NM_007194.4(CHEK2):c.1016A>G (p.His339Arg) AND Familial cancer of breast

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jun 22, 2021
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:: RCV001865716.7

Allele description [Variation Report for NM_007194.4(CHEK2):c.1016A>G (p.His339Arg)]

NM_007194.4(CHEK2):c.1016A>G (p.His339Arg)

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.1016A>G (p.His339Arg)

HGVS:

NC_000022.11:g.28696980T>C
NG_008150.2:g.49887A>G
NM_001005735.2:c.1145A>G
NM_001257387.2:c.353A>G
NM_001349956.2:c.815A>G
NM_007194.4:c.1016A>GMANE SELECT
NM_145862.2:c.1009-1107A>G
NP_001005735.1:p.His382Arg
NP_001244316.1:p.His118Arg
NP_001336885.1:p.His272Arg
NP_009125.1:p.His339Arg
LRG_302t1:c.1016A>G
LRG_302:g.49887A>G
LRG_302p1:p.His339Arg
NC_000022.10:g.29092968T>C
NG_008150.1:g.49855A>G
NM_007194.3:c.1016A>G

Protein change:

H118R

Links:

dbSNP: rs1555914365

NCBI 1000 Genomes Browser:

rs1555914365

Molecular consequence:

NM_145862.2:c.1009-1107A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001005735.2:c.1145A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001257387.2:c.353A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001349956.2:c.815A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_007194.4:c.1016A>G - 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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11327855[uid] (0)
Conserved Domains
coat protein VP20 [Cherry rasp leaf virus]
coat protein VP20 [Cherry rasp leaf virus]
gi|52137000|ref|YP_081447.1|

Protein
Sphingomonas sp. jr10 16S ribosomal RNA gene, partial sequence
Sphingomonas sp. jr10 16S ribosomal RNA gene, partial sequence
gi|300507132|gb|HM241215.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002146848	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jun 22, 2021)	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

SCV002146848

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jun 22, 2021)

germline

clinical testing

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

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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

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 Invitae, SCV002146848.3

#	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. 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: "Probably Damaging"; Align-GVGD: "Class C0"). This variant has not been reported in the literature in individuals with CHEK2-related conditions. ClinVar contains an entry for this variant (Variation ID: 479604). This variant is not present in population databases (ExAC no frequency). This sequence change replaces histidine with arginine at codon 339 of the CHEK2 protein (p.His339Arg). The histidine residue is highly conserved and there is a small physicochemical difference between histidine and arginine.

#	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 8, 2024

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