rs61750117

Variant names:

• chr12-6018629-G-A
• rs61750117
• NM_000552.5:c.4789C>T

Your query was ambiguous. Multiple possible variants found:

• chr12-6018629-G-A
• chr12-6018629-G-C
• chr12-6018629-G-T

Variant summary

Our verdict is Pathogenic. The variant received 15 ACMG points: 15P and 0B. PS3 PS4 PS2_Supporting PP1_Moderate PP4_Moderate PP3 PM2_Supporting

This summary comes from the ClinGen Evidence Repository: NM_000552.4(VWF):c.4789C>T (p.Arg1597Trp) missense variant has been identified in at least 40 probands reported to have type 2A VWD. This variant has been reported in at least 16 probands meeting PP4 laboratory phenotype criteria. (PS4_VeryStrong; PMIDs: 31939074, 22102197, 26791163, 27214365, 22329792, 14630825, 33807613, 23702511, 25689060, 27766062, 1380739, 16961623, 19277422, 22871923, 23355534). At least one patient with this variant displayed excessive mucocutaneous bleeding as well as laboratory phenotypes of very low VWF activity (VWF:RCo 11%), low VWF:RCo/VWF:Ag ratio of 0.28, and loss of high molecular weight multimers, which together are highly specific for VWD type 2A. Additionally, a normal RIPA assay was reported for this patient (PP4_moderate, PMID:25689060 Patient 7). The variant has been reported to segregate with VWD type 2A through >2 affected meioses in at least 2 families (PP1_moderate; PMID:22329792, 27766062). This variant has been identified as a de novo occurrence with unconfirmed parental relationships in at least 1 individual with VWD type 2A (PS2_supporting; PMID:27214365). The Grpmax filtering allele frequency in gnomAD v4.1 is 0 which is lower than the ClinGen VWD VCEP threshold of <0.0001 (PM2_Supporting), a single allele is present in the European (Finnish) population. ADAMTS susceptibility assay, in 293 EBNA cells and hydrodynamic mouse model, expressing recombinant R1597W VWF showed increased susceptibility indicating that this variant has a damaging effect on protein function and the hydrodynamic model is a strong recapitulation human patients with a multimer profile was skewed toward lower molecular weight multimers, reduced VWF:Ag, and reduced thrombus formation. (PMID:16322474, 29186156, 22372972)(PS3). The computational predictor CADD gives a PHRED score of 27.4, which is above the ClinGen VWD VCEP threshold of >20 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 2A based on the ACMG/AMP criteria applied, as specified by the ClinGen VWD VCEP: PP1_moderate, PP4_moderate, PS4_VeryStrong, PP3, PM2_supporting, PS2_supporting, PS3. LINK:https://erepo.genome.network/evrepo/ui/classification/CA114117/MONDO:0015628/081

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 6.8e-7 (0 hom.)
• Consequence: VWF NM_000552.5 missense
• Clinical Significance: Pathogenic reviewed by expert panel P:13 O:2
• Conservation: PhyloP100: 2.56
• Publications: 38 publications found

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]

VWF Gene-Disease associations (from GenCC):

• hereditary von Willebrand disease

  Inheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
• von Willebrand disease 2

  Inheritance: AD, AR Classification: DEFINITIVE, STRONG Submitted by: Laboratory for Molecular Medicine, Labcorp Genetics (formerly Invitae)
• von Willebrand disease type 2B

  Inheritance: AD Classification: DEFINITIVE, SUPPORTIVE Submitted by: ClinGen, Orphanet
• von Willebrand disease 1

  Inheritance: AD Classification: STRONG, SUPPORTIVE Submitted by: Orphanet, Labcorp Genetics (formerly Invitae)
• von Willebrand disease type 2A

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• von Willebrand disease type 2M

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• von Willebrand disease 3

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
• von Willebrand disease type 2N

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Pathogenic. The variant received 15 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000552.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	VWF	NM_000552.5	MANE Select	c.4789C>T	p.Arg1597Trp	missense	Exon 28 of 52	NP_000543.3	P04275-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	VWF	ENST00000261405.10	TSL:1 MANE Select	c.4789C>T	p.Arg1597Trp	missense	Exon 28 of 52	ENSP00000261405.5	P04275-1
	VWF	ENST00000895679.1		c.4789C>T	p.Arg1597Trp	missense	Exon 29 of 53	ENSP00000565738.1
	VWF	ENST00000895680.1		c.2967+10713C>T		intron	N/A	ENSP00000565739.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 6.84e-7 AC: 1 AN: 1461766 Hom.: 0 Cov.: 41 AF XY: 0.00 AC XY: 0 AN XY: 727166

African (AFR) AF: 0.00 AC: 0 AN: 33476

American (AMR) AF: 0.00 AC: 0 AN: 44724

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26136

East Asian (EAS) AF: 0.00 AC: 0 AN: 39700

South Asian (SAS) AF: 0.00 AC: 0 AN: 86254

European-Finnish (FIN) AF: 0.0000187 AC: 1 AN: 53380

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5764

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 1111948

Other (OTH) AF: 0.00 AC: 0 AN: 60384

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000378

ClinVar

ClinVar submissions

Significance: Pathogenic

Revision: reviewed by expert panel

Pathogenic	VUS	Benign	Condition
5	-	-	not provided (6)
2	-	-	Hereditary von Willebrand disease (3)
2	-	-	von Willebrand disease type 2 (2)
2	-	-	Von Willebrand disease type 2A (2)
1	-	-	Inborn genetic diseases (1)
1	-	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.39
BayesDel_addAF	Pathogenic	0.43	D
BayesDel_noAF	Pathogenic	0.37
CADD	Pathogenic	28
DANN	Pathogenic	1.0
DEOGEN2	Uncertain	0.67	D
Eigen	Pathogenic	0.87
Eigen_PC	Pathogenic	0.74
FATHMM_MKL	Uncertain	0.94	D
LIST_S2	Pathogenic	0.99	D
M_CAP	Pathogenic	0.43	D
MetaRNN	Pathogenic	0.99	D
MetaSVM	Pathogenic	1.0	D
MutationAssessor	Pathogenic	4.1	H
PhyloP100		2.6
PrimateAI	Uncertain	0.55	T
PROVEAN	Uncertain	-2.6	D
REVEL	Pathogenic	0.75
Sift	Uncertain	0.0020	D
Sift4G	Pathogenic	0.0010	D
Polyphen		1.0	D
Vest4		0.85
MutPred		0.86		Gain of catalytic residue at G1595 (P = 0.0166)
MVP		0.89
MPC		0.52
ClinPred		0.98	D
GERP RS		5.0
Varity_R		0.92
gMVP		0.95
Mutation Taster		=12/88	disease causing (ClinVar)

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

Other links and lift over

dbSNP: rs61750117; hg19: chr12-6127795; COSMIC: COSV54616988; COSMIC: COSV54616988;