12-6019297-C-T

Position:

• chr12-6019297-C-T

Variant summary

Our verdict is Pathogenic. Variant got 13 ACMG points: 13P and 0B. PS4 PP1_Moderate PP3 PP4 PM2_Supporting PS3

This summary comes from the ClinGen Evidence Repository: NM_000552.5(VWF):c.4121G>A is a missense variant predicted to cause substitution of Arginine by Histidine at amino acid 1374. This variant is absent from gnomAD v4.1 (PM2_Supporting). The computational predictor computational predictor REVEL gives a score of 0.879, which is above the ClinGen VWD VCEP threshold of >0.644 and predicts a damaging effect on VWF function (PP3). Family M proband I.1 (PMID:7734373) with this variant displayed excessive mucocutaneous bleeding as well as laboratory phenotypes of a complete set of vWF multimers present but relative reduction of the larger multimers, low VWF:RCo/VWF:Ag ratio (<0.4), and VWF:RCo <3-10 IU/dl (PP4). Additional consistent phenotypes included FVIII activity consistent with VWF antigen. This variant has been reported in >8 additional probands with consistent laboratory phenotypes (PS4_VeryStrong; PMIDs: 7620154, 9031470, 11154147, 7734373, 38315875, 28083987, 28536718). The variant has been reported to segregate with VWD type [2A/2M] through at least 2 affected meioses in at least 2 families (PP1_Moderate; PMID:7734373, PMID:7620154). A platelet binding assay in COS-7 cells expressing the recombinant VWF variant showed decreased binding indicating that this variant has a damaging effect on protein function relative to the rVWF wild-type control (PMID:10845912, PS3). In summary, this variant meets the criteria to be classified as Pathogenic for autosomal dominant VWD type 2 based on the ACMG/AMP criteria applied, as specified by the ClinGen VWD VCEP: PS3, PS4_VeryStrong, PM2_supporting, PP1_Moderate, PP3, PP4.Recent analysis (PMID:38315875) reports that patients with R1374H have severely reduced VWF:GPIbR/VWF:Ag and a modest decrease in VWF:CB/VWF:Ag ratios. This can be explained by 2 defects, (1) a reduced VWF A1 domain binding to GPIb and (2) an altered VWF multimeric pattern in which patients showed a slightly diminished proportion of HMWM and little increase of low and intermediate multimers. They hypothesize that the slight reduction of HMWM (characteristic of type 2A) is primarily responsible for marginally reduced VWF:CB/VWF:Ag ratio, whereas the markedly reduced VWF:GPIbR/VWF:Ag ratio is mainly because of a type 2M defect (diminished binding of A1-GPIb) and propose a subtype designation of 2M/2A for this variant. LINK:https://erepo.genome.network/evrepo/ui/classification/CA228541/MONDO:0013304/081

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000014 (0 hom.)
• Consequence: VWF ENST00000261405.10 missense
• Clinical Significance: Pathogenic reviewed by expert panel P:14 O:1
• Conservation: PhyloP100: 6.75

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 13 ACMG points.

• 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.4121G>A	p.Arg1374His	missense_variant	28/52	ENST00000261405.10	NP_000543.3
VWF	XM_047429501.1	c.4121G>A	p.Arg1374His	missense_variant	28/52		XP_047285457.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
VWF	ENST00000261405.10	c.4121G>A	p.Arg1374His	missense_variant	28/52	1	NM_000552.5	ENSP00000261405	P1
VWF	ENST00000538635.5	n.421-25363G>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000137 AC: 2 AN: 1461642 Hom.: 0 Cov.: 38 AF XY: 0.00000138 AC XY: 1 AN XY: 727132

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: 0.00000180

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:14 Other:1

Revision: reviewed by expert panel

Submissions by phenotype

von Willebrand disease type 2 Pathogenic:5

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	clinical testing	Genetics and Molecular Pathology, SA Pathology	Jan 19, 2022	- -
Pathogenic, criteria provided, single submitter	clinical testing	ISTH-SSC Genomics in Thrombosis and Hemostasis, KU Leuven, Center for Molecular and Vascular Biology	-	- -
Pathogenic, criteria provided, single submitter	research	Laboratory of Hematology, Radboud University Medical Center	Dec 28, 2021	- -
Pathogenic, criteria provided, single submitter	research	NIHR Bioresource Rare Diseases, University of Cambridge	Feb 01, 2019	- -

