rs267606789
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PVS1_StrongPM2PP5_Moderate
The NM_000129.4(F13A1):c.1984C>T(p.Arg662Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000843 in 1,613,880 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★).
Frequency
Genomes: 𝑓 0.00023 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000069 ( 0 hom. )
Consequence
F13A1
NM_000129.4 stop_gained
NM_000129.4 stop_gained
Scores
2
5
Clinical Significance
Conservation
PhyloP100: -0.772
Genes affected
F13A1 (HGNC:3531): (coagulation factor XIII A chain) This gene encodes the coagulation factor XIII A subunit. Coagulation factor XIII is the last zymogen to become activated in the blood coagulation cascade. Plasma factor XIII is a heterotetramer composed of 2 A subunits and 2 B subunits. The A subunits have catalytic function, and the B subunits do not have enzymatic activity and may serve as plasma carrier molecules. Platelet factor XIII is comprised only of 2 A subunits, which are identical to those of plasma origin. Upon cleavage of the activation peptide by thrombin and in the presence of calcium ion, the plasma factor XIII dissociates its B subunits and yields the same active enzyme, factor XIIIa, as platelet factor XIII. This enzyme acts as a transglutaminase to catalyze the formation of gamma-glutamyl-epsilon-lysine crosslinking between fibrin molecules, thus stabilizing the fibrin clot. It also crosslinks alpha-2-plasmin inhibitor, or fibronectin, to the alpha chains of fibrin. Factor XIII deficiency is classified into two categories: type I deficiency, characterized by the lack of both the A and B subunits; and type II deficiency, characterized by the lack of the A subunit alone. These defects can result in a lifelong bleeding tendency, defective wound healing, and habitual abortion. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_pathogenic. Variant got 8 ACMG points.
PVS1
?
Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant is located in the 3'-most 50 bp of the penultimate exon, not predicted to undergo nonsense mediated mRNA decay. There are 16 pathogenic variants in the truncated region.
PM2
?
Very rare variant in population databases, with high coverage;
PP5
?
Variant 6-6151874-G-A is Pathogenic according to our data. Variant chr6-6151874-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 16539.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr6-6151874-G-A is described in Lovd as [Pathogenic].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
F13A1 | NM_000129.4 | c.1984C>T | p.Arg662Ter | stop_gained | 14/15 | ENST00000264870.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
F13A1 | ENST00000264870.8 | c.1984C>T | p.Arg662Ter | stop_gained | 14/15 | 1 | NM_000129.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000230 AC: 35AN: 152092Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000179 AC: 45AN: 251042Hom.: 0 AF XY: 0.000199 AC XY: 27AN XY: 135654
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GnomAD4 exome AF: 0.0000691 AC: 101AN: 1461788Hom.: 0 Cov.: 34 AF XY: 0.0000688 AC XY: 50AN XY: 727198
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GnomAD4 genome ? AF: 0.000230 AC: 35AN: 152092Hom.: 0 Cov.: 32 AF XY: 0.000350 AC XY: 26AN XY: 74278
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ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:2
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Factor XIII, A subunit, deficiency of Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jul 15, 1994 | - - |
F13A1-related disorder Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Nov 21, 2022 | The F13A1 c.1984C>T variant is predicted to result in premature protein termination (p.Arg662*). The c.1984C>T (p.Arg662*) variant has been reported as a recurrent causative variant in patients with Factor XIII deficiency (described as Arg-661-Stop based on legacy nomenclature in Mikkola et al. 1994. PubMed ID: 8025280; Jang et al. 2015. PubMed ID: 25004025). This variant is reported in 0.20% of alleles in individuals of European (Finnish) descent in gnomAD (http://gnomad.broadinstitute.org/variant/6-6152107-G-A). Nonsense variants in F13A1 are expected to be pathogenic. Based on the collective evidence, this variant is interpreted as pathogenic. - |
Computational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
Cadd
Pathogenic
Dann
Benign
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
MutationTaster
Benign
A
Vest4
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at