NM_000419.5(ITGA2B):c.1253del (p.Gly418fs) AND Glanzmann thrombasthenia

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Aug 14, 2020
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV001387239.4

Allele description [Variation Report for NM_000419.5(ITGA2B):c.1253del (p.Gly418fs)]

NM_000419.5(ITGA2B):c.1253del (p.Gly418fs)

Gene:

ITGA2B:integrin subunit alpha 2b [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

17q21.31

Genomic location:

Preferred name:

NM_000419.5(ITGA2B):c.1253del (p.Gly418fs)

HGVS:

NC_000017.11:g.44381022del
NG_008331.1:g.13487del
NM_000419.5:c.1253delMANE SELECT
NP_000410.2:p.Gly418fs
LRG_479:g.13487del
NC_000017.10:g.42458387del
NC_000017.10:g.42458390del

Protein change:

G418fs

Links:

dbSNP: rs2143465205

NCBI 1000 Genomes Browser:

rs2143465205

Molecular consequence:

NM_000419.5:c.1253del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:: Glanzmann thrombasthenia
Synonyms:: PLATELET GLYCOPROTEIN IIb-IIIa DEFICIENCY; Thrombasthenia of Glanzmann and Naegeli; Glanzmann thrombasthenia type A; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0100326; MedGen: C0040015; Orphanet: 849; OMIM: PS273800

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001587804	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Aug 14, 2020)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 21917754, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001587804

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Aug 14, 2020)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Glanzmann thrombasthenia: a review of ITGA2B and ITGB3 defects with emphasis on variants, phenotypic variability, and mouse models.

Nurden AT, Fiore M, Nurden P, Pillois X.

Blood. 2011 Dec 1;118(23):5996-6005. doi: 10.1182/blood-2011-07-365635. Epub 2011 Sep 13. Review.

PubMed [citation]

PMID:: 21917754

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV001587804.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

Loss-of-function variants in ITGA2B are known to be pathogenic (PMID: 21917754). For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals with ITGA2B-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change creates a premature translational stop signal (p.Gly418Alafs*13) in the ITGA2B gene. It is expected to result in an absent or disrupted protein product.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Feb 28, 2024

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