rs137852436

Positions:

chrX-154931623-C-T

Variant summary

Our verdict is Pathogenic. Variant got 16 ACMG points: 16P and 0B. PM1PM5PP3_StrongPP5_Very_Strong

The ENST00000360256.9(F8):c.2167G>A(p.Ala723Thr) variant causes a missense change. The variant allele was found at a frequency of 0.00000273 in 1,097,863 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 2 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. A723D) has been classified as Likely pathogenic.

Frequency

Genomes: not found (cov: 23)

Exomes 𝑓: 0.0000027 ( 0 hom. 2 hem. )

Consequence

F8
ENST00000360256.9 missense

Scores

Clinical Significance

Pathogenic criteria provided, multiple submitters, no conflicts P:9

Conservation

PhyloP100: 4.19

Variant links:

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]

F8 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Pathogenic. Variant got 16 ACMG points.

PM1

In a disulfide_bond (size 81) in uniprot entity FA8_HUMAN there are 126 pathogenic changes around while only 0 benign (100%) in ENST00000360256.9

PM5

Other missense variant is known to change same aminoacid residue: Variant chrX-154931622-G-T is described in Lovd as [Likely_pathogenic].

PP3

MetaRNN computational evidence supports a deleterious effect, 0.973

PP5

Variant X-154931623-C-T is Pathogenic according to our data. Variant chrX-154931623-C-T is described in ClinVar as [Pathogenic]. Clinvar id is 10246.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-154931623-C-T is described in Lovd as [Likely_pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
F8	NM_000132.4 linkuse as main transcript	c.2167G>A	p.Ala723Thr	missense_variant	14/26	ENST00000360256.9	NP_000123.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
F8	ENST00000360256.9 linkuse as main transcript	c.2167G>A	p.Ala723Thr	missense_variant	14/26	1	NM_000132.4	ENSP00000353393	P1	P00451-1
F8	ENST00000647125.1 linkuse as main transcript	c.*1833G>A		3_prime_UTR_variant, NMD_transcript_variant	14/14			ENSP00000496062

Frequencies

GnomAD3 genomes

Cov.:

GnomAD3 exomes

AF:

0.00000550

AC:

AN:

181821

Hom.:

AF XY:

0.0000149

AC XY:

AN XY:

67031

show subpopulations

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:

0.0000526

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.00000273

AC:

AN:

1097863

Hom.:

Cov.:

AF XY:

0.00000551

AC XY:

AN XY:

363295

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.0000284

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:

0.00000119

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

Cov.:

ExAC

AF:

0.0000165

AC:

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:9

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Hereditary factor VIII deficiency disease

Pathogenic:4

Pathogenic, no assertion criteria provided	literature only	OMIM	Jan 01, 1995	- -
Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Sep 17, 2024	Variant summary: F8 c.2167G>A (p.Ala723Thr) 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 5.5e-06 in 181821 control chromosomes. c.2167G>A has been reported in the literature in multiple individuals affected with mild/moderate Hemophilia A (example: Cygan_2016). These data indicate that the variant is very likely to be associated with disease. The following publication has been ascertained in the context of this evaluation (PMID: 27704658). ClinVar contains an entry for this variant (Variation ID: 10246). Based on the evidence outlined above, the variant was classified as pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	3billion	Feb 23, 2023	The variant is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: <0.001%). The variant is located in a mutational hot spot and/or well-established functional domain in which established pathogenic variants have been reported. In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.84; 3Cnet: 0.63). Same nucleotide change resulting in same amino acid change has been previously reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000010246 / PMID: 1908096). A different missense change at the same codon (p.Ala723Val) has been reported to be associated with F8 related disorder (PMID: 25854144). Therefore, this variant is classified as Pathogenic according to the recommendation of ACMG/AMP guideline. -
Pathogenic, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Jun 25, 2019	The F8 c.2167G>A (p.Ala723Thr) variant, which was also previously referred to as p.Ala704Thr, is a missense variant. Across a selection of the available literature, it has been identified in at least four unrelated individuals with mild-to-moderate hemophilia A (Higuchi et al. 1991; Antonarakis et al. 1995; Inaba et al. 2013). For three cases, factor VIII activity was reported as falling within 2-29%. In the fourth case, the lowest FVIII:C level was recorded clinically was 0.034 IU/mL. This variant is reported at a frequency of 0.000053 in the South Asian population of the Genome Aggregation Database, where it is found on a single hemizygous allele. Coverage of this genomic region is good, suggesting the variant is rare. In addition, multiple in silico algorithms predict the variant, which is located in the F5/8 type A2 domain, to have a deleterious effect. Based on this evidence and application of the ACMG criteria, the p.Ala723Thr variant is classified as pathogenic for hemophilia A, FVIII deficiency. -

not provided

Pathogenic:3

Pathogenic, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Nov 24, 2023	The F8 c.2167G>A; p.Ala723Thr variant (rs137852436), also known as Ala704Thr, has been reported in multiple individuals diagnosed with mild to moderate hemophilia A (see link to FVIII database and references therein, Higuchi 1991, Markoff 2009). The variant is reported in the ClinVar database (Variation ID: 10246) and is observed on only 1 allele in the Genome Aggregation Database, indicating it is not a common polymorphism. The alanine at codon 723 is highly conserved, and additional variants at this position (c.2168C>A; p.Ala723Asp and c.2168C>T; p.Ala723Val) have been described in individuals with hemophilia A and are considered pathogenic (see link to FVIII database and references therein). Based on available information, the p.Ala723Thr variant is considered pathogenic. References: Link to Factor VIII variant database: http://www.factorviii-db.org/ 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. 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. -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Mar 27, 2024	In silico analysis supports that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 22883072, 31064749, 27380589, 19473423, 27704658, 18691168, 8547094, 15625837, 11857744, 16972227, 24845853, 23625609, 21645180, 23711237, 11179760, 20331761, 23617593, 32224444, 25550078, 1908096, 9452104, 15921397, 29296726, 33245802, 33706050, 32897612) -
Pathogenic, criteria provided, single submitter	clinical testing	Mayo Clinic Laboratories, Mayo Clinic	Sep 04, 2024	PP1_strong, PP3, PM1, PM2, PM6, PS4_moderate -

Hereditary factor VIII deficiency disease;C5676879:Thrombophilia, X-linked, due to factor 8 defect

Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Fulgent Genetics, Fulgent Genetics

Apr 07, 2022

- -

Hereditary factor IX deficiency disease

Pathogenic:1

Pathogenic, criteria provided, single submitter

research

NIHR Bioresource Rare Diseases, University of Cambridge

Feb 01, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Uncertain

0.34

BayesDel_addAF

Pathogenic

0.54

BayesDel_noAF

Pathogenic

0.54

CADD

Uncertain

DANN

Pathogenic

1.0

DEOGEN2

Uncertain

0.48

FATHMM_MKL

Uncertain

0.87

LIST_S2

Benign

0.82

M_CAP

Pathogenic

0.81

MetaRNN

Pathogenic

0.97

MetaSVM

Pathogenic

1.1

MutationAssessor

Benign

1.4

MutationTaster

Benign

0.95

PrimateAI

Benign

0.46

PROVEAN

Benign

-2.0

REVEL

Pathogenic

0.84

Sift

Benign

0.10

Sift4G

Uncertain

0.015

Polyphen

1.0

Vest4

0.69

MutPred

0.90

Loss of sheet (P = 0.0817);

MVP

1.0

MPC

1.6

ClinPred

0.74

GERP RS

5.4

Varity_R

0.52

gMVP

0.99

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over