Variant: NM_000419.3(ITGA2B):c.1787T>C

CA115846

2900 (ClinVar)

Gene: N/A

Condition: Glanzmann thrombasthenia

Inheritance Mode: Autosomal recessive inheritance

UUID: c6b42f33-92f7-4a71-822b-932469bd66ae

HGVS expressions

NM_000419.3(ITGA2B):c.1787T>C
NC_000017.11:g.44379780A>G
CM000679.2:g.44379780A>G
NC_000017.10:g.42457148A>G
CM000679.1:g.42457148A>G
NC_000017.9:g.39812674A>G
NG_008331.1:g.14726T>C
ENST00000262407.6:c.1787T>C
ENST00000648408.1:c.1218T>C
ENST00000262407.5:c.1787T>C
ENST00000592462.5:n.582T>C
NM_000419.3:c.1787T>C
NM_000419.4:c.1787T>C
NM_000419.5:c.1787T>C

Pathogenic

• Met criteria codes: PP4_Strong PM2_Supporting PM3_Strong PP1

• Not Met criteria codes: PP3

Expert Panel

Platelet Disorders VCEP

Criteria Specification Information

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

Evidence submitted by expert panel

Platelet Disorders VCEP

The NM_000419.5(ITGA2B):c.1787T>C (p.Ile596Thr) missense variant has been reported in the homozygous state in at least 2 apparently unrelated individuals (PMID: 22513797, 20020534) and in the compound heterozygous state in 4 individuals (PMID: 9215749, 9734640, 34552732, 25373348). The second variants in these patients are c.3060+2T>C (classified Pathogenic by the PD-VCEP; without confirmation of trans phase), Glu355Lys (classified Pathogenic by the PD-VCEP; with confirmation of trans phase), c.2841+1G>T, and c.408G>C (latter two not considered here to avoid circularity) respectively (PM3_Strong). The proband from PMID: 22513797 meets criteria for PP4_Strong including mucocutaneous bleeding; abnormal platelet aggregometry in response to at least 2 agonist and normal response to ristocetin; absent surface expression of GPIIb-IIIa on flow cytometry; and full sequencing of ITGA2B and ITGB3. It was found to co-segregate with disease in 1 additional family member (PP1). Ile596Thr is reported in gnomAD v4.0.0 at a frequency of 0.00008305 (98/1179968 alleles) in the non-Finnish European population, below the PM2_supporting threshold of <0.0001. In summary, this variant is classified Pathogenic for autosomal recessive Glanzmann thrombasthenia. GT-specific codes applied: PP4_Strong, PM2_Supporting, PM3_Strong, PP1. (PD-VCEP specifications version 2)

Met criteria codes

• PP4_Strong: Proband from PMID: 22513797 meet criteria for PP4_Strong including mucocutaneous bleeding; abnormal platelet aggregometry in response to at least 2 agonist and normal response to ristocetin; absent surface expression of GPIIb-IIIa on flow cytometry; and full sequencing of ITGA2B and ITGB3.
• PM2_Supporting: Ile596Thr is reported in gnomAD v4.0.0 at a frequency of 0.00008305 (98/1179968 alleles) in the non-Finnish European population, below the PM2_supporting threshold of <0.0001.
• PM3_Strong: The variant has been observed in the homozygous state in at least 2 apparently unrelated individuals (PMID: 22513797, 20020534; 1pt) and in the compound heterozygous state in 4 individuals (PMID: 9215749, 9734640, 34552732, 25373348). The second variants in these patients are c.3060+2T>C (classified Pathogenic by the PD-VCEP without confirmation of trans phase 0.5pt), Glu355Lys (classified Pathogenic by the PD-VCEP with confirmation of trans phase 1pt), c.2841+1G>T, and c.408G>C (latter two not considered here to avoid circularity) respectively. Total 2.5pt; PM3_Strong
• PP1: Patient 3 is the 16yo sister of the proband, Patient 4. Both siblings are diagnosed with GT, homozygous for the variant and meet phenotype criteria, thus meeting PP1

Not Met criteria codes

• PP3: In-silico evidence is available from PMID: 29385657: the authors suggest that Ile596 is a likely mutational hot spot; it is relatively well conserved both between species and within human α‐subunits. They report that the Thr introduces an ‐OH alcoholic function close to Arg551, which competes for H‐bonds with residues Asp542, Ser594 and Asp591 changing interatom distances and creating an additional H‐bond within connecting loops extending from the lower region of the thigh. However, the Ile596Thr variant has a REVEL score <0.7: 0.628.

Approved on: 2023-11-17

Published on: 2023-11-03