NM_007194.4(CHEK2):c.1100del (p.Thr367fs) AND Colorectal cancer

Germline classification:: Pathogenic (3 submissions)
Last evaluated:: Jun 9, 2023
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:: RCV002463641.10

Allele description [Variation Report for NM_007194.4(CHEK2):c.1100del (p.Thr367fs)]

NM_007194.4(CHEK2):c.1100del (p.Thr367fs)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

22q12.1

Genomic location:

Preferred name:

NM_007194.4(CHEK2):c.1100del (p.Thr367fs)

Other names:

NP_009125.1:p.Thr367MetfsTer15

HGVS:

NC_000022.11:g.28695869del
NG_008150.2:g.50998del
NM_001005735.2:c.1229del
NM_001257387.2:c.437del
NM_001349956.2:c.899del
NM_007194.4:c.1100delMANE SELECT
NM_145862.2:c.1013del
NP_001005735.1:p.Thr410fs
NP_001244316.1:p.Thr146fs
NP_001336885.1:p.Thr300fs
NP_009125.1:p.Thr367fs
NP_665861.1:p.Thr338fs
LRG_302t1:c.1100del
LRG_302:g.50998del
LRG_302p1:p.Thr367fs
NC_000022.10:g.29091857del
NC_000022.10:g.29091857delG
NG_008150.1:g.50966del
NM_001005735.1:c.1229del
NM_001005735.1:c.1229delC
NM_001005735.2:c.1229delC
NM_007194.3:c.1100delC
NM_007194.4:c.1100delCMANE SELECT
c.1100delC
p.T367MFS*15
p.T367MfsX15
p.Thr367Metfs*15
p.Thr367MetfsX15
p.Thr367fs
p.Thr410fs

Protein change:

T146fs

Links:

OMIM: 604373.0001; dbSNP: rs555607708

NCBI 1000 Genomes Browser:

rs555607708

Molecular consequence:

NM_001005735.2:c.1229del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001257387.2:c.437del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001349956.2:c.899del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_007194.4:c.1100del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_145862.2:c.1013del - frameshift variant - [Sequence Ontology: SO:0001589]

Functional consequence:

Uncertain function

Condition(s)

Name:: Colorectal cancer
Synonyms:: Colorectal cancer, somatic; Malignant Colorectal Neoplasm
Identifiers:: MONDO: MONDO:0005575; MedGen: C0346629; OMIM: 114500

Recent activity

Clear Turn Off Turn On

PREDICTED: Trichoplusia ni calmodulin-like protein 4 (LOC113509060), mRNA
PREDICTED: Trichoplusia ni calmodulin-like protein 4 (LOC113509060), mRNA
gi|1496262867|ref|XM_026892334.1|

Nucleotide
Streptococcus pneumoniae strain NCTC7465 chromosome 1, complete sequence
Streptococcus pneumoniae strain NCTC7465 chromosome 1, complete sequence
gi|983365893|ref|NZ_LN831051.1|

Nucleotide
Mus musculus 0 day neonate eyeball cDNA, RIKEN full-length enriched library, clo...
Mus musculus 0 day neonate eyeball cDNA, RIKEN full-length enriched library, clone:E130116K20 product:choline acetyltransferase, full insert sequence
gi|74226155|dbj|AK143147.1|

Nucleotide
Mus musculus zinc finger protein 971 (Zfp971), transcript variant 2, mRNA
Mus musculus zinc finger protein 971 (Zfp971), transcript variant 2, mRNA
gi|294345412|ref|NM_001177400.1|

Nucleotide
Mus musculus R4-type mRNA for choline acetyltransferase, N-terminal
Mus musculus R4-type mRNA for choline acetyltransferase, N-terminal
gi|220378|dbj|D12493.1|MUSCATR4

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002758585	Human Genetics Bochum, Ruhr University Bochum	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Jul 1, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004027697	Institute of Human Genetics, University of Leipzig Medical Center	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Jun 9, 2023)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004171175	Institute of Human Genetics, University Hospital of Duesseldorf	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic	germline	not provided	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002758585

Human Genetics Bochum, Ruhr University Bochum

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Jul 1, 2022)

germline

clinical testing

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

SCV004027697

Institute of Human Genetics, University of Leipzig Medical Center

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Jun 9, 2023)

unknown

clinical testing

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

SCV004171175

Institute of Human Genetics, University Hospital of Duesseldorf

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic

germline

not provided

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	yes	not provided	not provided	not provided	not provided	not provided	clinical testing, not provided
not provided	unknown	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Human Genetics Bochum, Ruhr University Bochum, SCV002758585.1

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

Description

ACMG criteria used to clasify this variant: PVS1, PS3, PS4

#	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 Institute of Human Genetics, University of Leipzig Medical Center, SCV004027697.1

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

Description

Criteria applied: PVS1,PS3,PS4,PM2_SUP

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

From Institute of Human Genetics, University Hospital of Duesseldorf, SCV004171175.1

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

#	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: Nov 3, 2024

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