NM_007194.4(CHEK2):c.1596del (p.Thr533fs) AND not provided

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

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Mar 1, 2024
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000235161.9

Allele description

NM_007194.4(CHEK2):c.1596del (p.Thr533fs)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

22q12.1

Genomic location:

Preferred name:

NM_007194.4(CHEK2):c.1596del (p.Thr533fs)

HGVS:

NC_000022.11:g.28687934del
NG_008150.2:g.58934del
NM_001005735.2:c.1725del
NM_001257387.2:c.933del
NM_001349956.2:c.1395del
NM_007194.4:c.1596delMANE SELECT
NM_145862.2:c.1509del
NP_001005735.1:p.Thr576fs
NP_001244316.1:p.Thr312fs
NP_001336885.1:p.Thr466fs
NP_009125.1:p.Thr533fs
NP_665861.1:p.Thr504fs
LRG_302t1:c.1596del
LRG_302:g.58934del
LRG_302p1:p.Thr533fs
NC_000022.10:g.29083921del
NC_000022.10:g.29083922del
NG_008150.1:g.58902del
NM_007194.3:c.1596del
NM_007194.3:c.1596delC
NM_007194.4:c.1596delCMANE SELECT
p.T533Qfs*33
p.T533QfsX33

Protein change:

T312fs

Links:

dbSNP: rs587781519

NCBI 1000 Genomes Browser:

rs587781519

Molecular consequence:

NM_001005735.2:c.1725del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001257387.2:c.933del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001349956.2:c.1395del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_007194.4:c.1596del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_145862.2:c.1509del - frameshift variant - [Sequence Ontology: SO:0001589]

Observations:

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
SCV000211015	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Uncertain significance (May 2, 2022)	germline	clinical testing	Citation Link,
SCV004810721	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Uncertain significance (Mar 1, 2024)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000211015

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Uncertain significance
(May 2, 2022)

germline

clinical testing

Citation Link,

SCV004810721

CeGaT Center for Human Genetics Tuebingen

criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)

Uncertain significance
(Mar 1, 2024)

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	yes	1	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From GeneDx, SCV000211015.15

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

Description

Not observed at significant frequency in large population cohorts (gnomAD); Frameshift variant predicted to result in protein truncation as the last 11 amino acids are replaced with 32 different amino acids, although loss-of-function variants have not been reported downstream of this position in the protein; Observed in individuals with breast cancer (Girard 2019); This variant is associated with the following publications: (PMID: 29615459, 30303537)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From CeGaT Center for Human Genetics Tuebingen, SCV004810721.3

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		1	not provided	not provided	not provided

Last Updated: Jun 17, 2024

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