The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
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Variant: NM_000212.2(ITGB3):c.1199G>A (p.Cys400Tyr)

CA123244

13562 (ClinVar)

Gene: ITGB3
Condition: Glanzmann thrombasthenia
Inheritance Mode: Autosomal recessive inheritance
UUID: c4ac081e-5a79-4468-b274-f8d363e98a9a
Approved on: 2024-06-06
Published on: 2024-06-07

HGVS expressions

NM_000212.2:c.1199G>A
NM_000212.2(ITGB3):c.1199G>A (p.Cys400Tyr)
NC_000017.11:g.47291027G>A
CM000679.2:g.47291027G>A
NC_000017.10:g.45368393G>A
CM000679.1:g.45368393G>A
NC_000017.9:g.42723392G>A
NG_008332.2:g.42186G>A
ENST00000696963.1:c.1199G>A
ENST00000559488.7:c.1199G>A
ENST00000559488.5:c.1199G>A
ENST00000560629.1:c.1164G>A
ENST00000571680.1:c.1199G>A
NM_000212.3:c.1199G>A
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Pathogenic

Met criteria codes 5
PP4_Strong PM2_Supporting PP1 PP3 PM3_Strong
Not Met criteria codes 1
PS3

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

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Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Platelet Disorders VCEP
The NM_000212.2(ITGB3):c.1199G>A (p.Cys400Tyr) missense has been identified in at least 4 probands, including GT11 and GT15a of PMID: 29675921 meeting the criteria for PP4_strong; including mucocutaneous bleeding, impaired aggregation with all agonists except ristocetin, and reduced surface expression of αIIbβ3 measured by flow cytometry. ITGA2B and ITGB3 were sequenced across all exons and intron/exon boundaries. Siblings GT15a and GT15b are both compound heterozygous for Cys400Tyr and pathogenic variant c.1525del (PP1; PMID: 29675921) with confirmation of trans phase was reported in PMID: 18788610. Additionally, two homozygous patients have been reported (PMIDs: 8781422, 35198519) (PM3_Strong). This variant is absent from gnomAD v4.1.0 (PM2_Supporting). The computational predictor REVEL gives a score of 0.968, which predicts a damaging effect on ITGB3 function (PP3). 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: PM2_supporting, PM3_strong, PP1, PP3, PP4_strong. (VCEP specifications version 2; date of approval 06/06/2024)
Met criteria codes
PP4_Strong
GT11 and GT15a of PMID: 29675921 meet the criteria for PP4_strong; including mucocutaneous bleeding, impaired aggregation with all agonists except ristocetin, and reduced surface expression of αIIbβ3 measured by flow cytometry. ITGA2B and ITGB3 were sequenced across all exons and intron/exon boundaries.
PM2_Supporting
This variant is absent from gnomAD v4.1.0 (PM2_Supporting).
PP1
Siblings GT15a and GT15b are both compound heterozygous for Cys400Tyr and c.1525del (PMID: 29675921).
PP3
The computational predictor REVEL gives a score of 0.968, which is above the ClinGen PD VCEP threshold of >0.7 and predicts a damaging effect on ITGB3 function (PP3).
PM3_Strong
Two homozygous patients have been reported (PMIDs: 8781422, 35198519) 1pt and GT15a of PMID: 29675921 is compound heterozygous for Cys400Tyr and c.1525del (classified Pathogenic by the PD-VCEP), confirmation of trans phase was reported in PMID: 18788610 1pt. Total: 2pt (PM3_Strong).
Not Met criteria codes
PS3
Transfection studies in both PMID: 8781422 and PMID: 11806996 showed reduced surface expression but did not meet the PS3_moderate criteria. Additionally, both studies found fibrinogen binding was unaffected.
Curation History
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