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Variant: NM_000419.5:c.2941C>T

CA399790399

Gene: ITGA2B
Condition: Glanzmann thrombasthenia
Inheritance Mode: Autosomal recessive inheritance
UUID: bd273211-4fdf-46e1-b2f1-940633954c3d
Approved on: 2023-01-17
Published on: 2023-02-15

HGVS expressions

NM_000419.5:c.2941C>T
NC_000017.11:g.44374661G>A
CM000679.2:g.44374661G>A
NC_000017.10:g.42452029G>A
CM000679.1:g.42452029G>A
NC_000017.9:g.39807555G>A
NG_008331.1:g.19845C>T
ENST00000262407.6:c.2941C>T
ENST00000648408.1:n.2372C>T
ENST00000262407.5:c.2941C>T
ENST00000587295.5:n.253+1172C>T
ENST00000588098.1:n.35C>T
ENST00000592462.5:n.2452C>T
NM_000419.3:c.2941C>T
NM_000419.4:c.2941C>T
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Pathogenic

Met criteria codes 5
PP4_Moderate PM2_Supporting PVS1_Moderate PS3 PP1
Not Met criteria codes 1
PM3

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 c.2941C>T (p.Gln981Ter) variant in exon 28 is a nonsense variant predicted to cause a premature stop codon in biologically-relevant-exon 28 and is predicted to lead to nonsense mediated decay in a gene in which loss-of-function is an established disease mechanism. Additionally, In two siblings, it has been shown that this mutation results in exon 28 being spliced out of the final protein product (PMID: 8111043, PVS1_Moderate). Surface expression of αIIb measured by Western blot in COS-1 cells transiently co-transfected with c.2941C>T (p.Gln981Ter) αIIb and wild type αIIb showed decreased expression at 0% of WT levels, indicating that this variant impacts protein function (PMID: 1932748)(PS3). At least two patients (Patient 1 and Patient 2 from PMID:8111043) 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 to 0% as measured by flow cytometry. However, ITGA2B and ITGB3 were not reported to be sequenced across all exons and intron/exon boundaries (PP4_Moderate). This variant has also been reported to segregate with Glanzmann thrombasthenia in the proband (confirmed by bleeding phenotype and platelet aggregometry) plus the proband's affected sister. The c.2941C>T (p.Gln981Ter) variant is inherited from the patients' father and an unspecified ITGA2B variant is inherited from their mother (PP1_Supporting, PMID: 8111043). Finally, this variant is absent from gnomAD v2.1.1 (PM2_Supporting). In summary, this variant meets the criteria to be classified as Pathogenic for autosomal recessive Glanzmann Thrombasthenia based on the ACMG/AMP criteria applied, as specified by the ClinGen PD VCEP: PVS1, PS3, PP4_Moderate, PP1 and PM2_Supporting (VCEP specifications version 2.1).
Met criteria codes
PP4_Moderate
At least two patients (Patient 1 and Patient 2 PMID:8111043 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 to 0% as measured by flow cytometry. However, ITGA2B and ITGB3 were not reported to be sequenced across all exons and intron/exon boundaries (PP4_Moderate).
PM2_Supporting
This variant is absent from gnomAD v2.1.1 (PM2_Supporting).
PVS1_Moderate
The c.2941C>T (p.Gln981Ter) variant in exon 28 is a nonsense variant predicted to cause a premature stop codon in biologically-relevant-exon 28 of 30 and is predicted to lead to nonsense mediated decay in a gene in which loss-of-function is an established disease mechanism. In two siblings, it has been shown that this mutation results in alternative splicing in which exon 28 is skipped (PMID: 8111043, PVS1_Moderate).
PS3
Surface expression of αIIb measured by Western blot in COS-1 cells transiently co-transfected with an (exon 28 null variant) αIIb and wild type αIIb showed decreased expression at 0% of WT levels, indicating that this variant impacts protein function (PMID: 1932748)(PS3).
PP1
The variant has been reported to segregate with Glanzmann thrombasthenia in the proband (confirmed by bleeding phenotype and platelet aggregometry) plus the proband's affected sister. The c.2941C>T (p.Gln981Ter) is inherited from the patients' father and an unspecified ITGA2B variant is inherited from their mother (PP1_Supporting, PMID: 8111043).
Not Met criteria codes
PM3
This variant has been detected in at least 1 proband with Glanzmann thrombasthenia. This individual was compound heterozygous for this variant and a variant that were confirmed in trans by family testing (paternal variant = c.2941C>T (p.Gln981Ter) and maternal allele is unspecified (PMID: 8111043). PM3 is not met.
Curation History
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