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.2898_2902dup

CA915940725

1210173 (ClinVar)

Gene: ITGA2B
Condition: Glanzmann thrombasthenia
Inheritance Mode: Autosomal recessive inheritance
UUID: e4b07930-d42f-47df-990a-6f83818fe71f
Approved on: 2024-08-20
Published on: 2024-08-20

HGVS expressions

NM_000419.5:c.2898_2902dup
NC_000017.11:g.44374704_44374708dup
CM000679.2:g.44374704_44374708dup
NC_000017.10:g.42452072_42452076dup
CM000679.1:g.42452072_42452076dup
NC_000017.9:g.39807598_39807602dup
NG_008331.1:g.19802_19806dup
ENST00000262407.6:c.2898_2902dup
ENST00000648408.1:c.2329_2333dup
ENST00000262407.5:c.2898_2902dup
ENST00000587295.5:c.253+1129_253+1133dup
ENST00000592462.5:n.2409_2413dup
NM_000419.3:c.2898_2902dup
NM_000419.4:c.2898_2902dup

Likely Pathogenic

Met criteria codes 4
PM3_Supporting PVS1_Strong PM2_Supporting PP4_Moderate

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Platelet Disorders Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines Version 2.1

PDF
Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Platelet Disorders VCEP
The ITGA2B NM_000419.5:c.2898_2902dup variant has been experimentally determined to result in two mRNA products: a major product lacking exon 28 and a minor product containing exon 28 with a disrupted reading frame and native stop codon loss (PMID: 16463284), altering the entire transmembrane domain which is critically important. Exon 28 skipping is an in frame event predicted to lead to the production of a protein lacking amino acids 948-981. Loss of exon 28 has been demonstrated to result in the production of GPIIb/IIIa heterodimers that fail to complete post-translational processing and are retained intracellularly where they undergo degradation (PMID: 1932748), suggesting exon 28 is critical to protein function (PVS1). This variant has been observed in homozygosity (PM3_supporting) in one individual with a phenotype specific for Glanzmann's thrombasthenia (GT) (GT24, PMID: 16463284); history of bleeding and impaired aggregation to at least two agonists, but normal or only mildly reduced agglutination with ristocetin (PP4_Moderate). Furthermore, this variant is absent from population databases, including gnomADv4.1.0 (PM2_supporting). In summary, this variant meets criteria to be classified as likely pathogenic for GT. GT-specific criteria applied: PVS1_strong, PP4_moderate, PM2_supporting, and PM3_supporting.
Met criteria codes
PM3_Supporting
This variant was reported in homozygosity in one individual (GT24 in PMID: 16463284), sufficient to apply PM3_Supporting.
PVS1_Strong
This variant introduces a frameshift in exon 28/30. Reverse transcription coupled with PCR and sequencing of platelet-derived mRNA from an affected individual homozygous for the variant indicated two mRNA products are present: a major product lacking exon 28 (which restores the reading frame) and a minor product containing exon 28 with a disrupted reading frame and native stop codon loss (PMID: 16463284) altering the entire transmembrane domain which is critically important. Exon 28 skipping is an in frame event predicted to lead to the production of a protein lacking amino acids 948-981, roughly 3% of the total protein. Loss of exon 28 has been demonstrated to result in the production of GPIIb/IIIa heterodimers that fail to complete post-translational processing and are retained intracellularly where they undergo degradation (PMID: 1932748), suggesting exon 28 is critical to protein function.
PM2_Supporting
This variant is absent from gnomADv4.1.0 (PM2_supporting).
PP4_Moderate
All requirements for PP4_moderate are met (GT24 in PMID: 16463284): history of bleeding and impaired aggregation to at least two agonists, but normal or only mildly reduced agglutination with ristocetin.
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