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.3970G>A (p.Gly1324Ser)

CA114147

300 (ClinVar)

Gene: VWF
Condition: von Willebrand disease type 2M
Inheritance Mode: Autosomal dominant inheritance
UUID: 8c83fcdc-3afc-44f1-a269-c2f1e73f9298
Approved on: 2024-08-13
Published on: 2024-08-13

HGVS expressions

NM_000552.4:c.3970G>A
NM_000552.4(VWF):c.3970G>A (p.Gly1324Ser)
NC_000012.12:g.6019448C>T
CM000674.2:g.6019448C>T
NC_000012.11:g.6128614C>T
CM000674.1:g.6128614C>T
NC_000012.10:g.5998875C>T
NG_009072.1:g.110223G>A
NG_009072.2:g.110223G>A
ENST00000261405.10:c.3970G>A
ENST00000261405.9:c.3970G>A
ENST00000538635.5:n.421-25514G>A
NM_000552.3:c.3970G>A
NM_000552.5:c.3970G>A
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Pathogenic

Met criteria codes 6
PP4_Moderate PM2_Supporting PS3 PP1 PP3 PS4_Moderate
Not Met criteria codes 1
PM5

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.3970G>A (p.Gly1324Ser) variant is a missense variant predicted to cause substitution of Glycine by Serine at amino acid 1324. At least 1 patient with this variant displayed excessive mucocutaneous bleeding as well as laboratory phenotypes of a normal multimer pattern, low VWF:RCo/VWF:Ag ratio, and a decreased GP1b binding assay, which together are highly specific for VWD type 2M (PP4_moderate, PMID: 30084138). The variant has been reported to segregate with VWD type 2M through 2 affected meioses from 1 family (PP1; PMID: 29341351). At least 3 additional VWD type 2M probands have been reported with this variant (PMIDs: 29341351, 22102201, 1409710; PS4_moderate). The Grpmax filtering allele frequency in gnomAD v4.1 is 0.000003650 (based on 2/91074 alleles in the South Asian population), which is lower than the ClinGen VWD VCEP threshold of <0.0001 (PM2_Supporting). The computational predictor REVEL gives a score of 0.718, which is above the ClinGen VWD VCEP threshold of >0.644 and predicts a damaging effect on VWF function (PP3). A platelet binding assay in COS-7 cells expressing recombinant VWF showed decreased binding indicating that this variant has a damaging effect on protein function. In a direct binding assay, the ristocetin-induced binding of rvWF(G1324S) to platelets was markedly reduced compared with rvWF(wt). (PMID: 1409710) (PS3). In summary, this variant meets the criteria to be classified as Pathogenic for autosomal dominant VWD type 2M based on the ACMG/AMP criteria applied, as specified by the ClinGen VWD VCEP: PS3, PM2_supporting, PP1, PP3, PP4_moderate, PS4_moderate. (VCEP specifications version Pilot; date of approval).
Met criteria codes
PP4_Moderate
At least 1 patient with this variant displayed excessive mucocutaneous bleeding as well as laboratory phenotypes of a normal multimer pattern, low VWF:RCo/VWF:Ag ratio, and a decreased GP1b binding assay, which together are highly specific for VWD type 2M (PP4_moderate PMID: 30084138). Additional consistent phenotypes were also reported in the patient including FVIII activity consistent with VWF antigen level.
PM2_Supporting
The Grpmax filtering allele frequency in gnomAD v4.1 is 0.000003650 (based on 2/91074 alleles in the South Asian population), which is lower than the ClinGen VWD VCEP threshold of <0.0001 (PM2_Supporting).
PS3
A platelet binding assay in COS-7 cells expressing recombinant VWF showed decreased binding indicating that this variant has a damaging effect on protein function. In a direct binding assay, the ristocetin-induced binding of rvWF(G1324S) to platelets was markedly reduced compared with rvWF(wt). (PMID: 1409710) (PS3).
PP1
The variant has been reported to segregate with VWD type 2M through 2 affected meioses from 1 family (PP1; PMID: 29341351).
PP3
The computational predictor REVEL gives a score of 0.718, 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 0.00 for all splicing types, indicating that the variant has no impact on splicing.
PS4_Moderate
At least 3 additional VWD type 2M probands have been reported with this variant (PMIDs: 29341351, 22102201, 1409710; PS4_moderate)
Not Met criteria codes
PM5
Another missense variant in the same codon has been reported in a patient with VWD type 2 [c.3971G>C, p.Gly1324Ala] (PMID: 9198195). However, this is not considered here to avoid circularity (PM5 not met).
Curation History
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