NM_000419.5:c.624+2C>A

CA399805557

Gene: ITGA2B

Condition: Glanzmann's thrombasthenia

Inheritance Mode: Autosomal recessive inheritance

UUID: 13d2b130-2f9d-48c6-8316-be8a93767b03

Approved on: 2020-09-06

Published on: 2021-01-28

HGVS expressions

NM_000419.5:c.624+2C>A
NM_000419.3:c.624+2C>A
NM_000419.4:c.624+2C>A
ENST00000262407.5:c.624+2C>A
ENST00000589645.5:n.80C>A
ENST00000592253.5:n.58C>A
ENST00000592944.1:n.311C>A
NC_000017.11:g.44385284G>T
CM000679.2:g.44385284G>T
NC_000017.10:g.42462652G>T
CM000679.1:g.42462652G>T
NC_000017.9:g.39818178G>T
NG_008331.1:g.9222C>A

Pathogenic

• Met criteria codes: PM2_Supporting PVS1 PP4_Moderate

• Not Met criteria codes: PS3 PM3

Expert Panel

Platelet Disorders VCEP

Criteria Specification Information

Evidence submitted by expert panel

Platelet Disorders VCEP

The canonical splice site variant NM_000419.4:c.624+2C>A predicted to affect splicing at intron 5 causing a frameshift and premature stop codon that leads to NMD (confirmed in by RT-PCR in patient cells). This variant is absent from all population databases but has been reported in one compound heterozygous proband with a phenotype highly specific to GT (PMID: 9920835). In summary, this variant meets criteria to be classified as Pathogenic for GT. GT-specific criteria applied: PVS1, PM2_Supporting, and PP4_Moderate.

Met criteria codes

• PM2_Supporting: This variant is absent from all population cohorts in gnomAD, ExAC, 1000 Genomes, and ESP.
• PVS1: The NM_000419.5:c.624+2C>A canonical splice variant is predicted to affect splicing at intron 5 causing a frameshift and premature stop codon that leads to NMD. The frameshift inducing inclusion of intron 5 was confirmed by exontrap analysis in CHO cells and by RT-PCR of patient mRNA which was present at an extremely low amount consistent with the instability of the transcript.
• PP4_Moderate: Proband of PMID: 9920835 meets the criteria for PP4; including mucocutaneous bleeding and impaired aggregation with all agonists except ristocetin. The proband has a normal platelet count of 286,0000/ul with a history of bleeding episodes, including unprovoked bruising. Platelets failed to aggregate either spontaneously or in response to adenosine diphosphate (ADP), epinephrine, or collagen, but showed a normal response to ristocetin. Surface level of platelet GPIIb-IIIa was analyzed by flow cytometry and it was found that GPIIb and GPIIIa were about 10% of the control values.

Not Met criteria codes

• PS3: The low representation of transcripts from the splice variant GPIIb allele suggested a poor functionality of its translational product. However, because the possibility existed that the abnormal GPIIb form could accumulate, the authors performed a heterologous overexpression to analyze its interaction with GPIIIa. CHO cells inherently expressing human GPIIIa (CHO-GPIIIa cells) were stably transfected with either the construct pCEP4-GPIIb or pCEP4-[intron 5]GPIIb. Cells transfected with the void plasmid showed surface expression of GPIIIa associated with endogenous alpha subunits. Cells transfected with normal GPIIb showed surface exposure of GPIIb accompanied by a significant increase in the fluorescence signal of GPIIIa, whereas no surface fluorescence changes in GPIIb-IIIa were observed in cells transfected with the mutant [intron 5]GPIIb cDNA. This evidence is not considered as PVS1 was applied for a loss of function variant and the construct introduced in the CHO cells is not the variant found in genomic DNA (c.624+2C>A) but the resulting altered mRNA (intron 5 inclusion) so it is not direct evidence for this variant.
• PM3: Proband of PMID: 9920835 is a compound heterozygote with the paternally derived c.624+2C>A variant and the maternal c.2113T>C (p.Cys705Arg). Not considered here to avoid a circular argument.