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_000419.5:c.1642C>T

CA399802364

Gene: ITGA2B (HGNC:3674)
Condition: Glanzmann thrombasthenia (MONDO:0100326)
Inheritance Mode: Autosomal recessive inheritance
UUID: bdc06307-e375-4cad-a8a9-98626be2be20
Approved on: 2023-06-01
Published on: 2023-06-02

HGVS expressions

NM_000419.5:c.1642C>T
NC_000017.11:g.44380112G>A
CM000679.2:g.44380112G>A
NC_000017.10:g.42457480G>A
CM000679.1:g.42457480G>A
NC_000017.9:g.39813006G>A
NG_008331.1:g.14394C>T
ENST00000262407.6:c.1642C>T
ENST00000648408.1:n.1073C>T
ENST00000262407.5:c.1642C>T
ENST00000592226.5:n.1115C>T
ENST00000592462.5:n.437C>T
NM_000419.3:c.1642C>T
NM_000419.4:c.1642C>T
More

Pathogenic

Met criteria codes 3
PVS1 PP4_Moderate PM2_Supporting
Not Met criteria codes 1
PM3

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 c.1642C>T (p.Gln548Ter) variant in exon 17 is a nonsense variant predicted to cause a premature stop codon in biologically-relevant-exon 17 and is predicted to lead to nonsense mediated decay in a gene in which loss-of-function is an established disease mechanism (PVS1). At least one patient (Patient 1 in PMID: 23624894) with this variant displayed mucocutaneous bleeding and impaired aggregation with all agonists except ristocetin, which is highly specific for Glanzmann thrombasthenia. Additionally, αIIbβ3 surface expression was reduced to 0% (<25%), as measured by flow cytometry. Molecular genetic analysis was performed for the ITGA2B, but no genotyping was performed for ITGB3 (PP4_moderate). This variant has been detected in at least 1 proband with Glanzmann thrombasthenia (PMID:23624894). This individual was compound heterozygous for this variant and the NM_000419.3:c.1750C>T (Arg584Ter) variant, which was classified as Pathogenic by the PD VCEP (but occurs at too high a frequency to consider for PM3). This variant is absent from gnomAD v2.1.1 (PM2_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, PP4_Moderate, PM2_Supporting (VCEP specifications version 2).
Met criteria codes
PVS1
The c.1642C>T (p.Gln548Ter) variant in exon 17 is a nonsense variant predicted to cause a premature stop codon in biologically-relevant-exon 17 and is predicted to lead to nonsense mediated decay in a gene in which loss-of-function is an established disease mechanism (PVS1).
PP4_Moderate
At least one patient (Patient 1 in PMID: 23624894) with this variant displayed mucocutaneous bleeding and impaired aggregation with all agonists except ristocetin, which is highly specific for Glanzmann thrombasthenia. Additionally, αIIbβ3 surface expression was reduced to 0% (<25%), as measured by flow cytometry. Molecular genetic analysis was performed for the ITGA2B, but no genotyping was performed for ITGB3 (PP4_moderate).
PM2_Supporting
This variant is absent from gnomAD v2.1.1 (PM2_Supporting).
Not Met criteria codes
PM3
This variant has been detected in at least 1 proband with Glanzmann thrombasthenia (PMID:23624894). This individual was compound heterozygous for this variant and the NM_000419.3:c.1750C>T (Arg584Ter) variant, which was classified as Pathogenic by the PD VCEP. These variants were confirmed in trans by parental testing. NM_000419.3:c.1750C>T (Arg584Ter) does not meet PM2 so is not considered here.
Curation History
The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. If you have questions about the information contained on this website, please see a health care professional.
ClinGen Terms of Use.
¤ Powered by BCM's Genboree.