ClinGen Coagulation Factor Deficiency Variant Curation Expert Panel, Clingen	Feb 09, 2024	The c.1834C>T (p.Arg612Cys) variant is present in 3 hemizygotes in gnomAD v2.1.1, so PM2_Supporting in not met. The REVEL score of 0.88 which meets PP3 criteria (threshold >0.6). Thirty-two patients were reported with mild-moderate hemophilia A in a single publication and over 100 individuals were identified in the My Life Our Future Cohort, meeting F8 phenotype criteria for PP4_Moderate and PS4_Very strong (PMID: 18691168, 29296726). This variant has been associated with mostly mild, but also moderate and severe, hemophilia A with and without inhibitors to factor replacement therapies. This may be in part because the variant has also been associated with discrepant factor VIII activity levels, with chromogenic assays (two-stage) being 2-fold lower than one stage assays (EAHAD database; PMID: 32232366). The variant has been reported to segregate with hemophilia A in greater than 6 meioses across two families (PP1_Strong; PMID: 9292523). This variant has also been found to have at least one de novo occurrence in the mother of a proband, where the proband was found to have the unaffected maternal grandfather's allele via haplotype analysis (PS2; PMID: 9292523). Additionally, this variant has been reported in patients with and without a history of inhibitors to factor replacement products (EAHAD database). 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: PS2, PS4_Very strong, PP1_Strong, PP3 and PP4_Moderate. -
Pathogenic, no assertion criteria provided	literature only	OMIM	Jan 01, 1995	- -
Pathogenic, no assertion criteria provided	research	ISTH-SSC Genomics in Thrombosis and Hemostasis, KU Leuven, Center for Molecular and Vascular Biology	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	Genetics and Molecular Pathology, SA Pathology	Jun 15, 2022	PS3, PS4, PP3, PP5 -

not provided Pathogenic:3

Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Mar 08, 2024	Published functional studies demonstrate that R612C reduces factor VIII activity, and leads to intracellular accumulation and subsequent degradation of the F8 protein (PMID: 10691849); This variant is associated with the following publications: (PMID: 12195713, 11858487, 7794769, 8281136, 35014236, 31064749, 1908096, 7728145, 15682412, 1301932, 9569189, 21251204, 19473423, 11554935, 26057490, 11341489, 10404764, 29296726, 33245802, 32897612, 35047849, 10691849) -
Pathogenic, criteria provided, single submitter	clinical testing	Mayo Clinic Laboratories, Mayo Clinic	Apr 06, 2022	PP1_strong, PP3, PP5, PM3_supporting, PS3, PS4_moderate -
Pathogenic, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Jun 26, 2023	The F8 c.1834C>T; p.Arg612Cys variant (rs137852428), also known as Arg593Cys, is reported in multiple patients associated with mild or moderate hemophilia (See Factor VIII database and references therein, Antonarakis 1995, Diamond 1992, Higuchi 1991, Markoff 2009, Trampus Bajika 2015). This variant is reported in ClinVar (Variation ID: 10236), and found in the general Latino/Admixed American population with an allele frequency of 0.01% (4/27431 alleles, including 3 hemizygotes) in the Genome Aggregation Database. The arginine at codon 612 is highly conserved and computational analyses predict that this variant is deleterious (REVEL: 0.808). Based on available information, this variant is considered to be pathogenic. References: Factor VIII variant database: https://f8-db.eahad.org/index.php Antonarakis SE et al. Molecular etiology of factor VIII deficiency in hemophilia A. Hum Mutat. 1995;5(1):1-22. PMID: 7728145. 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. PMID: 1301932. 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 Aug 15;88(16):7405-9. PMID: 1908096. 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 Jul;15(4):932-41. PubMed: 19473423. Trampus Bakija A et al. Specific and global coagulation tests in patients with mild haemophilia A with a double mutation (Glu113Asp, Arg593Cys). Blood Transfus. 2015 Oct;13(4):622-30. PubMed: 26057490. -

Familial aortopathy Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Mar 08, 2024

- -

Hereditary factor IX deficiency disease Pathogenic:1

Pathogenic, criteria provided, single submitter

research

NIHR Bioresource Rare Diseases, University of Cambridge

Feb 01, 2019

- -

Thrombophilia, X-linked, due to factor 8 defect Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Mendelics

May 04, 2022

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.15
BayesDel_addAF	Pathogenic	0.31	D
BayesDel_noAF	Pathogenic	0.46
CADD	Uncertain	25
DANN	Pathogenic	1.0
DEOGEN2	Pathogenic	0.91	D
FATHMM_MKL	Benign	0.34	N
LIST_S2	Benign	0.64	T
M_CAP	Pathogenic	0.85	D
MetaRNN	Pathogenic	0.99	D
MetaSVM	Pathogenic	1.1	D
MutationAssessor	Uncertain	2.4	M
PrimateAI	Benign	0.34	T
PROVEAN	Pathogenic	-5.3	D
REVEL	Pathogenic	0.81
Sift	Uncertain	0.0010	D
Sift4G	Pathogenic	0.0010	D
Polyphen		1.0	D
Vest4		0.72
MutPred		0.85		Loss of helix (P = 0.0033);
MVP		1.0
MPC		1.8
ClinPred		0.96	D
GERP RS		5.2
Varity_R		0.65
gMVP		0.97

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.13		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: rs137852428; hg19: chrX-154182236; COSMIC: COSV64269271;