not provided Pathogenic:4 Other:1

Pathogenic, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	Apr 06, 2021	In the published literature, this variant has been reported as a pathogenic variant associated with Types 1, 2A, and 2M von Willebrand Disease (PMID: 22329792 (2012), 25696906 (2014)). Functional studies identify R1374H as a deleterious change located in the A1 domain that has been observed in patients with a loss of high molecular weight multimers, increased mature VWF turnover, and loss of platelet binding (PMID: 7620154 (1995), 16985174 (2007), 23340442 (2013), 25185554 (2013)). Based on the available information, this variant is classified as pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Aug 03, 2023	Published functional studies demonstrate a damaging effect, including decreased or absent platelet binding (Hilbert et al., 1995; Tischer et al., 2014); Not observed at significant frequency in large population cohorts (gnomAD); Variant considered pathogenic by a well-established clinical consortium and/or database; In silico analysis supports that this missense variant does not alter protein structure/function; Also known as p.R611H using alternate nomenclature; This variant is associated with the following publications: (PMID: 31064749, 34758185, 33556167, 31589614, 25696906, 7620154, 22329792, 26879396, 23340442, 26988807, 7734373, 16985174, 29924855, 26200876, 23349392, 18805962, 19277422, 19404524, 18384353, 17087728, 11776047, 10845912, 25185554) -
Pathogenic, criteria provided, single submitter	clinical testing	Mayo Clinic Laboratories, Mayo Clinic	Mar 28, 2024	PP1, PP3, PP5, PM2_moderate, PM5, PS3, PS4_moderate -
not provided, no classification provided	literature only	Academic Unit of Haematology, University of Sheffield	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Sep 11, 2023	The VWF c.4121G>A; p.Arg1374His variant (rs61750072), also known as R611H, is reported in the literature in multiple individuals and segregates with disease in families affected with von Willebrand disease type 2A or type 2M (Borras 2017, Castaman 1995, Corrales 2009, Flood 2013, Goodeve 2007, Hilbert 1995). This variant is also reported in ClinVar (Variation ID: 100330). It is absent from the Genome Aggregation Database, indicating it is not a common polymorphism. The arginine at codon 1374 is highly conserved, and computational analyses predict that this variant is deleterious (REVEL: 0.879). Functional analyses of the variant protein show decreased multimer formation and a loss of platelet binding (Ajzenberg 2000, Hilbert 1995, Tischer 2014). Additionally, other amino acid substitutions at this codon (Cys, Leu, Ser) have been reported in individuals with von Willebrand disease type 2A or type 2M and are considered pathogenic (Borras 2017, Corrales 2009, Flood 2013, Hilbert 1995, Veyradier 2016). Based on available information, this variant is considered to be pathogenic. References: Ajzenberg N et al. Effect of recombinant von Willebrand factor reproducing type 2B or type 2M mutations on shear-induced platelet aggregation. Blood. 2000 Jun 15;95(12):3796-803. PMID: 10845912. Borras N et al. Molecular and clinical profile of von Willebrand disease in Spain (PCM-EVW-ES): comprehensive genetic analysis by next-generation sequencing of 480 patients. Haematologica. 2017 Dec;102(12):2005-2014. PMID: 28971901. Castaman G et al. A novel candidate mutation (Arg611-->His) in type I 'platelet discordant' von Willebrand's disease with desmopressin-induced thrombocytopenia. Br J Haematol. 1995 Mar;89(3):656-8. PMID: 7734373. Corrales I et al. Rapid molecular diagnosis of von Willebrand disease by direct sequencing. Detection of 12 novel putative mutations in VWF gene. Thromb Haemost. 2009 Mar;101(3):570-6. PMID: 19277422. Flood VH et al. Collagen binding provides a sensitive screen for variant von Willebrand disease. Clin Chem. 2013 Apr;59(4):684-91. PMID: 23340442. Goodeve A et al. Phenotype and genotype of a cohort of families historically diagnosed with type 1 von Willebrand disease in the European study, Molecular and Clinical Markers for the Diagnosis and Management of Type 1 von Willebrand Disease (MCMDM-1VWD). Blood. 2007 Jan 1;109(1):112-21. PMID: 16985174. Hilbert L et al. Identification of two mutations (Arg611Cys and Arg611His) in the A1 loop of von Willebrand factor (vWF) responsible for type 2 von Willebrand disease with decreased platelet-dependent function of vWF. Blood. 1995 Aug 1;86(3):1010-8. PMID: 7620154. Tischer A et al. Misfolding of vWF to pathologically disordered conformations impacts the severity of von Willebrand disease. Biophys J. 2014 Sep 2;107(5):1185-1195. PMID: 25185554. Veyradier A et al. A Laboratory Phenotype/Genotype Correlation of 1167 French Patients From 670 Families With von Willebrand Disease: A New Epidemiologic Picture. Medicine (Baltimore). 2016 Mar;95(11):e3038. PMID: 26986123. -

