12-6019472-C-T

Position:

• chr12-6019472-C-T

Variant summary

Our verdict is Pathogenic. Variant got 15 ACMG points: 15P and 0B. PP4_Moderate PM2_Supporting PP3 PP1 PS2_Moderate PS4 PS3

This summary comes from the ClinGen Evidence Repository: The NM_000552.5(VWF):c.3946G>A variant in VWF is a missense variant predicted to cause substitution of valine by methionine at amino acid 1316. This variant is absent from gnomADv4.1 (PM2_Supporting). This variant has been reported in at least 9 probands showing excessive mucocutaneous bleeding as well as a laboratory phenotype of loss of high molecular weight multimers and/or enhanced platelet aggregation at low doses of ristocetin (PS4_VeryStrong, PMID:19060241, PMID:27885890, PMID:28640903). At least 1 patient showed excessive mucocutaneous bleeding, loss of high molecular weight multimers, and enhanced platelet aggregation at low doses of ristocetin, which together are specific for VWD type 2B, along with consistent features of thrombocytopenia and low VWF antigen/activity ratio (PP4_Moderate, PMID:28640903). Two additional affected patients harbored the variant in an apparent de novo heterozygous state (PS2_Moderate, PMID:7909449, PMID:2010538). The variant has been reported to segregate with VWD type 2B through 3 affected meioses from 1 family (PP1; PMID:19060241). The computational predictor REVEL gives a score of 0.74, which is above the ClinGen VWD VCEP threshold of >0.644 and predicts a damaging effect on VWF function (PP3). A knock-in mouse model expressing VWF p.Val1316Met has shown prolonged bleeding time, absence of high-MW multimers, large platelet aggregates, decreased in vitro platelet adhesion to thrombin or collagen, and enhanced in vivo VWF/platelet string formation, indicating that this variant has a damaging effect on protein function that is consistent with phenotypes of VWD Type 2B (PMID:27212476, PS3). In summary, this variant meets the criteria to be classified as Pathogenic for von Willebrand disease type 2A. ACMG/AMP criteria applied as specified by the ClinGen von Willebrand disease Variant Curation Expert Panel: PS3, PS4_VeryStrong, PP4_Moderate, PS2_Moderate, PP1, PP3, PM2_Supporting. LINK:https://erepo.genome.network/evrepo/ui/classification/CA114127/MONDO:0015629/081

• Frequency: Genomes: not found (cov: 32)
• Consequence: VWF NM_000552.5 missense
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:12 O:2
• Conservation: PhyloP100: 5.25

Genes affected

VWF (HGNC:12726): (von Willebrand factor) This gene encodes a glycoprotein involved in hemostasis. The encoded preproprotein is proteolytically processed following assembly into large multimeric complexes. These complexes function in the adhesion of platelets to sites of vascular injury and the transport of various proteins in the blood. Mutations in this gene result in von Willebrand disease, an inherited bleeding disorder. An unprocessed pseudogene has been found on chromosome 22. [provided by RefSeq, Oct 2015]

ACMG classification

Verdict is Pathogenic. Variant got 15 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
VWF	NM_000552.5	c.3946G>A	p.Val1316Met	missense_variant	28/52	ENST00000261405.10
VWF	XM_047429501.1	c.3946G>A	p.Val1316Met	missense_variant	28/52

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
VWF	ENST00000261405.10	c.3946G>A	p.Val1316Met	missense_variant	28/52	1	NM_000552.5	P1
VWF	ENST00000538635.5	n.421-25538G>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 38

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:12 Other:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Hereditary von Willebrand disease Pathogenic:3 Other:1

not provided, no classification provided	literature only	GeneReviews	-	- -
Likely pathogenic, no assertion criteria provided	research	ISTH-SSC Genomics in Thrombosis and Hemostasis, KU Leuven, Center for Molecular and Vascular Biology	-	- -
Pathogenic, no assertion criteria provided	clinical testing	Clinical Molecular Genetics Laboratory, Johns Hopkins All Children's Hospital	Jan 23, 2006	- -
Pathogenic, criteria provided, single submitter	research	NIHR Bioresource Rare Diseases, University of Cambridge	Feb 01, 2019	- -

von Willebrand disease type 2 Pathogenic:3

Pathogenic, criteria provided, single submitter	clinical testing	Genetics and Molecular Pathology, SA Pathology	Nov 09, 2023	The VWF c.3946G>A variant is classified as Pathogenic (PS3_Strong, PS4_Strong, PM2_Moderate, PP3_Supporting) The VWF c.3946G>A variant is a single nucleotide change in exon 28/52 of the VWF gene, which is predicted to change the amino acid valine at position 1316 in the protein to methionine. The variant has been reported in dbSNP (rs61749397) and in the HGMD database: CM910400. Well-established functional studies in mouse models have shown a deleterious effect of this variant resulting in diminished platelet aggregation (PMID: 24270421 and PMID: 20317142) (PS3_Strong). The variant has been commonly reported in probands with a clinical presentation of von Willebrand Disease type 2B (PS4_Strong). This variant is absent from population databases (PM2_Moderate). Computational predictions support a deleterious effect on the gene or gene product (REVEL >0.7.) (PP3_Supporting). It has been reported as Pathogenic by other diagnostic laboratories (ClinVar Variation ID: 290). -
Pathogenic, no assertion criteria provided	clinical testing	Angelo Bianchi Bonomi Hemophilia and Thrombosis Center, Fondazione IRCCS Ca Granda Ospedale Maggiore Policlinico	Apr 26, 2022	- -
Pathogenic, criteria provided, single submitter	research	NIHR Bioresource Rare Diseases, University of Cambridge	Feb 01, 2019	- -

not provided Pathogenic:2 Other:1

not provided, no classification provided	literature only	Academic Unit of Haematology, University of Sheffield	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Sep 01, 2020	- -
Pathogenic, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	Apr 27, 2018	- -

