NM_007194.4(CHEK2):c.908+1493_1095+388del AND Predisposition to cancer

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jun 22, 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:: RCV003325286.1

Allele description [Variation Report for NM_007194.4(CHEK2):c.908+1493_1095+388del]

NM_007194.4(CHEK2):c.908+1493_1095+388del

Gene:

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

Variant type:

Deletion

Cytogenetic location:

22q12.1

Genomic location:

Preferred name:

NM_007194.4(CHEK2):c.908+1493_1095+388del

HGVS:

NC_000022.11:g.28696516_28702015del
NG_008150.2:g.44855_50354del
NM_001005735.2:c.1037+1493_1224+388del
NM_001257387.2:c.245+1493_432+388del
NM_001349956.2:c.707+1493_894+388del
NM_007194.4:c.908+1493_1095+388delMANE SELECT
NM_145862.2:c.908+1493_1009-640del
LRG_302t1:c.908+1493_1095+388del
LRG_302:g.44855_50354del
NC_000022.10:g.29092504_29098003del

Molecular consequence:

NM_001005735.2:c.1037+1493_1224+388del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001257387.2:c.245+1493_432+388del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001349956.2:c.707+1493_894+388del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_007194.4:c.908+1493_1095+388del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_145862.2:c.908+1493_1009-640del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001005735.2:c.1037+1493_1224+388del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001257387.2:c.245+1493_432+388del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001349956.2:c.707+1493_894+388del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_007194.4:c.908+1493_1095+388del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_145862.2:c.908+1493_1009-640del - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Name:: Predisposition to cancer
Identifiers:

Recent activity

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PREDICTED: Homo sapiens calpain 9 (CAPN9), transcript variant X4, mRNA
PREDICTED: Homo sapiens calpain 9 (CAPN9), transcript variant X4, mRNA
gi|2217263323|ref|XM_011544019.3|

Nucleotide
cbRhyMega
cbRhyMega
Rhynchostegium megapolitanum (megapolitan feathermoss), genomic and transcriptomic data

BioProject
LOC109950870 [Prunus persica]
LOC109950870 [Prunus persica]
Gene ID:109950870

Gene
LOC109950872 [Prunus persica]
LOC109950872 [Prunus persica]
Gene ID:109950872

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004031206	St. Jude Molecular Pathology, St. Jude Children's Research Hospital	criteria provided, single submitter (St. Jude Assertion Criteria 2020)	Pathogenic (Jun 22, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004031206

St. Jude Molecular Pathology, St. Jude Children's Research Hospital

criteria provided, single submitter

(St. Jude Assertion Criteria 2020)

Pathogenic
(Jun 22, 2023)

germline

clinical testing

Citation Link

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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 St. Jude Molecular Pathology, St. Jude Children's Research Hospital, SCV004031206.1

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

Description

The CHEK2 c.908+1493_1095+388del variant is a gross deletion of the genomic region encompassing exons 9-10 of the CHEK2 gene. The 5' end is likely confined to intron 8. The 3' end of this event is likely confined to intron 10. This deletion is expected to result in an absent or disrupted protein product. A deletion of this region has been reported in individuals with breast cancer, prostate cancer, thrombocythemia, thyroid cancer, medulloblastoma, and renal cell carcinoma (PMID: 16551709, 17085682, 21876083, 22058216, 25583358, 29753700, 29978187). Of note, this deletion is also referred to as del5395, and is reported to be a Slavic founder variant. In summary, this variant meets criteria to be 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 3, 2023

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