Hereditary von Willebrand disease Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Dec 01, 2022	Variant summary: VWF c.4121G>A (p.Arg1374His) results in a non-conservative amino acid change located in the von Willebrand factor, type A domain (IPR002035) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 250960 control chromosomes. c.4121G>A has been widely reported in the literature as a heterozygous genotype in a dominant transmission in multiple individuals affected with Von Willebrand Disease (example, Hilbert_1995, Boender_2018). These data indicate that the variant is very likely to be associated with disease. Several publicatios report experimental evidence evaluating an impact on protein function (example, Hilbert_1995). The most pronounced variant effect results in a significant decrease in the high MW multimeric forms. Risocetin and Botrocetin induced binding of mutated rvWFs to platelets were also markedly decreased. Seven clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -
Pathogenic, criteria provided, single submitter	research	NIHR Bioresource Rare Diseases, University of Cambridge	Feb 01, 2019	- -

Prolonged bleeding time;C1458140:Abnormal bleeding Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Centre for Mendelian Genomics, University Medical Centre Ljubljana

Jan 01, 2017

- -

von Willebrand disease type 1;C1282968:Von Willebrand disease type 2A;C1282974:von Willebrand disease type 2M Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Versiti Diagnostic Laboratories, Versiti, Inc

Apr 25, 2019

The missense variant VWF c.4121G>A, p.Arg1374His (p.R1374; legacy p.R611H) in exon 28 changes amino acid arginine at codon 1374 to histidine. The arginine at this residue is highly conserved among species. This amino acid change occurs in the A1 domain, a functional domain that binds platelets (GP1b) and collagen (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 variant has been previously reported in patients with type 2A (Goodeve, 2007; Corrales, 2009; Flood, 2013; Perez-Rodriguez, 2018), type 2M or type 1 VWD (Ajzenberg, 2000; Rayes, 2007; Flood, 2013). This variant has been observed in multiple patients with type 2 VWD in our laboratory cohort. Functional studies of the variant in mammalian cells demonstrated decreased expression and a decrease in the high molecular weight multimers (Hilbert, 1995; Ajenberg, 2000). To date, this variant has not been reported in the general population (GnomAD). In summary, the collective evidence supports VWF c.4121G>A, p.Arg1374His as a pathogenic variant for type 2 VWD. -

von Willebrand disease type 1 Pathogenic:1

Pathogenic, criteria provided, single submitter

research

Laboratory of Hematology, Radboud University Medical Center

Dec 28, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.32
BayesDel_addAF	Pathogenic	0.57	D
BayesDel_noAF	Pathogenic	0.58
CADD	Pathogenic	29
DANN	Pathogenic	1.0
DEOGEN2	Uncertain	0.61	D
Eigen	Pathogenic	0.92
Eigen_PC	Pathogenic	0.80
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Uncertain	0.96	D
M_CAP	Pathogenic	0.86	D
MetaRNN	Pathogenic	0.97	D
MetaSVM	Pathogenic	1.0	D
MutationAssessor	Pathogenic	3.8	H
MutationTaster	Benign	1.0	D
PrimateAI	Benign	0.46	T
PROVEAN	Benign	-1.4	N
REVEL	Pathogenic	0.88
Sift	Pathogenic	0.0	D
Sift4G	Pathogenic	0.0	D
Polyphen		1.0	D
Vest4		0.79
MutPred		0.81		Gain of catalytic residue at K1371 (P = 0.0023);
MVP		0.93
MPC		1.0
ClinPred		1.0	D
GERP RS		5.0
Varity_R		0.69
gMVP		0.84

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: rs61750072; hg19: chr12-6128463; COSMIC: COSV54615184; COSMIC: COSV54615184;