12-6019474-C-T

Variant summary

Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PP4_ModeratePP3PM2_SupportingPS4_Moderate

This summary comes from the ClinGen Evidence Repository: The missense variant NM_000552.5(VWF):c.3944G>A (p.Arg1315His) is a rare variant which occurs at a Grpmax filtering allele frequency in gnomAD v4.1 is 0.00002255 (based on 4/60004 alleles in the Admixed American population), which is lower than the ClinGen VWD VCEP threshold of <0.0001 (PM2_supporting). The computational predictor REVEL gives a score of 0.815, which is above the ClinGen VWD VCEP threshold of >0.644 and predicts a damaging effect on VWF function (PP3). Portuguese patient P30, with this variant, (PMID:26988807) displayed excessive mucocutaneous bleeding (bleeding score 7) as well as a laboratory phenotype of normal multimers, low VWF:RCo/VWF:Ag ratio (VWF:RCo 11%, VWF:Ag 16%, ratio 0.69) and an abnormal collagen binding assay (VWF:CB 19%), which together are highly specific for VWD type 2M (PP4_moderate). At least 3 additional probands have been reported with this variant and VWD reported as type 1 (but with VWF:RCo/VWF:Ag ratio <0.7) or type 2M (PMID:26986123, 25689060, 16985174; PS4_moderate). In summary, the variant meets the criteria to be classified as Likely Pathogenic for von Willebrand disease type 2M based on the ACMG/AMP criteria applied, as specified by the ClinGen VWD VCEP: PM2_supporting, PP3, PP4_moderate, PS4_moderate. LINK:https://erepo.genome.network/evrepo/ui/classification/CA228504/MONDO:0015630/081

Frequency

Genomes: 𝑓 0.0000066 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000018 ( 0 hom. )

Consequence

VWF
NM_000552.5 missense

Scores

12
4
3

Clinical Significance

Likely pathogenic reviewed by expert panel P:5U:1O:1

Conservation

PhyloP100: 6.99
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Likely_pathogenic. Variant got 6 ACMG points.

PS4
For more information check the summary or visit ClinGen Evidence Repository.
PM2
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
VWFNM_000552.5 linkuse as main transcriptc.3944G>A p.Arg1315His missense_variant 28/52 ENST00000261405.10 NP_000543.3 P04275-1
VWFXM_047429501.1 linkuse as main transcriptc.3944G>A p.Arg1315His missense_variant 28/52 XP_047285457.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
VWFENST00000261405.10 linkuse as main transcriptc.3944G>A p.Arg1315His missense_variant 28/521 NM_000552.5 ENSP00000261405.5 P04275-1
VWFENST00000538635.5 linkuse as main transcriptn.421-25540G>A intron_variant 4

Frequencies

GnomAD3 genomes
AF:
0.00000657
AC:
1
AN:
152192
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0000654
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.0000239
AC:
6
AN:
250994
Hom.:
0
AF XY:
0.0000295
AC XY:
4
AN XY:
135700
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.0000867
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.0000544
Gnomad SAS exome
AF:
0.0000327
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.000163
GnomAD4 exome
AF:
0.0000178
AC:
26
AN:
1461606
Hom.:
0
Cov.:
38
AF XY:
0.0000193
AC XY:
14
AN XY:
727108
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.0000671
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000252
Gnomad4 SAS exome
AF:
0.0000116
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000126
Gnomad4 OTH exome
AF:
0.000116
GnomAD4 genome
AF:
0.00000657
AC:
1
AN:
152192
Hom.:
0
Cov.:
32
AF XY:
0.0000135
AC XY:
1
AN XY:
74342
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.0000654
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.0000847
Hom.:
0
Bravo
AF:
0.000151
ESP6500AA
AF:
0.00
AC:
0
ESP6500EA
AF:
0.000116
AC:
1
ExAC
AF:
0.0000330
AC:
4

ClinVar

Significance: Likely pathogenic
Submissions summary: Pathogenic:5Uncertain:1Other:1
Revision: reviewed by expert panel
LINK: link

