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.3092del

CA915940323

Gene: ITGA2B
Condition: Glanzmann thrombasthenia
Inheritance Mode: Autosomal recessive inheritance
UUID: 5b384cb7-ff65-4031-a5b8-0ac479f14ece

HGVS expressions

NM_000419.5:c.3092del
NC_000017.11:g.44372392del
CM000679.2:g.44372392del
NC_000017.10:g.42449760del
CM000679.1:g.42449760del
NC_000017.9:g.39805286del
NG_008331.1:g.22114del
ENST00000262407.6:c.3092del
ENST00000648408.1:n.2406del
ENST00000262407.5:c.3092del
ENST00000587295.5:n.285del
ENST00000588098.1:n.69del
NM_000419.3:c.3092del
NM_000419.4:c.3092del

Likely Pathogenic

Met criteria codes 4
PM3_Supporting PM2_Supporting PP4_Strong PM4

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.3092del (p.Leu1031ArgfsTer?) variant causes a frameshift and subsequent stop loss. This results in the addition of 90 amino acids to the ITGA2B protein, beyond the cytoplasmic domain (PM4). The variant is absent from gnomAD v2.1.1 (PM2_Supporting). At least one patient (Patient GT11 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 reduced between 5% and 20% and function was pathological, as measured by flow cytometry (PP4_strong). This patient is compound heterozygous for the maternal c.3092del variant and Leu214Pro (classified Pathogenic by the PD-EP), without confirmation of trans phase (PM3_supporting). 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_supporting, PM4. (VCEP specifications version 2; date of approval xx/xx/xxxx)
Met criteria codes
PM3_Supporting
GT11 of PMID: 25373348 is compound heterozygous for the maternal c.3092del variant and Leu214Pro (classified Pathogenic by the PD-EP), without confirmation of trans phase (0.5pt; PM3_supporting).
PM2_Supporting
This variant is absent from gnomAD v2.1.1 (PM2_Supporting).
PP4_Strong
At least one patient (Patient GT11 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 reduced between 5% and 20% and function was pathological, as measured by flow cytometry. ITGA2B and ITGB3 were sequenced across all exons and intron/exon boundaries (PP4_strong).
PM4
The c.3092del variant causes a frameshift and subsequent stop loss, Leu1031ArgfsTer97. This results in the addition of 90 amino acids to the ITGA2B protein, beyond the cytoplasmic domain.
Approved on: 2021-12-02
Published on: 2022-06-12
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