Von Willebrand disease type 2B Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Versiti Diagnostic Laboratories, Versiti, Inc	Sep 20, 2019	The missense variant VWF c.3946G>A, p.Val1316Met (p.V1316M; mature protein p.V553M) in exon 28 changes amino acid valine at codon 1316 to methionine. The valine at this residue is highly conserved among species. This amino acid change occurs in the A1 domain, a functional domain that binds GPIba (Springer, 2014). Pathogenic variants in VWF are associated with autosomal dominant or autosomal recessive von Willebrand disease (VWD), characterized by quantitative or qualitative deficiencies in von Willebrand factor and resulting in prolonged bleeding. This sequence variant has been previously reported in patients with type 2B VWD. Patients with this variant have a unique phenotype of severe thrombocytopenia, bleeding, giant platelets, and spontaneous platelet aggregation in vitro (Jackson, 2009; Poon, 2010; Espitia, 2017; Rotz, 2017). To date, this variant has not been reported in the general population (GnomAD, Exome Variant Server, ExAC, Variation Viewer). Functional studies of the p.V1316M variant in COS-7 cells mimic the patient laboratory phenotype: binding is significantly increased in the absence of agonist, in the presence of ristocetin, or in the presence of low concentrations of botrocetin, and platelet aggregation is increased by SIPA (Ajzenberg, 2000). In summary, the collective evidence supports VWF c.3946G>A, p.Val1316Met as a pathogenic variant for type 2B VWD. -
Pathogenic, no assertion criteria provided	literature only	OMIM	May 01, 2010	- -

not specified Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

May 09, 2019

The VWF c.3946G>A; p.Val1316Met variant (rs61749397), also known in traditional nomenclature as p.Val553Met, is described in the literature in individuals and families with von Willebrand disease type 2B (Casana 1998, Federici 2009, Goodeve 2010, Jackson 2009, Randi 1991). This variant been described in at least one family to segregate with disease with autosomal dominant inheritance (Jackson 2009) and has also been found to occur de novo (Randi 1990). This variant is absent from general population databases (Exome Variant Server, Genome Aggregation Database), indicating it is not a common polymorphism, and it is reported as pathogenic by several laboratories in ClinVar (Variation ID: 290). The valine at codon 1316 is highly conserved, and computational analyses (SIFT, PolyPhen-2) predict that this variant is deleterious. Further, a mouse model expressing the p.Val1316Met variant exhibits similar physiological symptoms as human patients with this variant, including increased bleeding, reduced platelet aggregation, and macrothrombocytopenia (Adam 2016,Kauskot 2016). Based on available information, the p.Val1316Met variant is considered to be pathogenic. References: Adam F et al. A genetically-engineered von Willebrand disease type 2B mouse model displays defects in hemostasis and inflammation. Sci Rep. 2016 May 23;6:26306. Casana P et al. Search for mutations in a segment of the exon 28 of the human von Willebrand factor gene: new mutations, R1315C and R1341W, associated with type 2M and 2B variants. Am J Hematol. 1998 Sep;59(1):57-63. Federici AB et al. Clinical and molecular predictors of thrombocytopenia and risk of bleeding in patients with von Willebrand disease type 2B: a cohort study of 67 patients. Blood. 2009 Jan 15;113(3):526-34. Goodeve AC. The genetic basis of von Willebrand disease. Blood Rev. 2010 May;24(3):123-34 Jackson SC et al. The Montreal platelet syndrome kindred has type 2B von Willebrand disease with the VWF V1316M mutation. Blood. 2009 Apr 2;113(14):3348-51. Kauskot A et al. LIM kinase/cofilin dysregulation promotes macrothrombocytopenia in severe von Willebrand disease-type 2B. JCI Insight. 2016 Oct 6;1(16):e88643. Randi AM et al. Molecular basis of von Willebrand disease type IIB. Candidate mutations cluster in one disulfide loop between proposed platelet glycoprotein Ib binding sequences. J Clin Invest. 1991 Apr;87(4):1220-6. -

von Willebrand disease type 1;C1264040:von Willebrand disease type 2;C1264041:von Willebrand disease type 3 Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Fulgent Genetics, Fulgent Genetics

Aug 06, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.45
BayesDel_addAF	Pathogenic	0.41	D
BayesDel_noAF	Pathogenic	0.35
CADD	Pathogenic	27
DANN	Uncertain	1.0
DEOGEN2	Uncertain	0.62	D
Eigen	Pathogenic	0.88
Eigen_PC	Pathogenic	0.76
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Pathogenic	0.99	D
M_CAP	Pathogenic	0.45	D
MetaRNN	Pathogenic	0.93	D
MetaSVM	Pathogenic	0.98	D
MutationAssessor	Pathogenic	3.7	H
MutationTaster	Benign	1.0	A
PrimateAI	Uncertain	0.64	T
PROVEAN	Benign	-1.1	N
REVEL	Pathogenic	0.74
Sift	Uncertain	0.0090	D
Sift4G	Uncertain	0.0030	D
Polyphen		1.0	D
Vest4		0.89
MutPred		0.75		Gain of catalytic residue at V1316 (P = 0);
MVP		0.87
MPC		0.93
ClinPred		0.99	D
GERP RS		5.0
Varity_R		0.29
gMVP		0.85

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: rs61749397; hg19: chr12-6128638;