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NM_007194.4(CHEK2):c.860del (p.Lys287fs) AND not provided

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Aug 17, 2016
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:
RCV000255418.2

Allele description [Variation Report for NM_007194.4(CHEK2):c.860del (p.Lys287fs)]

NM_007194.4(CHEK2):c.860del (p.Lys287fs)

Gene:
CHEK2:checkpoint kinase 2 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
22q12.1
Genomic location:
Preferred name:
NM_007194.4(CHEK2):c.860del (p.Lys287fs)
HGVS:
  • NC_000022.11:g.28703554del
  • NG_008150.2:g.43314del
  • NM_001005735.2:c.989del
  • NM_001257387.2:c.197del
  • NM_001349956.2:c.659del
  • NM_007194.4:c.860delMANE SELECT
  • NM_145862.2:c.860del
  • NP_001005735.1:p.Lys330fs
  • NP_001244316.1:p.Lys66fs
  • NP_001336885.1:p.Lys220fs
  • NP_009125.1:p.Lys287fs
  • NP_665861.1:p.Lys287fs
  • LRG_302t1:c.860del
  • LRG_302:g.43314del
  • LRG_302p1:p.Lys287fs
  • NC_000022.10:g.29099541del
  • NC_000022.10:g.29099542del
  • NG_008150.1:g.43282del
  • NM_007194.3:c.860del
  • NM_007194.3:c.860delA
Protein change:
K220fs
Links:
dbSNP: rs886039731
NCBI 1000 Genomes Browser:
rs886039731
Molecular consequence:
  • NM_001005735.2:c.989del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001257387.2:c.197del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001349956.2:c.659del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_007194.4:c.860del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_145862.2:c.860del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000322682GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Likely pathogenic
(Aug 17, 2016) 		germlineclinical testing

Citation Link

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From GeneDx, SCV000322682.7

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

This deletion of one nucleotide in CHEK2 is denoted c.860delA at the cDNA level and p.Lys287ArgfsX17 (K287RfsX17) at the protein level. The normal sequence, with the base that is deleted in braces, is ATCA[A]GATT. The deletion causes a frameshift which changes a Lysine to an Arginine at codon 287, and creates a premature stop codon at position 17 of the new reading frame. Although this variant has not, to our knowledge, been reported in the literature, it is predicted to cause loss of normal protein function through either protein truncation or nonsense-mediated mRNA decay. Based on the currently available information, we consider this deletion to be a likely pathogenic variant.

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

Last Updated: Sep 29, 2024