NM_007194.4(CHEK2):c.1434del (p.Glu479fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Aug 14, 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:: RCV000222773.6

Allele description [Variation Report for NM_007194.4(CHEK2):c.1434del (p.Glu479fs)]

NM_007194.4(CHEK2):c.1434del (p.Glu479fs)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

22q12.1

Genomic location:

Preferred name:

NM_007194.4(CHEK2):c.1434del (p.Glu479fs)

HGVS:

NC_000022.10:g.29090047del
NC_000022.11:g.28694060del
NG_008150.2:g.52808del
NM_001005735.2:c.1563del
NM_001257387.2:c.771del
NM_001349956.2:c.1233del
NM_007194.4:c.1434delMANE SELECT
NM_145862.2:c.1347del
NP_001005735.1:p.Glu522fs
NP_001244316.1:p.Glu258fs
NP_001336885.1:p.Glu412fs
NP_009125.1:p.Glu479fs
NP_665861.1:p.Glu450fs
LRG_302t1:c.1434del
LRG_302:g.52808del
LRG_302p1:p.Glu479fs
NC_000022.10:g.29090047del
NC_000022.10:g.29090047delT
NC_000022.10:g.29090048del
NG_008150.1:g.52776del
NM_007194.3:c.1434del
NM_007194.3:c.1434delA
p.E478EFS*4

Protein change:

E258fs

Links:

dbSNP: rs786202601

NCBI 1000 Genomes Browser:

rs786202601

Molecular consequence:

NM_001005735.2:c.1563del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001257387.2:c.771del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001349956.2:c.1233del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_007194.4:c.1434del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_145862.2:c.1347del - 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
SCV000279829	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Aug 14, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000279829

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Pathogenic
(Aug 14, 2023)

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	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From GeneDx, SCV000279829.10

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

Description

Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss of function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 32805687, 27751358, 37490054)

#	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

Last Updated: Mar 5, 2024

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