The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
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Variant: NM_000419.5:c.3091del

CA915940322

Gene: ITGA2B
Condition: Glanzmann thrombasthenia
Inheritance Mode: Autosomal recessive inheritance
UUID: f12400d0-86e4-4239-befa-8c185f729db0

HGVS expressions

NM_000419.5:c.3091del
NC_000017.11:g.44372396del
CM000679.2:g.44372396del
NC_000017.10:g.42449764del
CM000679.1:g.42449764del
NC_000017.9:g.39805290del
NG_008331.1:g.22113del
ENST00000262407.6:c.3091del
ENST00000648408.1:n.2405del
ENST00000262407.5:c.3091del
ENST00000587295.5:n.284del
ENST00000588098.1:n.68del
NM_000419.3:c.3091del
NM_000419.4:c.3091del

Likely Pathogenic

Met criteria codes 4
PM3 PM4 PP4_Strong PM2_Supporting

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
Platelet Disorders VCEP
The NM_000419.5(ITGA2B):c.3091del variant causes a frameshift and subsequent stop loss, Leu1031TrpfsTer97. This results in the addition of 90 amino acids to the ITGA2B protein, beyond the cytoplasmic domain (PM4). This variant is absent from gnomAD v2.1.1 (PM2_Supporting). At least one patient (Patient GT10 in PMID:25373348) with this variant displayed mucocutaneous bleeding and impaired aggregation with all agonists except ristocetin, which is highly specific for Glanzmann thrombasthenia. Additionally, αIIbβ3 surface expression was severely reduced, as measured by flow cytometry (PP4_strong). GT10 of PMID: 25373348 is compound heterozygous for the paternal c.1210+105A>G (classified Likely Pathogenic by the PD-EP) and the maternal c.3091delC variants (PM3). In summary this variant meets criteria to be classified as Likely Pathogenic for autosomal recessive Glanzmann Thrombasthenia based on the ACMG/AMP criteria applied, as specified by the ClinGen PD VCEP: PP4_strong, PM2_supporting, PM3, PM4. (VCEP specifications version 2; date of approval 03/15/2022)
Met criteria codes
PM3
GT10 of PMID: 25373348 is compound heterozygous for the paternal c.1210+105A>G (classified Likely Pathogenic by the PD-EP) and the maternal c.3091delC variants (1pt; PM3).
PM4
The c.3091del variant causes a frameshift and subsequent stop loss, Leu1031TrpfsTer97. This results in the addition of 90 amino acids to the ITGA2B protein, beyond the cytoplasmic domain.
PP4_Strong
At least one patient (Patient GT10 in PMID:25373348) with this variant displayed mucocutaneous bleeding and impaired aggregation with all agonists except ristocetin, which is highly specific for Glanzmann thrombasthenia. Additionally, αIIbβ3 surface expression was severely reduced, as measured by flow cytometry. ITGA2B and ITGB3 were sequenced across all exons and intron/exon boundaries (PP4_strong).
PM2_Supporting
This variant is absent from gnomAD v2.1.1 (PM2_Supporting).
Approved on: 2022-04-07
Published on: 2022-12-07
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