rs121918451

Positions:

• chr17-47300488-G-T

Variant summary

Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PM3 PS3_Supporting PVS1_Strong PM2_Supporting PP4_Moderate

This summary comes from the ClinGen Evidence Repository: NM_000212.2(ITGB3):c.1924G>T (p.Glu642Ter) in exon 12 of 15 is a nonsense variant predicted to cause a premature stop codon in biologically-relevant-exon and is predicted to lead to nonsense mediated decay in a gene in which loss-of-function is an established disease mechanism. However, RT-PCR analysis in the proband of PMID:9845537 found that, instead, a shortened transcript was produced (in similar quantities to the normal allele) with in-frame skipping of exons 11 and 12 (reported by authors as exons 10 and 11, using alternate numbering), resulting in removal of 14% of the protein (PVS1_strong). CHO cells were transiently cotransfected with the plasmid pcDNA3-GPIIb and either WT or mutant pcDNA3-GPIIIa with this variant. To investigate the surface exposure of GPIIb-IIIa, intact cells were labeled with biotin, and the GPIIb-IIIa complexes were immunoprecipitated with anti-GPIIb (M3) or anti-GPIIIa (P37) MoAbs. No biotin-labeled products were found in cells cotransfected with normal GPIIb and mutant GPIIIa. Additionally, to examine the intracellular presence of GPIIb and/or GPIIIa as either monomers or heterodimers, total cell lysates were labeled with biotin, and GPIIb, GPIIIa, or GPIIb-IIIa complexes were immunoprecipitated. Unlike in extracts from cells coexpressing normal subunits, heterodimers failed to immunoprecipitate using a complex-specific MoAb, suggesting that the mutant ΔGPIIIa does not complex with GPIIb. Pulse-chase experiments further verified that the mutant ΔGPIIIa does not complex to GPIIb (PMID:9845537; PS3_supporting). This variant has been detected homozygous in at least 2 probands with Glanzmann thrombasthenia (PMIDs: 14985172, 9845537; PM3). At least one patient (Patient II.1 in PMID:14985172) with this variant displayed mucocutaneous bleeding and impaired aggregation with all agonists except ristocetin, which is highly specific for Glanzmann thrombasthenia (PP4_moderate). Additionally, αIIbβ3 surface expression was reduced to <5%, as measured by flow cytometry and Western blot. 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_strong, PS3_supporting, PP4_moderate, PM3, PM2_supporitng. (VCEP specifications version 2; date of approval 12/21/21). LINK:https://erepo.genome.network/evrepo/ui/classification/CA123249/MONDO:0100326/011

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000014 (0 hom.)
• Consequence: ITGB3 NM_000212.3 stop_gained
• Clinical Significance: Pathogenic reviewed by expert panel P:3
• Conservation: PhyloP100: 7.06

Genes affected

ITGB3 (HGNC:6156): (integrin subunit beta 3) The ITGB3 protein product is the integrin beta chain beta 3. Integrins are integral cell-surface proteins composed of an alpha chain and a beta chain. A given chain may combine with multiple partners resulting in different integrins. Integrin beta 3 is found along with the alpha IIb chain in platelets. Integrins are known to participate in cell adhesion as well as cell-surface mediated signalling. [provided by RefSeq, Jul 2008]

ENSG00000259753 (HGNC:):

ACMG classification

Verdict is Pathogenic. Variant got 10 ACMG points.

• PVS1: For more information check the summary or visit ClinGen Evidence Repository.
• PS3: For more information check the summary or visit ClinGen Evidence Repository.
• PM2: For more information check the summary or visit ClinGen Evidence Repository.
• PM3: For more information check the summary or visit ClinGen Evidence Repository.
• PP4: For more information check the summary or visit ClinGen Evidence Repository.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ITGB3	NM_000212.3	c.1924G>T	p.Glu642*	stop_gained	12/15	ENST00000559488.7	NP_000203.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ITGB3	ENST00000559488.7	c.1924G>T	p.Glu642*	stop_gained	12/15	1	NM_000212.3	ENSP00000452786.2
ENSG00000259753	ENST00000560629.1	n.1888G>T		non_coding_transcript_exon_variant	12/18	2		ENSP00000456711.2
ITGB3	ENST00000696963.1	c.1924G>T	p.Glu642*	stop_gained	12/14			ENSP00000513002.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000137 AC: 2 AN: 1461226 Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0 AN XY: 726994

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000180

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:3

Revision: reviewed by expert panel

Submissions by phenotype

Glanzmann thrombasthenia Pathogenic:1

Pathogenic, reviewed by expert panel

curation

ClinGen Platelet Disorders Variant Curation Expert Panel, ClinGen

Dec 21, 2021

NM_000212.2(ITGB3):c.1924G>T (p.Glu642Ter) in exon 12 of 15 is a nonsense variant predicted to cause a premature stop codon in biologically-relevant-exon and is predicted to lead to nonsense mediated decay in a gene in which loss-of-function is an established disease mechanism. However, RT-PCR analysis in the proband of PMID: 9845537 found that, instead, a shortened transcript was produced (in similar quantities to the normal allele) with in-frame skipping of exons 11 and 12 (reported by authors as exons 10 and 11, using alternate numbering), resulting in removal of 14% of the protein (PVS1_strong). CHO cells were transiently cotransfected with the plasmid pcDNA3-GPIIb and either WT or mutant pcDNA3-GPIIIa with this variant. To investigate the surface exposure of GPIIb-IIIa, intact cells were labeled with biotin, and the GPIIb-IIIa complexes were immunoprecipitated with anti-GPIIb (M3) or anti-GPIIIa (P37) MoAbs. No biotin-labeled products were found in cells cotransfected with normal GPIIb and mutant GPIIIa. Additionally, to examine the intracellular presence of GPIIb and/or GPIIIa as either monomers or heterodimers, total cell lysates were labeled with biotin, and GPIIb, GPIIIa, or GPIIb-IIIa complexes were immunoprecipitated. Unlike in extracts from cells coexpressing normal subunits, heterodimers failed to immunoprecipitate using a complex-specific MoAb, suggesting that the mutant ΔGPIIIa does not complex with GPIIb. Pulse-chase experiments further verified that the mutant ΔGPIIIa does not complex to GPIIb (PMID: 9845537; PS3_supporting). This variant has been detected homozygous in at least 2 probands with Glanzmann thrombasthenia (PMIDs: 14985172, 9845537; PM3). At least one patient (Patient II.1 in PMID: 14985172) with this variant displayed mucocutaneous bleeding and impaired aggregation with all agonists except ristocetin, which is highly specific for Glanzmann thrombasthenia (PP4_moderate). Additionally, αIIbβ3 surface expression was reduced to <5%, as measured by flow cytometry and Western blot. 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_strong, PS3_supporting, PP4_moderate, PM3, PM2_supporitng. (VCEP specifications version 2; date of approval 12/21/21). -

Glanzmann thrombasthenia 2 Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

Dec 15, 1998

- -

not provided Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

May 18, 2023

For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 13565). This premature translational stop signal has been observed in individual(s) with Glanzmann thrombasthenia (PMID: 9845537). This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Glu642*) in the ITGB3 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in ITGB3 are known to be pathogenic (PMID: 21917754). -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.63	D
BayesDel_noAF	Pathogenic	0.65
CADD	Pathogenic	51
DANN	Uncertain	1.0
Eigen	Pathogenic	1.1
Eigen_PC	Pathogenic	0.98
FATHMM_MKL	Pathogenic	1.0	D
Vest4		0.97
GERP RS		5.1

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.070		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs121918451; hg19: chr17-45377854;