rs387906434

Variant summary

Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1PM2PP5_Very_Strong

The ENST00000360256.9(F8):​c.209_212del​(p.Phe70Ter) variant causes a frameshift change. The variant allele was found at a frequency of 0.000000913 in 1,095,552 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. Variant has been reported in ClinVar as Pathogenic (β˜…β˜…). Variant results in nonsense mediated mRNA decay.

Frequency

Genomes: not found (cov: 22)
Exomes 𝑓: 9.1e-7 ( 0 hom. 0 hem. )

Consequence

F8
ENST00000360256.9 frameshift

Scores

Not classified

Clinical Significance

Pathogenic criteria provided, multiple submitters, no conflicts P:5

Conservation

PhyloP100: 4.57
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]

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ACMG classification

Classification made for transcript

Verdict is Pathogenic. Variant got 18 ACMG points.

PVS1
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant X-154999531-TACAA-T is Pathogenic according to our data. Variant chrX-154999531-TACAA-T is described in ClinVar as [Pathogenic]. Clinvar id is 10159.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-154999531-TACAA-T is described in Lovd as [Likely_pathogenic].

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
F8NM_000132.4 linkuse as main transcriptc.209_212del p.Phe70Ter frameshift_variant 2/26 ENST00000360256.9 NP_000123.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
F8ENST00000360256.9 linkuse as main transcriptc.209_212del p.Phe70Ter frameshift_variant 2/261 NM_000132.4 ENSP00000353393 P1P00451-1
F8ENST00000423959.5 linkuse as main transcriptc.104_107del p.Phe35Ter frameshift_variant 2/63 ENSP00000409446
F8ENST00000453950.1 linkuse as main transcriptc.191_194del p.Phe64Ter frameshift_variant 3/53 ENSP00000389153
F8ENST00000647125.1 linkuse as main transcriptc.187_190del p.Leu63ArgfsTer11 frameshift_variant, stop_lost, NMD_transcript_variant 2/14 ENSP00000496062

Frequencies

GnomAD3 genomes
Cov.:
22
GnomAD4 exome
AF:
9.13e-7
AC:
1
AN:
1095552
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
361164
show subpopulations
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
Cov.:
22

ClinVar

Significance: Pathogenic
Submissions summary: Pathogenic:5
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

Hereditary factor VIII deficiency disease Pathogenic:4
Pathogenic, criteria provided, single submitterclinical testingARUP Laboratories, Molecular Genetics and Genomics, ARUP LaboratoriesJan 14, 2021The F8 c.209_212delTTGT; p.Phe70Ter variant (rs387906434), also known as c.208_211delTTTG, is published in the medical literature in numerous individuals with severe hemophilia A (Becker 1996, Habart 2003, Liu 1998, F8 database and references therein). Samples from affected individuals with this variant typically exhibit less than 1% of wildtype clotting activity (Habart 2003, Liu 1998, F8 database and references therein). This variant is absent from general population databases (Exome Variant Server, Genome Aggregation Database), indicating it is not a common polymorphism. This variant deletes 4 nucleotides, leads to an immediate stop codon and is predicted to result in a truncated protein or mRNA subject to non-sense mediated decay. Considering available information, this variant is considered to be pathogenic. References: Link to F8 database: http://www.factorviii-db.org Becker J et al. Characterization of the factor VIII defect in 147 patients with sporadic hemophilia A: family studies indicate a mutation type-dependent sex ratio of mutation frequencies. Am J Hum Genet. 1996 Apr;58(4):657-70. -
Pathogenic, criteria provided, single submitterclinical testingNeuberg Centre For Genomic Medicine, NCGM-The F8 c.209_212del (p.Phe70Ter) variant has been reported in hemizygous state in individuals affected with Hemophilia A (Habart 2003). This variant has been reported to the ClinVar database as Pathogenic. The p.Phe70Ter variant is novel (not in any individuals) in gnomAD Exomes and is novel (not in any individuals) in 1000 Genomes. This variant is predicted to cause loss of normal protein function through protein truncation. Loss of function variants have been previously reported to be disease causing. For these reasons, this variant has been classified as Pathogenic. -
Pathogenic, criteria provided, single submitterclinical testingGenetics and Molecular Pathology, SA PathologyMay 05, 2021- -
Pathogenic, no assertion criteria providedliterature onlyOMIMJan 01, 1995- -
not provided Pathogenic:1
Pathogenic, criteria provided, single submitterclinical testingMayo Clinic Laboratories, Mayo ClinicApr 16, 2024PM2_moderate, PM6, PS4_moderate, PVS1 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

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.

Other links and lift over

dbSNP: rs387906434; hg19: chrX-154227806; API