The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
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Variant: NM_000552.4(VWF):c.3437A>G (p.Tyr1146Cys)

CA228408

31009 (ClinVar)

Gene: VWF
Condition: von Willebrand disease type 2A
Inheritance Mode: Autosomal dominant inheritance
UUID: a771d414-f2f6-4f3d-b08a-bb4f6c8303ef
Approved on: 2024-08-13
Published on: 2024-08-19

HGVS expressions

NM_000552.4:c.3437A>G
NM_000552.4(VWF):c.3437A>G (p.Tyr1146Cys)
NC_000012.12:g.6022841T>C
CM000674.2:g.6022841T>C
NC_000012.11:g.6132007T>C
CM000674.1:g.6132007T>C
NC_000012.10:g.6002268T>C
NG_009072.1:g.106830A>G
NG_009072.2:g.106830A>G
ENST00000261405.10:c.3437A>G
ENST00000261405.9:c.3437A>G
ENST00000538635.5:n.421-28907A>G
NM_000552.3:c.3437A>G
NM_000552.5:c.3437A>G
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Pathogenic

Met criteria codes 5
PS3 PS4_Very Strong PP4 PP3 PM2_Supporting
Not Met criteria codes 1
PP1

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen von Willebrand Disease Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for VWF Version 1.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
von Willebrand Disease VCEP
The NM_000552.4(VWF):c.3437A>G (p.Tyr1146Cys) missense variant has been reported in at least 22 VWD type 2A patients. The Grpmax filtering allele frequency in gnomAD v4.1 is 0 (based on 1/37812 alleles in the African/African-American population), which is lower than the ClinGen VWD VCEP threshold of<0.0001 (PM2_Supporting). The computational predictor REVEL gives a score of 0.872, which is above the ClinGen VWD VCEP threshold of >0.644 and predicts a damaging effect on VWF function (PP3). At least 1 patient with this variant displayed excessive mucocutaneous bleeding as well as a laboratory phenotypes of low VWF activity (VWF:RCo 16, VWF:CB 7) and VWF:Ag of 20 for a low VWF:CB activity/VWF:Ag ratio of 0.35, which is specific for VWD type 2A. (PP4; PMID: 24598842). Eight additional VWD 2A patients, with confirmatory lab values including very low VWF:RCo, low VWF:GPIb, and or low VWF activity/ VWF:Ag ratio, have been reported (PMIDs: 22871923, 16985174, 35452508, 20351307; PS4_VeryStrong). Multimer analysis in 293 cells expressing recombinant variant VWF showed reduced high molecular weight multimers indicating that this variant has a damaging effect on protein function (PMID: 20351307 Figure 3, PMID: 27533707 Figure 2; PS3). 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: PS4_VeryStrong, PS3, PM2_supporting, PP3, PP4.
Met criteria codes
PS3
Multimer analysis in 293 cells expressing recombinant variant VWF showed reduced high molecular weight multimers indicating that this variant has a damaging effect on protein function (PMID: 20351307 Figure 3, PMID: 27533707 Figure 2; PS3).
PS4_Very Strong
At least 22 patients, heterozygous for the variant, have been reported with type 2A. Eight are included here with confirmatory lab values including very low VWF:RCo, low VWF:GPIb, and or low VWF activity/ VWF:Ag ratio (PMIDs: 22871923, 16985174, 35452508, 20351307; PS4_VeryStrong).
PP4
At least 1 patient with this variant displayed excessive mucocutaneous bleeding as well as a laboratory phenotypes of low VWF activity (VWF:RCo 16, VWF:CB 7) and VWF:Ag of 20 for a low VWF:CB activity/VWF:Ag ratio of 0.35, which is specific for VWD type 2A. (PP4; PMID: 24598842).
PP3
The computational predictor REVEL gives a score of 0.872, which is above the ClinGen VWD VCEP threshold of >0.644 and predicts a damaging effect on VWF function (PP3). The computational splicing predictor SpliceAI gives a score of 0.01 for splice acceptor gain, indicating that the variant likely has no impact on splicing.
PM2_Supporting
The Grpmax filtering allele frequency in gnomAD v4.1 is 0 (based on 1/37812 alleles in the African/African-American population), which is lower than the ClinGen VWD VCEP threshold of<0.0001 (PM2_Supporting).
Not Met criteria codes
PP1
The variant has been reported to segregate with VWD type 2A through just 1 affected meiosis from family 16 (PP1_NotMet; PMID: 30722078).
Curation History
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