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NM_007194.4(CHEK2):c.274C>A (p.Pro92Thr) AND Familial cancer of breast

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jan 22, 2019
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:
RCV001070634.9

Allele description [Variation Report for NM_007194.4(CHEK2):c.274C>A (p.Pro92Thr)]

NM_007194.4(CHEK2):c.274C>A (p.Pro92Thr)

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.274C>A (p.Pro92Thr)
HGVS:
  • NC_000022.11:g.28734448G>T
  • NG_008150.2:g.12419C>A
  • NM_001005735.2:c.274C>A
  • NM_001257387.2:c.-504C>A
  • NM_001349956.2:c.274C>A
  • NM_007194.4:c.274C>AMANE SELECT
  • NM_145862.2:c.274C>A
  • NP_001005735.1:p.Pro92Thr
  • NP_001336885.1:p.Pro92Thr
  • NP_009125.1:p.Pro92Thr
  • NP_665861.1:p.Pro92Thr
  • LRG_302t1:c.274C>A
  • LRG_302:g.12419C>A
  • LRG_302p1:p.Pro92Thr
  • NC_000022.10:g.29130436G>T
  • NG_008150.1:g.12387C>A
  • NM_007194.3:c.274C>A
Protein change:
P92T
Links:
dbSNP: rs1555932172
NCBI 1000 Genomes Browser:
rs1555932172
Molecular consequence:
  • NM_001257387.2:c.-504C>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001005735.2:c.274C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001349956.2:c.274C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_007194.4:c.274C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_145862.2:c.274C>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

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

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001235896Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Jan 22, 2019) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical 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, SCV001235896.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

This variant has not been reported in the literature in individuals with CHEK2-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change replaces proline with threonine at codon 92 of the CHEK2 protein (p.Pro92Thr). The proline residue is highly conserved and there is a small physicochemical difference between proline and threonine. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C35"). 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.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024