chr12-6019496-G-A

Position:

• chr12-6019496-G-A

Variant summary

Our verdict is Pathogenic. Variant got 14 ACMG points: 14P and 0B. PS2_Supporting PP4_Moderate PP3 PP1 PM2_Supporting PS3 PS4

This summary comes from the ClinGen Evidence Repository: NM_000552.4(VWF):c.3922C>T (p.Arg1308Cys) missense variant is predicted to cause substitution of arginine by cysteine at amino acid 1308. This variant has been reported in at least 30 probands, of which at least 19 reported sufficient phenotypic information to confirm type 2B VWD. (PS4; PMIDs: 18805962, 22077376, 1419803, 2010538, 16246252). Patient 9 of PMID:2010538, has sufficient information to meet PP4_moerate: lacked HMWM in plasma and had a moderately heightened RIPA (0.6–0.7), as well as low VWF:RCo/VWF:Ag ratio (<0.45), with Platelet-type VWD excluded by mixing experiments to confirm that the defect was in the patient plasma and not in the patient platelets. The variant has been reported to segregate with VWD type 2B through at least 2 affected meioses from 1 family (PP1; PMID:2010538). This variant has been identified as a de novo occurrence with unconfirmed parental relationships in 1 individual with VWD type 2B (PPS2_supporting; PMID:2010538). This variant is absent from gnomAD v4.1 (PM2_Supporting). GP1bα binding assay in COS-7 cells expressing recombinant VWF, variant alone or together with WT, showed increased binding at low doses of ristocetin, indicating that this variant has a gain of function effect on the protein (PMID:16246252) (PS3). Similar results have been reported in multiple studies (PMIDs: 26345337, 8630394). The computational predictor REVEL gives a score of 0.673, which is above the ClinGen VWD VCEP threshold of >0.644 and predicts a damaging effect on VWF function (PP3). In summary, this variant meets the criteria to be classified as Pathogenic for autosomal dominant VWD type 2B based on the ACMG/AMP criteria applied, as specified by the ClinGen VWD VCEP: PS3_supporting, PS4_VeryStrong, PM2_supporting, PS2_supporting, PP1, PP3, PP4_moderate. LINK:https://erepo.genome.network/evrepo/ui/classification/CA114125/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:10 O:1
• Conservation: PhyloP100: 6.15

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 14 ACMG points.

• PS2: For more information check the summary or visit ClinGen Evidence Repository.
• PS3: For more information check the summary or visit ClinGen Evidence Repository.
• PS4: For more information check the summary or visit ClinGen Evidence Repository.
• PM2: 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
VWF	NM_000552.5	c.3922C>T	p.Arg1308Cys	missense_variant	28/52	ENST00000261405.10	NP_000543.3
VWF	XM_047429501.1	c.3922C>T	p.Arg1308Cys	missense_variant	28/52		XP_047285457.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
VWF	ENST00000261405.10	c.3922C>T	p.Arg1308Cys	missense_variant	28/52	1	NM_000552.5	ENSP00000261405	P1
VWF	ENST00000538635.5	n.421-25562C>T		intron_variant, non_coding_transcript_variant		4
VWF	ENST00000539641.1			downstream_gene_variant		3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 38

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:10 Other:1

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Pathogenic:3 Other:1

Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Feb 26, 2024	Published functional studies demonstrate significantly increased GPIb binding in both homozygous and heterozygous states and moderately increased collagen binding (PMID: 23179108); Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 22077376, 1672694, 26345337, 31064749, 30924991, 30817071, 33556167, 35452508, 32573891, 31939074, 27766062, 23179108, 2010538, 36226571) -
Pathogenic, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Feb 21, 2023	The VWF c.3922C>T; p.Arg1308Cys variant (rs61749387), also known as R545C, is reported in the literature in multiple individuals affected with von Willebrand disease type 2B (Ahmad 2013, Baronciani 2005, Freitas 2019, Randi 1991, Ranger 2012). This variant is reported in ClinVar (Variation ID: 289), and is absent from the Genome Aggregation Database, indicating it is not a common polymorphism. The arginine at codon 1308 is moderately conserved, and computational analyses are uncertain whether this variant is neutral or deleterious (REVEL: 0.673). Additionally, other amino acid substitutions at this codon (Leu, Pro, Ser, His) have been reported in individuals with von Willebrand disease type 2B (Baronciani 2005, Hatta 2015, Meyer 1997, Nurden 2006). Based on available information, this variant is considered to be pathogenic. References: Ahmad F et al. Characterisation of mutations and molecular studies of type 2 von Willebrand disease. Thromb Haemost. 2013 Jan;109(1):39-46. PMID: 23179108 Baronciani L et al. Expression studies on a novel type 2B variant of the von Willebrand factor gene (R1308L) characterized by defective collagen binding. J Thromb Haemost. 2005 Dec;3(12):2689-94. PMID: 16246252 Freitas SDS et al. Genetic variants of VWF gene in type 2 von Willebrand disease. Haemophilia. 2019 Mar;25(2):e78-e85. PMID: 30817071 Hatta K et al. A family having type 2B von Willebrand disease with a novel VWF p.R1308S mutation: Detection of characteristic platelet aggregates on peripheral blood smears as the key aspect of diagnosis. Thromb Res. 2015 Oct;136(4):813-7. PMID: 26278967 Meyer D et al. Gene defects in 150 unrelated French cases with type 2 von Willebrand disease: from the patient to the gene. INSERM Network on Molecular Abnormalities in von Willebrand Disease. Thromb Haemost. 1997 Jul;78(1):451-6. PMID: 9198195 Nurden P et al. Impaired megakaryocytopoiesis in type 2B von Willebrand disease with severe thrombocytopenia. Blood. 2006 Oct 15;108(8):2587-95. PMID: 16720832 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. PMID: 2010538 Ranger A et al. Pregnancy in type 2B VWD: a case series. Haemophilia. 2012 May;18(3):406-12. PMID: 22077376 -
Pathogenic, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	Aug 26, 2021	The variant has been reported in multiple individuals with type 2B von Willebrand disease in the published literature (PMIDs: 31939074 (2020), 30817071 (2019), 1419803 (1992), and 2010538 (1991)). It has been shown to result in enhanced sensitivity to ADAMT13-mediated proteolysis (PMID: 26345337 (2015)), increased affinity for GpIbα, increased absence of high molecular weight multimers (PMIDs: 2010538 (1991), 16246252 (2005)), 23179108 (2013), 17155947 (2007)), and a reduced binding to collagen type I and III (PMID: 16246252 (2005)). Therefore, the variant is classified as pathogenic. -
not provided, no classification provided	literature only	Academic Unit of Haematology, University of Sheffield	-	- -

