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.2929_2930del

CA915940726

Gene: ITGA2B
Condition: Glanzmann thrombasthenia
Inheritance Mode: Autosomal recessive inheritance
UUID: aee242a3-5ff9-4bcf-ade0-8064f7f01e8b
Approved on: 2021-12-21
Published on: 2021-12-23

HGVS expressions

NM_000419.5:c.2929_2930del
NC_000017.11:g.44374672_44374673del
CM000679.2:g.44374672_44374673del
NC_000017.10:g.42452040_42452041del
CM000679.1:g.42452040_42452041del
NC_000017.9:g.39807566_39807567del
NG_008331.1:g.19833_19834del
ENST00000262407.6:c.2929_2930del
ENST00000648408.1:n.2360_2361del
ENST00000262407.5:c.2929_2930del
ENST00000587295.5:n.253+1160_253+1161del
ENST00000588098.1:n.23_24del
ENST00000592462.5:n.2440_2441del
NM_000419.3:c.2929_2930del
NM_000419.4:c.2929_2930del
More

Likely Pathogenic

Met criteria codes 3
PVS1_Strong PP4_Moderate PM2_Supporting
Not Met criteria codes 1
PM3

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:c.2929_2930del (p.Glu979SerfsTer56) variant in ITGA2B is a frameshift variant that may cause a premature stop codon that is predicted to escape nonsense mediated decay, however it leads to alteration of a functionally important region (alters amino acids 979-1034, which includes the transmembrane domain) in a gene where loss-of-function is an established disease mechanism (PVS1_Strong). At least one patient (Proband GT 26 in PMID: 16463284) with this variant displayed mucocutaneous bleeding and impaired aggregation with all agonists except ristocetin, which is highly specific for Glanzmann thrombasthenia (PP4_moderate). This variant is absent from gnomAD v2.1.1 (PM2_Supporting). In summary, this variant meets the 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: PVS1_strong, PP4_moderate, and PM2_supporting. (VCEP specifications version 2; date of approval 12/21/2021).
Met criteria codes
PVS1_Strong
The c.2929_2930del (p.Glu979SerfsTer56) variant in ITGA2B is a frameshift variant that may cause a premature stop codon that is predicted to escape nonsense mediated decay, however it leads to alteration of a functionally important region (alters amino acids 979-1034, which includes the transmembrane domain) in a gene where loss-of-function is an established disease mechanism (PVS1_Strong).
PP4_Moderate
At least one patient (Proband GT 26 in PMID: 16463284) with this variant displayed mucocutaneous bleeding and impaired aggregation with all agonists except ristocetin, which is highly specific for Glanzmann thrombasthenia (PP4_moderate).
PM2_Supporting
This variant is absent from gnomAD v2.1.1 (PM2_Supporting).
Not Met criteria codes
PM3
This variant has been detected in at least one individual with Glanzmann thrombasthenia. The individual was heterozygous for this variant, however a second ITGA2B variant was not observed (GT 26, PMID: 16463284, 0 pts).
Curation History
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