NM_007194.4(CHEK2):c.1059_1064del (p.Leu354_Leu355del) AND Familial cancer of breast

This record was updated by the submitter. Please see the current version.

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Dec 16, 2022
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:: RCV003607967.1

Allele description

NM_007194.4(CHEK2):c.1059_1064del (p.Leu354_Leu355del)

Gene:

CHEK2:checkpoint kinase 2 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

22q12.1

Genomic location:

Preferred name:

NM_007194.4(CHEK2):c.1059_1064del (p.Leu354_Leu355del)

HGVS:

NC_000022.11:g.28696933_28696938del
NG_008150.2:g.49930_49935del
NM_001005735.2:c.1188_1193del
NM_001257387.2:c.396_401del
NM_001349956.2:c.858_863del
NM_007194.4:c.1059_1064delMANE SELECT
NM_145862.2:c.1009-1064_1009-1059del
NP_001005735.1:p.Leu397_Leu398del
NP_001244316.1:p.Leu133_Leu134del
NP_001336885.1:p.Leu287_Leu288del
NP_009125.1:p.Leu354_Leu355del
LRG_302t1:c.1059_1064del
LRG_302:g.49930_49935del
LRG_302p1:p.Leu354_Leu355del
NC_000022.10:g.29092920_29092925del
NC_000022.10:g.29092921_29092926del

Molecular consequence:

NM_001005735.2:c.1188_1193del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001257387.2:c.396_401del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001349956.2:c.858_863del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_007194.4:c.1059_1064del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_145862.2:c.1009-1064_1009-1059del - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:: Familial cancer of breast
Synonyms:: Breast cancer, familial; Hereditary breast cancer
Identifiers:: MONDO: MONDO:0016419; MedGen: C0346153; OMIM: 114480

Recent activity

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PREDICTED: Puma concolor nuclear RNA export factor 3-like (LOC112870711), mRNA
PREDICTED: Puma concolor nuclear RNA export factor 3-like (LOC112870711), mRNA
gi|1435044736|ref|XM_025933797.1|

Nucleotide
cytochrome P450 2A6 [Homo sapiens]
cytochrome P450 2A6 [Homo sapiens]
gi|189339233|ref|NP_000753.3|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004487924	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Dec 16, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004487924

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Dec 16, 2022)

germline

clinical testing

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

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

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV004487924.1

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

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. This variant has not been reported in the literature in individuals affected with CHEK2-related conditions. This variant is not present in population databases (gnomAD no frequency). This variant, c.1059_1064del, results in the deletion of 2 amino acid(s) of the CHEK2 protein (p.Leu354_Leu355del), but otherwise preserves the integrity of the reading frame.

#	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 8, 2024

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