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.428T>G (p.Leu143Trp)

CA123252

13567 (ClinVar)

Gene: ITGB3
Condition: Glanzmann thrombasthenia
Inheritance Mode: Autosomal recessive inheritance
UUID: ce6d64be-3f9d-41cb-ada5-71ebdf8c6cb9
Approved on: 2024-06-06
Published on: 2024-06-07

HGVS expressions

NM_000212.2:c.428T>G
NM_000212.2(ITGB3):c.428T>G (p.Leu143Trp)
NC_000017.11:g.47284509T>G
CM000679.2:g.47284509T>G
NC_000017.10:g.45361875T>G
CM000679.1:g.45361875T>G
NC_000017.9:g.42716874T>G
NG_008332.2:g.35668T>G
ENST00000696963.1:c.428T>G
ENST00000559488.7:c.428T>G
ENST00000559488.5:c.428T>G
ENST00000560629.1:c.393T>G
ENST00000571680.1:c.428T>G
NM_000212.3:c.428T>G
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Pathogenic

Met criteria codes 6
PS3 PP1 PP3 PP4_Moderate PM3 PM2_Supporting
Not Met criteria codes 2
PM5 BS1

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 ITGB3 missense variant NM_000212.2:c.428T>G replaces the leucine residue with a tryptophan residue (p.Leu143Trp). This variant has been observed in homozygosity in at least 14 individuals reported to have Glanzmann's thrombasthenia (GT) (PMID: 9376589, PMID: 26096001, PMID: 16463284, PMID: 36672149; PM3). PMID: 16463284 suggests this variant is a founder variant in Indian populations. At least one patient has a phenotype specific for GT (Patient MK, PMID: 9376589) with a history of bleeding and impaired aggregation to at least two agonists, but normal or only mildly reduced agglutination with ristocetin. Additionally, flow cytometry showed <10% expression of αIIbβ3 (PP4_Moderate). This variant has also been observed to segregate with disease in two affected family members (Patients L and M, PMID: 26096001; PP1). Additionally, in silico tools predict the variant is damaging to protein function (REVEL score 0.98; PP3) and transient expression of ITGB3 carrying the variant in 293 cells led to a reduced level of αIIbβ3 and αIIb receptor expression on the cell surface (<5% compared to cells expressing wild type ITGB3, PMID: 11806996; PS3). The highest population minor allele frequency in gnomAD v4.1.0 is 0.00009881 (9/91082 alleles) in the South Asian population, which is lower than the ClinGen PD VCEP threshold (<0.0001; PM2_Supporting). In summary, this variant meets criteria to be classified as pathogenic for GT. GT-specific criteria applied: PS3, PP4_moderate, PP1, PP3, PM2_supporting, PM3.
Met criteria codes
PS3
PMID: 11806996: ITGB3 cDNA carrying the c.428T>G variant and wild type ITGA2B cDNA were transiently co-transfected into 293 cells. αIIbβ3 and αIIb receptor expression on the cell surface was measured by flow cytometry and immunoprecipitation and both were shown to be reduced to <5% compared to wild type.
PP1
This variant was observed in homozygosity in a proband (Patient L in PMID: 26096001) and their affected sibling (also in homozygosity; Patient M in PMID: 26096001).
PP3
REVEL score of 0.98 is above the >.0.7 threshold, in support of a deleterious effect.
PP4_Moderate
All requirements for PP4_moderate are met (Patient MK, PMID: 9376589): history of bleeding and impaired aggregation to at least two agonists, but normal or only mildly reduced agglutination with ristocetin. Additionally, flow cytometry showed <10% expression of αIIbβ3, however full sequencing of intron-exon boundaries of ITGA2B and ITGB3 was not performed.
PM3
This variant has been observed in homozygosity at least 14 individuals (Patient MK, PMID: 9376589; Patient L, PMID: 26096001; GT-08, GT-16, GT-32, GT-33, GT-39, GT-40, GT-48, GT-50, GT-53, GT-60-1, GT-64, PMID: 16463284, PMID: 36672149 pt 13) and in compound heterozygosity in one individual (GT-09, PMID: 16463284), PM3
PM2_Supporting
The highest population minor allele frequency in gnomAD v4.1.0 is 0.00009881 (9/91082 alleles) in the South Asian population, which is lower than the ClinGen PD VCEP threshold (<0.0001; PM2_Supporting). PMID: 16463284 suggests this variant is a founder variant in Indian populations.
Not Met criteria codes
PM5
Another missense variant NM_000212.3(ITGB3):c.428T>C (p.Leu143Ser) in the same codon has been classified as likely pathogenic for Glanzmann thrombasthenia by the ClinGen PD VCEP but is not considered here to avoid circularity.
BS1
The highest MAF in gnomAD v4.0.0 is 0.0001043 (9/86258 alleles) in the South Asian population which is above the <0.0001 threshold for PM2_supporting but below the <0.00158 threshold for BS1. PMID: 16463284 suggests this variant is a founder variant in Indian populations.
Curation History
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