NM_000173.7(GP1BA):c.165_168del (p.Ser55fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Mar 3, 2023
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:: RCV003559936.2

Allele description [Variation Report for NM_000173.7(GP1BA):c.165_168del (p.Ser55fs)]

NM_000173.7(GP1BA):c.165_168del (p.Ser55fs)

Gene:

GP1BA:glycoprotein Ib platelet subunit alpha [Gene - OMIM - HGNC]

Variant type:

Microsatellite

Cytogenetic location:

17p13.2

Genomic location:

Preferred name:

NM_000173.7(GP1BA):c.165_168del (p.Ser55fs)

HGVS:

NC_000017.11:g.4932765TGAG[1]
NG_008767.2:g.5471TGAG[1]
NM_000173.7:c.165_168delMANE SELECT
NP_000164.5:p.Ser55fs
LRG_480t1:c.165_168del
LRG_480:g.5471TGAG[1]
LRG_480p1:p.Ser55fs
NC_000017.10:g.4836060TGAG[1]
NC_000017.10:g.4836060_4836063del

Protein change:

S55fs

Molecular consequence:

NM_000173.7:c.165_168del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004296473	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Mar 3, 2023)	germline	clinical testing	PubMed (5) [See all records that cite these PMIDs] 18791947, 11054083, 9233564, 9639514, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004296473

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Mar 3, 2023)

germline

clinical testing

PubMed (5)
[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

A case of Bernard-Soulier Syndrome due to a homozygous four bases deletion (TGAG) of GPIbalpha gene: lack of GPIbalpha but absence of bleeding.

Vettore S, Scandellari R, Scapin M, Lombardi AM, Duner E, Randi ML, Fabris F.

Platelets. 2008 Aug;19(5):388-91. doi: 10.1080/09537100801949976.

PubMed [citation]

PMID:: 18791947

Bernard-Soulier syndrome in a patient doubly heterozygous for two frameshift mutations in the glycoprotein ib alpha gene.

Afshar-Kharghan V, Craig FE, López JA.

Br J Haematol. 2000 Sep;110(4):919-24.

PubMed [citation]

PMID:: 11054083

See all PubMed Citations (5)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004296473.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (5)

Description

Algorithms developed to predict the effect of variants on protein structure and function are not available or were not evaluated for this variant. This sequence change creates a premature translational stop signal (p.Ser55Argfs*12) in the GP1BA gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 598 amino acid(s) of the GP1BA protein. This variant is not present in population databases (gnomAD no frequency). This premature translational stop signal has been observed in individuals with Bernard-Soulier syndrome (PMID: 11054083, 18791947). This variant is also known as p.Ser39fs. Experimental studies have shown that this premature translational stop signal affects GP1BA function (PMID: 11054083). This variant disrupts a region of the GP1BA protein in which other variant(s) (p.Trp540*) have been determined to be pathogenic (PMID: 9233564, 9639514). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic.

#	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: Sep 29, 2024

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