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NM_000212.3(ITGB3):c.774_775del (p.Cys258_Asp259delinsTer) AND Glanzmann thrombasthenia

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Sep 6, 2020
Review status:
3 stars out of maximum of 4 stars
reviewed by expert panel
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:
RCV001225289.2

Allele description [Variation Report for NM_000212.3(ITGB3):c.774_775del (p.Cys258_Asp259delinsTer)]

NM_000212.3(ITGB3):c.774_775del (p.Cys258_Asp259delinsTer)

Genes:
LOC130061044:ATAC-STARR-seq lymphoblastoid active region 12308 [Gene]
ITGB3:integrin subunit beta 3 [Gene - OMIM - HGNC]
Variant type:
Microsatellite
Cytogenetic location:
17q21.32
Genomic location:
Preferred name:
NM_000212.3(ITGB3):c.774_775del (p.Cys258_Asp259delinsTer)
HGVS:
  • NC_000017.11:g.47286417TG[1]
  • NG_008332.2:g.37576TG[1]
  • NM_000212.3:c.774_775delMANE SELECT
  • NP_000203.2:p.Cys258_Asp259delinsTer
  • LRG_481t1:c.774_775del
  • LRG_481:g.37576TG[1]
  • NC_000017.10:g.45363783TG[1]
  • NC_000017.11:g.47286419_47286420del
  • NM_000212.2:c.774_775del
Links:
dbSNP: rs2065103002
NCBI 1000 Genomes Browser:
rs2065103002
Molecular consequence:
  • NM_000212.3:c.774_775del - nonsense - [Sequence Ontology: SO:0001587]

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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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001397567ClinGen Platelet Disorders Variant Curation Expert Panel, ClinGen
reviewed by expert panel

(ClinGen Platelet ACMG Specifications v2)		Pathogenic
(Sep 6, 2020) 		germlinecuration

PubMed (1)
[See all records that cite this PMID]

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedcuration

Citations

PubMed

Functional and molecular characterization of inherited platelet disorders in the Iberian Peninsula: results from a collaborative study.

Sánchez-Guiu I, Antón AI, Padilla J, Velasco F, Lucia JF, Lozano M, Cid AR, Sevivas T, Lopez-Fernandez MF, Vicente V, González-Manchón C, Rivera J, Lozano ML.

Orphanet J Rare Dis. 2014 Dec 24;9:213. doi: 10.1186/s13023-014-0213-6.

PubMed [citation]
PMID:
25539746
PMCID:
PMC4302577

Details of each submission

From ClinGen Platelet Disorders Variant Curation Expert Panel, ClinGen, SCV001397567.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcuration PubMed (1)

Description

The frameshift variant NM_000212.2:c.774_775del results in the immediate creation of a premature stop codon in exon 5 of 15, which is expected to result in NMD. It is absent from population databases but has been reported in one compound heterozygous patient with a phenotype highly specific to GT (PMID: 25539746). In summary, based on the available evidence at this time, the variant is classified as Pathogenic. GT-specific criteria applied: PVS1, PM2_supporting, PP4_moderate.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 14, 2023