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NM_007194.4(CHEK2):c.569C>T (p.Ala190Val) AND not provided

Germline classification:
Uncertain significance (3 submissions)
Last evaluated:
Jun 22, 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:
RCV001531540.25

Allele description [Variation Report for NM_007194.4(CHEK2):c.569C>T (p.Ala190Val)]

NM_007194.4(CHEK2):c.569C>T (p.Ala190Val)

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.569C>T (p.Ala190Val)
HGVS:
  • NC_000022.11:g.28725000G>A
  • NG_008150.2:g.21867C>T
  • NM_001005735.2:c.698C>T
  • NM_001257387.2:c.-209C>T
  • NM_001349956.2:c.445-77C>T
  • NM_007194.4:c.569C>TMANE SELECT
  • NM_145862.2:c.569C>T
  • NP_001005735.1:p.Ala233Val
  • NP_009125.1:p.Ala190Val
  • NP_665861.1:p.Ala190Val
  • LRG_302t1:c.569C>T
  • LRG_302:g.21867C>T
  • LRG_302p1:p.Ala190Val
  • NC_000022.10:g.29120988G>A
  • NG_008150.1:g.21835C>T
  • NM_007194.3:c.569C>T
  • p.A190V
Protein change:
A190V
Links:
dbSNP: rs786203483
NCBI 1000 Genomes Browser:
rs786203483
Molecular consequence:
  • NM_001257387.2:c.-209C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001349956.2:c.445-77C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001005735.2:c.698C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_007194.4:c.569C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_145862.2:c.569C>T - missense variant - [Sequence Ontology: SO:0001583]
Observations:
1

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001746732CeGaT Center for Human Genetics Tuebingen
criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)
Uncertain significance
(Apr 1, 2021)
germlineclinical testing

Citation Link,

SCV001819902GeneDx
criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)
Uncertain significance
(Jul 20, 2020)
germlineclinical testing

Citation Link,

SCV004221749Quest Diagnostics Nichols Institute San Juan Capistrano
criteria provided, single submitter

(Quest Diagnostics criteria)
Uncertain significance
(Jun 22, 2023)
unknownclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing
not providedgermlineyes1not providednot providednot providednot providedclinical testing

Citations

PubMed

A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders.

Karbassi I, Maston GA, Love A, DiVincenzo C, Braastad CD, Elzinga CD, Bright AR, Previte D, Zhang K, Rowland CM, McCarthy M, Lapierre JL, Dubois F, Medeiros KA, Batish SD, Jones J, Liaquat K, Hoffman CA, Jaremko M, Wang Z, Sun W, Buller-Burckle A, et al.

Hum Mutat. 2016 Jan;37(1):127-34. doi: 10.1002/humu.22918. Epub 2015 Oct 29.

PubMed [citation]
PMID:
26467025
PMCID:
PMC4737317

Details of each submission

From CeGaT Center for Human Genetics Tuebingen, SCV001746732.20

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided1not providednot providednot provided

From GeneDx, SCV001819902.1

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

Description

Not observed in large population cohorts (Lek 2016); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge; This variant is associated with the following publications: (PMID: 29987844)

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

From Quest Diagnostics Nichols Institute San Juan Capistrano, SCV004221749.1

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

Description

This variant has not been reported in the published literature. It also has not been reported in large, multi-ethnic general populations (Genome Aggregation Database, http://gnomad.broadinstitute.org). Analysis of this variant using bioinformatics tools for the prediction of the effect of amino acid changes on protein structure and function yielded predictions that this variant is damaging. Based on the available information, we are unable to determine the clinical significance of this variant.

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

Last Updated: Oct 20, 2024