NM_007194.4(CHEK2):c.120CTC[1] (p.Ser42del) AND Familial cancer of breast

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Oct 4, 2018
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:: RCV000792203.8

Allele description [Variation Report for NM_007194.4(CHEK2):c.120CTC[1] (p.Ser42del)]

NM_007194.4(CHEK2):c.120CTC[1] (p.Ser42del)

Gene:

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

Variant type:

Microsatellite

Cytogenetic location:

22q12.1

Genomic location:

Preferred name:

NM_007194.4(CHEK2):c.120CTC[1] (p.Ser42del)

HGVS:

NC_000022.11:g.28734597GAG[1]
NG_008150.2:g.12265CTC[1]
NM_001005735.2:c.120CTC[1]
NM_001257387.2:c.-658CTC[1]
NM_001349956.2:c.120CTC[1]
NM_007194.4:c.120CTC[1]MANE SELECT
NM_145862.2:c.120CTC[1]
NP_001005735.1:p.Ser42del
NP_001336885.1:p.Ser42del
NP_009125.1:p.Ser42del
NP_665861.1:p.Ser42del
LRG_302t1:c.120CTC[1]
LRG_302:g.12265CTC[1]
LRG_302p1:p.Ser42del
NC_000022.10:g.29130585GAG[1]
NC_000022.10:g.29130585_29130587del
NM_007194.3:c.123_125delCTC

Protein change:

S42del

Links:

dbSNP: rs1294840272

NCBI 1000 Genomes Browser:

rs1294840272

Molecular consequence:

NM_001257387.2:c.-658CTC[1] - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001005735.2:c.120CTC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001349956.2:c.120CTC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_007194.4:c.120CTC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_145862.2:c.120CTC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]

Condition(s)

Name:: Familial cancer of breast
Synonyms:: Breast cancer, familial; Hereditary breast cancer
Identifiers:: MONDO: MONDO:0016419; MedGen: C0346153; OMIM: 114480

Recent activity

Clear Turn Off Turn On

ribosome-associated Tef1p biogenesis chaperone CHP1 [Saccharomyces cerevisiae S2...
ribosome-associated Tef1p biogenesis chaperone CHP1 [Saccharomyces cerevisiae S288C]
gi|6325031|ref|NP_015099.1|

Protein
txid7955[organism] AND (gins4[gene symbol] OR (BC078242 OR BC0782... (19)
txid7955[organism] AND (gins4[gene symbol] OR (BC078242 OR BC078242.* OR BC131877 OR BC131877.* OR CK676828 OR CK676828.* OR BC078242 OR BC078242.* OR BC131877 OR BC131877.* OR EE697537 OR EE697537.* OR EH534241 OR EH534241.* OR EH566551 OR EH566551.* OR GDQH01021507 OR GDQH01021507.* OR NM_001003546 OR NM_001003546.* OR XM_021478305 OR XM_021478305.*))
Search

GEO Profiles

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000931483	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Oct 4, 2018)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000931483

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Oct 4, 2018)

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

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000931483.4

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

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Experimental studies and prediction algorithms are not available for this variant, and the functional significance of the affected amino acid(s) is currently unknown. This variant has not been reported in the literature in individuals with CHEK2-related disease. This variant is not present in population databases (ExAC no frequency). This variant, c.123_125delCTC, results in the deletion of 1 amino acid(s) of the CHEK2 protein (p.Ser42del), but otherwise preserves the integrity of the reading frame.

#	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 29, 2024

ClinVar

Relating variation to medicine