VCV001879016.1 - ClinVar

NM_000212.3(ITGB3):c.401del (p.Glu134fs)

Germline

Top reviewed classifications are shown here.

Submission summary:

1 submission

1 submitter

1 condition

Reviewed by expert panel

Pathogenic

Nov 2022 by ClinGen Platel… FDA Recognized Database

for Glanzmann thrombasthenia

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_000212.3(ITGB3):c.401del (p.Glu134fs)

Variation ID: 1879016 Accession: VCV001879016.1

Type and length

Deletion, 1 bp

Location

Cytogenetic: 17q21.32 17: 47284482 (GRCh38) [ NCBI UCSC ] 17: 45361848 (GRCh37) [ NCBI UCSC ]

Timeline in ClinVar

	First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.	Last submission Help The date of the most recent submission for each type of classification for this variant.	Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline	Jan 21, 2023	Jan 21, 2023	Nov 15, 2022

HGVS

Nucleotide	Protein	Molecular consequence
NM_000212.3:c.401del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_000203.2:p.Glu134fs	frameshift
NC_000017.11:g.47284482del
NC_000017.10:g.45361848del
NG_008332.2:g.35641del
LRG_481:g.35641del
LRG_481t1:c.401del	LRG_481p1:p.Glu134Glyfs

... more HGVS ... less HGVS

Protein change

E134fs

Other names

NM_000212.3:c.401del

Canonical SPDI

NC_000017.11:47284481:A:

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

Global minor allele frequency (GMAF) Help The global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.

Allele frequency Help The frequency of the allele represented by this VCV record.

Links

VarSome

Genes

Gene	OMIM	ClinGen Gene Dosage Sensitivity Curation		Variation Viewer Help Links to Variation Viewer, a genome browser to view variation data from NCBI databases.	Related variants
Gene	OMIM	HI score Help The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.	TS score Help The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.		Within gene Help The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants.	All Help The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene.
ITGB3		No evidence available	No evidence available	GRCh38 GRCh37	622	811

Conditions - Germline

Condition Help The condition for this variant-condition (RCV) record in ClinVar.	Classification Help The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions)	Review status Help The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status.	Last evaluated Help The most recent date that a submitter evaluated this variant for the condition.	Variation/condition record Help The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page.
Glanzmann thrombasthenia	Pathogenic (1)	reviewed by expert panel	Nov 15, 2022	RCV002511517.1

Submissions - Germline

Classification Help The submitted germline classification for each SCV record. (Last evaluated)	Review status Help Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria)	Condition Help The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant.	Submitter Help The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar.	More information Help This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
Pathogenic (Nov 15, 2022)	reviewed by expert panel (ClinGen Platelet ACMG Specifications v2-1) Method: curation	Glanzmann thrombasthenia (Autosomal recessive inheritance) Affected status: unknown Allele origin: germline	ClinGen Platelet Disorders Variant Curation Expert Panel, ClinGen FDA Recognized Database Accession: SCV002820905.1 First in ClinVar: Jan 21, 2023 Last updated: Jan 21, 2023	Other databases https://erepo.clinicalgenome.org… https://erepo.clinicalgenome.org/evrepo/ui/interpretation/cef37463-2816-4dd5-b011-66e91f09a94b Comment: The c.401del (p.Glu134GlyfsTer10) variant in exon 4 is a nonsense variant predicted to cause a premature stop codon in biologically-relevant-exon 4 and is predicted to … (more) The c.401del (p.Glu134GlyfsTer10) variant in exon 4 is a nonsense variant predicted to cause a premature stop codon in biologically-relevant-exon 4 and is predicted to lead to nonsense mediated decay in a gene in which loss-of-function is an established disease mechanism (PVS1). This variant has been detected in at least 1 proband with Glanzmann thrombasthenia. This proband was homozygous for the variant (PMID: 3102915; PM3_Supporting). This variant is also 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, PM3_Supporting, PM2_Supporting (VCEP specifications version 2.1). (less)

Comment:

The c.401del (p.Glu134GlyfsTer10) variant in exon 4 is a nonsense variant predicted to cause a premature stop codon in biologically-relevant-exon 4 and is predicted to lead to nonsense mediated decay in a gene in which loss-of-function is an established disease mechanism (PVS1). This variant has been detected in at least 1 proband with Glanzmann thrombasthenia. This proband was homozygous for the variant (PMID: 3102915; PM3_Supporting). This variant is also 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, PM3_Supporting, PM2_Supporting (VCEP specifications version 2.1).

Germline Functional Evidence

There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Comment:

Citations for germline classification of this variant

Title	Author	Journal	Year	Link
https://erepo.clinicalgenome.org/evrepo/ui/interpretation/cef37463-2816-4dd5-b011-66e91f09a94b	-	-	-	-

Text-mined citations for this variant ...

Record last updated Aug 13, 2023

ClinVar Genomic variation as it relates to human health

NM_000212.3(ITGB3):c.401del (p.Glu134fs)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...