Evidence Repository
The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • No ClinVar Id was directly found from the curated document

Variant: NM_000212.3:c.1990G>T

CA400033003

Gene: ITGB3 (HGNC:3690)
Condition: Glanzmann thrombasthenia (MONDO:0100326)
Inheritance Mode: Autosomal recessive inheritance
UUID: 987c5c64-6ff8-412f-9906-26cf77b4102c
Approved on: 2023-01-17
Published on: 2023-02-15

HGVS expressions

NM_000212.3:c.1990G>T
NC_000017.11:g.47300554G>T
CM000679.2:g.47300554G>T
NC_000017.10:g.45377920G>T
CM000679.1:g.45377920G>T
NC_000017.9:g.42732919G>T
NG_008332.2:g.51713G>T
ENST00000559488.7:c.1990G>T
ENST00000559488.5:c.1990G>T
ENST00000560629.1:n.1955G>T
NM_000212.2:c.1990G>T
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Pathogenic

Met criteria codes 3
PM3_Supporting PVS1 PM2_Supporting
Not Met criteria codes 1
PP4

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(ITGB3):c.1990G>T (p.Glu664Ter) nonsense variant is predicted to cause a premature stop codon in biologically-relevant-exon 12/15 and is predicted to lead to nonsense mediated decay in a gene in which loss-of-function is an established mechanism (PVS1). This variant is absent from gnomAD v2.1.1 (PM2_Supporting). Patient 6, of PMID: 31029159, is reported to have a clinical diagnosis of GT and is homozygous for this variant (PM3_supporting). 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: PVS1, PM2_supporting, PM3_supporting (VCEP specifications version 2.1).
Met criteria codes
PM3_Supporting
Patient 6 is homozygous (by consanguinity) for this variant 0.5pt (PM3_supporting).
PVS1
The NM_000212.3(ITGB3):c.1990G>T (p.Glu664Ter) nonsense variant is predicted to cause a premature stop codon in biologically-relevant-exon 12/15 and is predicted to lead to nonsense mediated decay in a gene in which loss-of-function is an established mechanism (PVS1).
PM2_Supporting
This variant is absent from gnomAD v2.1.1 (PM2_Supporting).
Not Met criteria codes
PP4
Patient 7 of PMID: 31029159 is reported to have a clinical diagnosis of GT with a bleeding time of 17min, however insufficient information is provided including a lack of platelet aggregation results (PP4_NotMet).
Curation History
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