NM_007194.4(CHEK2):c.1343T>G (p.Ile448Ser) AND not specified

Germline classification:: Benign (5 submissions)
Last evaluated:: Aug 15, 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:: RCV000120559.16

Allele description [Variation Report for NM_007194.4(CHEK2):c.1343T>G (p.Ile448Ser)]

NM_007194.4(CHEK2):c.1343T>G (p.Ile448Ser)

Gene:

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

Variant type:

single nucleotide variant

Cytogenetic location:

22q12.1

Genomic location:

Preferred name:

NM_007194.4(CHEK2):c.1343T>G (p.Ile448Ser)

Other names:

p.I448S:ATT>AGT

HGVS:

NC_000022.11:g.28695159A>C
NG_008150.2:g.51708T>G
NM_001005735.2:c.1472T>G
NM_001257387.2:c.680T>G
NM_001349956.2:c.1142T>G
NM_007194.4:c.1343T>GMANE SELECT
NM_145862.2:c.1256T>G
NP_001005735.1:p.Ile491Ser
NP_001244316.1:p.Ile227Ser
NP_001336885.1:p.Ile381Ser
NP_009125.1:p.Ile448Ser
NP_665861.1:p.Ile419Ser
LRG_302t1:c.1343T>G
LRG_302:g.51708T>G
LRG_302p1:p.Ile448Ser
NC_000022.10:g.29091147A>C
NG_008150.1:g.51676T>G
NM_001005735.1:c.1472T>G
NM_007194.3:c.1343T>G
O96017:p.Ile448Ser
p.I448S

Protein change:

I227S

Links:

UniProtKB: O96017#VAR_021120; dbSNP: rs17886163

NCBI 1000 Genomes Browser:

rs17886163

Molecular consequence:

NM_001005735.2:c.1472T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001257387.2:c.680T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001349956.2:c.1142T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_007194.4:c.1343T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_145862.2:c.1256T>G - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

Recent activity

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PREDICTED: Perognathus longimembris pacificus calpain 3 (Capn3), transcript vari...
PREDICTED: Perognathus longimembris pacificus calpain 3 (Capn3), transcript variant X6, mRNA
gi|2240597664|ref|XM_048332895.1|

Nucleotide
PREDICTED: Perognathus longimembris pacificus calpain 3 (Capn3), transcript vari...
PREDICTED: Perognathus longimembris pacificus calpain 3 (Capn3), transcript variant X3, mRNA
gi|2240597658|ref|XM_048332892.1|

Nucleotide
Homo sapiens mRNA; cDNA DKFZp434L038 (from clone DKFZp434L038)
Homo sapiens mRNA; cDNA DKFZp434L038 (from clone DKFZp434L038)
gi|5912146|emb|AL117585.1|

Nucleotide
b4gat1 [Carassius gibelio]
b4gat1 [Carassius gibelio]
Gene ID:128017422

Gene
LOC113669287 [Pocillopora damicornis]
LOC113669287 [Pocillopora damicornis]
Gene ID:113669287

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000084713	ITMI	no classification provided	not provided	germline	reference population	PubMed (1) [See all records that cite this PMID]
SCV000806867	PreventionGenetics, part of Exact Sciences	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign (Jul 31, 2017)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV000860561	Eurofins Ntd Llc (ga)	criteria provided, single submitter (EGL ClinVar v180209 classification definitions)	Benign (Apr 6, 2018)	germline	clinical testing	Citation Link,
SCV002070843	Genetic Services Laboratory, University of Chicago	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign (May 3, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004024689	Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign (Aug 15, 2023)	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	1	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	no	not provided	not provided	not provided	not provided	not provided	clinical testing
African	germline	unknown	not provided	not provided	not provided	43	not provided	reference population
African_European	germline	unknown	not provided	not provided	not provided	46	not provided	reference population
Central_Asian	germline	unknown	not provided	not provided	not provided	50	not provided	reference population
East_Asian	germline	unknown	not provided	not provided	not provided	62	not provided	reference population
European	germline	unknown	not provided	not provided	not provided	331	not provided	reference population
Hispanic	germline	unknown	not provided	not provided	not provided	118	not provided	reference population
Whole_cohort	germline	unknown	not provided	not provided	not provided	681	not provided	reference population

Citations

PubMed

Germline variation in cancer-susceptibility genes in a healthy, ancestrally diverse cohort: implications for individual genome sequencing.

Bodian DL, McCutcheon JN, Kothiyal P, Huddleston KC, Iyer RK, Vockley JG, Niederhuber JE.

PLoS One. 2014;9(4):e94554. doi: 10.1371/journal.pone.0094554.

PubMed [citation]

PMID:: 24728327
PMCID:: PMC3984285

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 ITMI, SCV000084713.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	African	not provided	not provided	not provided	reference population	PubMed (1)
2	African_European	not provided	not provided	not provided	reference population	PubMed (1)
3	Central_Asian	not provided	not provided	not provided	reference population	PubMed (1)
4	East_Asian	not provided	not provided	not provided	reference population	PubMed (1)
5	European	not provided	not provided	not provided	reference population	PubMed (1)
6	Hispanic	not provided	not provided	not provided	reference population	PubMed (1)
7	Whole_cohort	not provided	not provided	not provided	reference population	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	43	not provided	discovery		not provided	0.0375	not provided	not provided
2	germline	unknown	46	not provided	discovery		not provided	0.0128	not provided	not provided
3	germline	unknown	50	not provided	discovery		not provided	0	not provided	not provided
4	germline	unknown	62	not provided	discovery		not provided	0	not provided	not provided
5	germline	unknown	331	not provided	discovery		not provided	0	not provided	not provided
6	germline	unknown	118	not provided	discovery		not provided	0	not provided	not provided
7	germline	unknown	681	not provided	discovery		not provided	0.0034	not provided	not provided

From PreventionGenetics, part of Exact Sciences, SCV000806867.1

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

#	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

From Eurofins Ntd Llc (ga), SCV000860561.1

#	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	unknown	not provided	not provided	not provided		1	not provided	not provided	not provided

From Genetic Services Laboratory, University of Chicago, SCV002070843.1

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	no	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, SCV004024689.1

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

#	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: Oct 20, 2024

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