Submissions by phenotype

not provided Pathogenic:2Uncertain:1Other:1
Likely pathogenic, criteria provided, single submitterclinical testingCenter for Genomic Medicine, Rigshospitalet, Copenhagen University HospitalJul 31, 2024- -
Likely pathogenic, criteria provided, single submitterclinical testingARUP Laboratories, Molecular Genetics and Genomics, ARUP LaboratoriesJun 28, 2023The VWF c.3944G>A; p.Arg1315His variant (rs61749396) is reported in the literature in multiple individuals affected with Von Willebrand disease types 1, 2m and 3 (Elayaperumal 2018, Goodeve 2007, Veyradier 2016). This variant is also reported in ClinVar (Variation ID: 100311) and is found in the general population with an overall allele frequency of 0.002% (6/250,994 alleles) in the Genome Aggregation Database. Additionally, other amino acid substitutions at this codon (Cys, Gly, Leu, Pro) have been reported in individuals with VWF and are considered disease causative (Elayaperumal 2018, Goodeve 2007, Veyradier 2016). Computational analyses predict that this variant is deleterious (REVEL: 0.815). Based on available information, this variant is considered to be likely pathogenic. References: Elayaperumal S et al. Type-3 von Willebrand disease in India-Clinical spectrum and molecular profile. Haemophilia. 2018 Nov;24(6):930-940. PMID: 29984440. 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. 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. -
Uncertain significance, criteria provided, single submitterclinical testingQuest Diagnostics Nichols Institute San Juan CapistranoSep 12, 2022The frequency of this variant in the general population, 0.000087 (3/34586 chromosomes, http://gnomad.broadinstitute.org), is uninformative in assessment of its pathogenicity. In the published literature, the variant has been reported in individuals affected with Type 1 von Willebrand disease (vWD) (PMID: 16985174 (2007)), Type 2 vWD with a collagen binding defect (PMID: 26986123 (2016), 28083987 (2017)), and Type 3 vWD (PMID: 29984440 (2018)). Analysis of this variant using bioinformatics tools for the prediction of the effect of amino acid changes on protein structure and function yielded predictions that this variant is damaging. Based on the available information, we are unable to determine the clinical significance of this variant. -
not provided, no classification providedliterature onlyAcademic Unit of Haematology, University of Sheffield-- -
von Willebrand disease type 2 Pathogenic:1
Likely pathogenic, criteria provided, single submitterclinical testingGenetics and Molecular Pathology, SA PathologyJul 26, 2019- -
Inborn genetic diseases Pathogenic:1
Pathogenic, criteria provided, single submitterclinical testingAmbry GeneticsJun 14, 2024The c.3944G>A (p.R1315H) alteration is located in exon 28 (coding exon 27) of the VWF gene. This alteration results from a G to A substitution at nucleotide position 3944, causing the arginine (R) at amino acid position 1315 to be replaced by a histidine (H). for autosomal dominant, autosomal recessive Von Willebrand disease; however, its clinical significance for autosomal dominant von Willebrand disease Type 2B is uncertain Based on data from gnomAD, the A allele has an overall frequency of 0.002% (6/250994) total alleles studied. The highest observed frequency was 0.016% (1/6124) of Other alleles. This variant has been identified in the heterozygous state or in conjunction with other VWF variants in individuals with features consistent with various forms of von Willebrand disease; in at least one instance, the variants were identified in trans (&Aacute;lvarez-Laderas, 2015; Fidalgo, 2017; Elayaperumal, 2018). Two other alterations at the same codon, c.3943C>T (p.R1315C) and c.3944G>T (p.R1315L), have been detected in multiple individuals with autosomal dominant/autosomal recessive loss of function von Willebrand disease forms (Baronciani, 2006; Elayaperumal, 2018). This amino acid position is well conserved in available vertebrate species. Based on internal structural analysis, R1315H is deleterious. The variant is moderately destabilizing to the local structure. The variant is not on an interface. The variant has no nearby pathogenic variants and has no nearby benign variants (Ribba, 2001; Ambry internal data). This alteration is predicted to be deleterious by in silico analysis. Based on the available evidence, this alteration is classified as pathogenic. -
von Willebrand disease type 1 Pathogenic:1
Likely pathogenic, no assertion criteria providedclinical testingZotz-Klimas Genetics Lab, MVZ Zotz KlimasOct 09, 2023- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.32
BayesDel_addAF
Pathogenic
0.32
D
BayesDel_noAF
Pathogenic
0.41
CADD
Pathogenic
28
DANN
Pathogenic
1.0
DEOGEN2
Uncertain
0.50
T
Eigen
Pathogenic
0.84
Eigen_PC
Pathogenic
0.75
FATHMM_MKL
Pathogenic
0.99
D
LIST_S2
Uncertain
0.96
D
M_CAP
Pathogenic
0.47
D
MetaRNN
Pathogenic
0.87
D
MetaSVM
Pathogenic
0.90
D
MutationAssessor
Pathogenic
3.8
H
PrimateAI
Uncertain
0.54
T
PROVEAN
Benign
-2.0
N
REVEL
Pathogenic
0.81
Sift
Pathogenic
0.0
D
Sift4G
Uncertain
0.0020
D
Polyphen
0.98
D
Vest4
0.75
MVP
0.92
MPC
1.0
ClinPred
0.97
D
GERP RS
5.0
Varity_R
0.60
gMVP
0.88

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: rs61749396; hg19: chr12-6128640; API