von Willebrand disease type 2 Pathogenic:3

Pathogenic, criteria provided, single submitter	clinical testing;research	ISTH-SSC Genomics in Thrombosis and Hemostasis, KU Leuven, Center for Molecular and Vascular Biology	-	- -
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	Laboratory of Hematology, Radboud University Medical Center	Dec 10, 2020	- -

Von Willebrand disease type 2B Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Versiti Diagnostic Laboratories, Versiti, Inc	Jul 09, 2019	The missense variant VWF c.3922C>T, p.Arg1308Cys (p.R1308C; legacy p.R545C) in exon 28 changes amino acid arginine at codon 1308 to cysteine. The arginine at this residue is not well conserved among species. This amino acid change occurs in the A1 domain, a functional domain that binds GPIb (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 von Willebrand disease (Randi, 1991; Ranger, 2012; Ahmad,2013; Frietas, 2019) and has been observed in multiple patients with type 2B von Willebrand disease in our laboratory cohort. Functional studies of the variant in mammalian cells show an increased affinity for GPIb or enhanced responsiveness with ristoceitin and preferential cleavage of high molecular weight multimers under fluid stress and natured conditions (Ahmad, 2013; Ma, 2015). To date, this variant has not been reported in the general population (gnomAD, Exome Variant Server). In summary, the collective evidence supports VWF c.3922C>T, p.Arg1308Cys as a dominant pathogenic variant for von Willebrand disease type 2B. -
Pathogenic, no assertion criteria provided	literature only	OMIM	May 01, 2010	- -

Hereditary von Willebrand disease Pathogenic:2

Pathogenic, criteria provided, single submitter	research	NIHR Bioresource Rare Diseases, University of Cambridge	Feb 01, 2019	- -
Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Apr 27, 2023	Variant summary: VWF c.3922C>T (p.Arg1308Cys) results in a non-conservative amino acid change located in the von Willebrand factor, type A (IPR002035) of the encoded protein sequence. Four of four in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 251060 control chromosomes. c.3922C>T has been reported in the literature in multiple individuals affected with Von Willebrand Disease (Ahmad_2013, Casonato_2017, Ranger_2012). These data indicate that the variant is very likely to be associated with disease. Experimental evidence evaluating an impact on protein function shows loss of high molecular weight multimers, increased affinity for GPIb and increased stability (Ahmad_2013, Ma_2015). The following publications have been ascertained in the context of this evaluation (PMID: 23179108, 28640903, 26345337, 22077376). Six clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 and all laboratories classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.18
BayesDel_addAF	Pathogenic	0.36	D
BayesDel_noAF	Pathogenic	0.28
CADD	Pathogenic	29
DANN	Pathogenic	1.0
DEOGEN2	Benign	0.40	T
Eigen	Uncertain	0.41
Eigen_PC	Uncertain	0.39
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Pathogenic	0.99	D
M_CAP	Pathogenic	0.69	D
MetaRNN	Pathogenic	0.96	D
MetaSVM	Uncertain	0.47	D
MutationAssessor	Benign	1.4	L
MutationTaster	Benign	1.0	A
PrimateAI	Benign	0.24	T
PROVEAN	Benign	1.1	N
REVEL	Pathogenic	0.67
Sift	Uncertain	0.0040	D
Sift4G	Pathogenic	0.0010	D
Polyphen		0.99	D
Vest4		0.81
MutPred		0.81		Loss of MoRF binding (P = 0.0038);
MVP		0.90
MPC		0.51
ClinPred		0.72	D
GERP RS		4.1
Varity_R		0.32
gMVP		0.80

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: rs61749387; hg19: chr12-6128662;