The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • No ClinVar Id was directly found from the curated document
  • ClinVar Id was derived from the Allele Registry.


Variant: NM_000419.5:c.555T>G

CA399805736

952995 (ClinVar)

Gene: ITGA2B (HGNC:3674)
Condition: Glanzmann thrombasthenia (MONDO:0010119)
Inheritance Mode: Autosomal recessive inheritance
UUID: a378c029-ae10-4b9e-9aad-49a358635fe2
Approved on: 2023-10-17
Published on: 2023-10-17

HGVS expressions

NM_000419.5:c.555T>G
NC_000017.11:g.44385570A>C
CM000679.2:g.44385570A>C
NC_000017.10:g.42462938A>C
CM000679.1:g.42462938A>C
NC_000017.9:g.39818464A>C
NG_008331.1:g.8936T>G
ENST00000262407.6:c.555T>G
ENST00000262407.5:c.555T>G
ENST00000592944.1:n.240T>G
NM_000419.3:c.555T>G
NM_000419.4:c.555T>G
NM_000419.5(ITGA2B):c.555T>G (p.Ile185Met)
More

Likely Pathogenic

Met criteria codes 3
PM3_Supporting PP4_Strong PM2_Supporting
Not Met criteria codes 2
PP3 BP4

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

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Platelet Disorders VCEP
The ITGA2B missense variant NM_000419.4:c.555T>G replaces the isoleucine residue with a methionine residue (p.Ile185Met). This variant has been observed in a proband with a phenotype specific for Glanzmann's thrombasthenia (GT; PP4_Strong) who also harbors a second ITGA2B variant (c.1882C>T, p.Arg628Ter) previously classified by the VCEP as pathogenic (phase unconfirmed; PM3_supporting). Furthermore, this variant has not been observed in population databases (absent from gnomAD v2.1.1 and v3; PM2_supporting). Although the in silico meta-predictor REVEL score for this variant is 0.134 (below the VCEP-established threshold of 0.25) and multiple other in silico tools also predict no impact on the gene product, splicing tools predict this variant creates an exonic cryptic donor site (SpliceAI delta score 0.89), potentially altering splicing. Given the conflicting in silico predictions for this variant, neither BP4 nor PP3 was applied. Experimental evidence is needed to clarify the effect of the variant on the gene product. In summary, this variant is classified as likely pathogenic for GT. GT-specific criteria applied: PM2_supporting, PP4_strong, PM3_supporting.
Met criteria codes
PM3_Supporting
This variant has been observed in combination with the VCEP-curated pathogenic ITGA2B variant c.1882C>T (p.Arg628Ter) in 1 proband (GT13, PMID: 25373348). However, the phase of these two variants was not confirmed. This occurrence with phase unknown scores 0.5 points, meeting PM3 at the downgraded strength level of supporting (PM3_supporting).
PP4_Strong
All requirements for PP4 at an upgraded strength of moderate (PP4_Strong) are met by proband GT13 in PMID 25373348: bleeding symptoms; lack of platelet aggregation in response to various agonists except normal response to ristocetin; flow cytometry showing 5-20% expression of αIIbβ3; direct sequencing of all exons and surrounding intronic regions of ITGA2B and ITGB3.
PM2_Supporting
This variant is not observed in gnomAD v2.1.1 or v3, meeting criteria for PM2.
Not Met criteria codes
PP3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP4
This variant has a REVEL score of 0.134, meeting the criteria for BP4. Other in silico tools also predict that this variant is "tolerated" (SIFT) and "benign" (PolyPhen2). However, three splicing tools (Human Splicing Finder, MaxEntScan, and NNSPLICE) predict this variant results in the activation of an exonic cryptic donor site, potentially altering splicing.
Curation History
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