NM_024675.4(PALB2):c.2004GGA[1] (p.Glu669del) AND Hereditary cancer-predisposing syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 25, 2021
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:: RCV002417267.2

Allele description [Variation Report for NM_024675.4(PALB2):c.2004GGA[1] (p.Glu669del)]

NM_024675.4(PALB2):c.2004GGA[1] (p.Glu669del)

Gene:

PALB2:partner and localizer of BRCA2 [Gene - OMIM - HGNC]

Variant type:

Microsatellite

Cytogenetic location:

16p12.2

Genomic location:

Preferred name:

NM_024675.4(PALB2):c.2004GGA[1] (p.Glu669del)

HGVS:

NC_000016.10:g.23630145TCC[1]
NG_007406.1:g.16208GGA[1]
NM_001407296.1:c.1944_1946GGA[1]
NM_001407297.1:c.2004_2006GGA[1]
NM_001407298.1:c.2004_2006GGA[1]
NM_001407299.1:c.2004_2006GGA[1]
NM_001407300.1:c.2004_2006GGA[1]
NM_001407301.1:c.2004_2006GGA[1]
NM_001407302.1:c.2004_2006GGA[1]
NM_001407304.1:c.1119_1121GGA[1]
NM_001407305.1:c.1119_1121GGA[1]
NM_001407306.1:c.1119_1121GGA[1]
NM_001407307.1:c.1119_1121GGA[1]
NM_001407308.1:c.1119_1121GGA[1]
NM_001407309.1:c.1119_1121GGA[1]
NM_001407310.1:c.1119_1121GGA[1]
NM_001407311.1:c.1119_1121GGA[1]
NM_001407312.1:c.216_218GGA[1]
NM_001407313.1:c.216_218GGA[1]
NM_024675.4:c.2004GGA[1]MANE SELECT
NP_001394225.1:p.Glu649del
NP_001394226.1:p.Glu669del
NP_001394227.1:p.Glu669del
NP_001394228.1:p.Glu669del
NP_001394229.1:p.Glu669del
NP_001394230.1:p.Glu669del
NP_001394231.1:p.Glu669del
NP_001394233.1:p.Glu374del
NP_001394234.1:p.Glu374del
NP_001394235.1:p.Glu374del
NP_001394236.1:p.Glu374del
NP_001394237.1:p.Glu374del
NP_001394238.1:p.Glu374del
NP_001394239.1:p.Glu374del
NP_001394240.1:p.Glu374del
NP_001394241.1:p.Glu73del
NP_001394242.1:p.Glu73del
NP_078951.2:p.Glu669del
NP_078951.2:p.Glu669del
LRG_308t1:c.2004_2006GGA[1]
LRG_308:g.16208GGA[1]
LRG_308p1:p.Glu669del
NC_000016.9:g.23641466TCC[1]
NM_024675.3:c.2004_2006GGA[1]
NM_024675.3:c.2007_2009delGGA

Protein change:

E374del

Molecular consequence:

NM_024675.4:c.2004GGA[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001407296.1:c.1944_1946GGA[1] - inframe_indel - [Sequence Ontology: SO:0001820]
NM_001407297.1:c.2004_2006GGA[1] - inframe_indel - [Sequence Ontology: SO:0001820]
NM_001407298.1:c.2004_2006GGA[1] - inframe_indel - [Sequence Ontology: SO:0001820]
NM_001407299.1:c.2004_2006GGA[1] - inframe_indel - [Sequence Ontology: SO:0001820]
NM_001407300.1:c.2004_2006GGA[1] - inframe_indel - [Sequence Ontology: SO:0001820]
NM_001407301.1:c.2004_2006GGA[1] - inframe_indel - [Sequence Ontology: SO:0001820]
NM_001407302.1:c.2004_2006GGA[1] - inframe_indel - [Sequence Ontology: SO:0001820]
NM_001407304.1:c.1119_1121GGA[1] - inframe_indel - [Sequence Ontology: SO:0001820]
NM_001407305.1:c.1119_1121GGA[1] - inframe_indel - [Sequence Ontology: SO:0001820]
NM_001407306.1:c.1119_1121GGA[1] - inframe_indel - [Sequence Ontology: SO:0001820]
NM_001407307.1:c.1119_1121GGA[1] - inframe_indel - [Sequence Ontology: SO:0001820]
NM_001407308.1:c.1119_1121GGA[1] - inframe_indel - [Sequence Ontology: SO:0001820]
NM_001407309.1:c.1119_1121GGA[1] - inframe_indel - [Sequence Ontology: SO:0001820]
NM_001407310.1:c.1119_1121GGA[1] - inframe_indel - [Sequence Ontology: SO:0001820]
NM_001407311.1:c.1119_1121GGA[1] - inframe_indel - [Sequence Ontology: SO:0001820]
NM_001407312.1:c.216_218GGA[1] - inframe_indel - [Sequence Ontology: SO:0001820]
NM_001407313.1:c.216_218GGA[1] - inframe_indel - [Sequence Ontology: SO:0001820]

Condition(s)

Name:: Hereditary cancer-predisposing syndrome
Synonyms:: Neoplastic Syndromes, Hereditary; Tumor predisposition; Cancer predisposition; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0015356; MeSH: D009386; MedGen: C0027672

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002719543	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (Aug 25, 2021)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002719543

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(Aug 25, 2021)

germline

clinical testing

Citation Link

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

Details of each submission

From Ambry Genetics, SCV002719543.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

The c.2007_2009delGGA variant (also known as p.E669del) is located in coding exon 5 of the PALB2 gene. This variant results from an in-frame GGA deletion at nucleotide positions 2007 to 2009. This results in the in-frame deletion of a glutamic acid at codon 669. This amino acid position is well conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis (Choi Y et al. PLoS ONE. 2012; 7(10):e46688). Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

#	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: May 1, 2024

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