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Variant: NM_000212.3:c.2356C>T

CA400034866

Gene: ITGB3
Condition: Glanzmann thrombasthenia
Inheritance Mode: Autosomal recessive inheritance
UUID: a6821494-10c9-4e64-8e3c-7bf1f427f06c
Approved on: 2023-05-16
Published on: 2023-05-16

HGVS expressions

NM_000212.3:c.2356C>T
NC_000017.11:g.47310193C>T
CM000679.2:g.47310193C>T
NC_000017.10:g.45387559C>T
CM000679.1:g.45387559C>T
NC_000017.9:g.42742558C>T
NG_008332.2:g.61352C>T
ENST00000559488.7:c.2356C>T
ENST00000559488.5:c.2356C>T
ENST00000560629.1:n.2266+2556C>T
NM_000212.2:c.2356C>T
NR_110880.1:n.363-6411G>A
NR_110881.1:n.227-6411G>A

Uncertain Significance

Met criteria codes 2
PM2_Supporting PP4_Moderate
Not Met criteria codes 4
PS3 PP3 PM3 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 NM_000212.3:c.2356C>T variant in ITGB3 predicts the missense change, Arg786Trp. It is absent from gnomAD v2.1.1 and v3 (PM2_supporting). The variant is reported in a compound heterozygous GT patient who has a GOF variant in trans with this variant (PMID: 29439184). The patient meets GT bleeding and laboratory phenotype criteria (PP4_moderate): Platelet aggregation was impaired in response to ADP and TRAP-6, but normal to ristocetin, with low-normal response to collagen (64 U; nv = 56-144). αIIbβ3 surface expression was reduced (CD41/CD42b 0.1 [nv = 0.43+-0.11], expression corrected for platelet volume), and PAC-1 binding induced by platelet stimulation impaired (33.6% with ADP [nv = 74.4+-22.3], 20.3% with TRAP-6 [nv = 80.1+-20.05]). Due to the gain of function variant the patient also shows the macrothrombocytopenia phenotype. The REVEL score (0.334) for this variant is low and does not meet PP3 (>0.7) or BP4 (>0.25) criteria. Functional evidence from transfection studies in CHO cells show that the variant does not affect αIIbβ3 expression or PAC-1 binding, but results in reduced CHO cell spreading (PMID: 29439184), not meeting criteria for PS3. In summary, this variant meets the criteria to be classified as uncertain significance for autosomal recessive Glanzmann Thrombasthenia based on the ACMG/AMP criteria applied, as specified by the ClinGen PD VCEP: PM2_Supporting, PP4_moderate (PD VCEP specifications version 2.1).
Met criteria codes
PM2_Supporting
Arg786Trp is absent from gnomAD v2.1.1 and v3, meeting criteria for PM2_Supporting
PP4_Moderate
Proband from PMID: 29439184 is confirmed compound heterozygous for a GOF (Asn331Ser) and LOF (Arg786Trp) variants. The patient meets GT bleeding and laboratory phenotype criteria (PP4_moderate): Platelet aggregation was impaired in response to ADP and TRAP-6, but normal to ristocetin, with low-normal response to collagen (64 U; nv = 56-144). αIIbβ3 surface expression was reduced (CD41/CD42b 0.1 [nv = 0.43+-0.11], expression corrected for platelet volume), and PAC-1 binding induced by platelet stimulation impaired (33.6% with ADP [nv = 74.4+-22.3], 20.3% with TRAP-6 [nv = 80.1+-20.05]). Due to the gain of function variant the patient also shows the macrothrombocytopenia phenotype.
Not Met criteria codes
PS3
Experimental evidence in CHO cells from PMID: 29439184 showed normal αIIbβ3 expression and PAC-1 binding, but showed reduced CHO cell spreading indicating impaired outside-in signaling. PS3 critieria not met.
PP3
REVEL score of 0.334 does not meet PP3 threshold of >0.7.
PM3
The patient of PMID: 29439184 is compound heterozygous for maternal Arg786Trp and paternal Asn331Ser variants. Not considered since Asn331Ser is a GOF variant related to macrothrombocytopenia.
BP4
REVEL score of 0.334 does not meet PP3 threshold of <0.25.
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