NM_000455.4(STK11):c.1150C>T (p.Arg384Trp) AND Malignant tumor of breast

Clinical significance:Uncertain significance

Review status:(0/4) 0 stars out of maximum of 4 stars

no assertion criteria provided

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV001356885.1

Allele description [Variation Report for NM_000455.4(STK11):c.1150C>T (p.Arg384Trp)]

NM_000455.4(STK11):c.1150C>T (p.Arg384Trp)

Gene:
STK11:serine/threonine kinase 11 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
19p13.3
Genomic location:
Preferred name:
NM_000455.4(STK11):c.1150C>T (p.Arg384Trp)
HGVS:
  • NC_000019.10:g.1226495C>T
  • NG_007460.2:g.42089C>T
  • NM_000455.4:c.1150C>T
  • NP_000446.1:p.Arg384Trp
  • LRG_319t1:c.1150C>T
  • LRG_319:g.42089C>T
  • LRG_319p1:p.Arg384Trp
  • NC_000019.9:g.1226494C>T
Protein change:
R384W
Links:
dbSNP: rs752015385
NCBI 1000 Genomes Browser:
rs752015385
Molecular consequence:
  • NM_000455.4:c.1150C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Malignant tumor of breast
Synonyms:
Breast cancer; Malignant breast neoplasm
Identifiers:
MONDO: MONDO:0007254; MedGen: C0006142

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001552167Department of Pathology and Laboratory Medicine,Sinai Health System - The Canadian Open Genetics Repository (COGR)

See additional submitters

no assertion criteria providedUncertain significanceunknownclinical testing

Summary from all submissions

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

Details of each submission

From Department of Pathology and Laboratory Medicine,Sinai Health System - The Canadian Open Genetics Repository (COGR), SCV001552167.1

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

Description

The STK11 p.Arg384Trp variant was identified in the literature although a frequency in an affected population was not provided (Cheng 2015). The variant was also identified in dbSNP as “with Uncertain significance allele”. The variant was not identified in ClinVar or LOVD 3.0. The variant was identified in control databases in 1 of 30920 chromosomes at a frequency of 0.00003 (Genome Aggregation Database Feb 27, 2017). The variant was observed in the African population in 1 of 8702 chromosomes (freq: 0.0001), while the variant was not observed in the European, Other, Latino, Ashkenazi Jewish, East Asian, Finnish, or South Asian populations. The p.Arg384 residue is not conserved in mammals and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) provide inconsistent predictions regarding the impact to the protein; this information is not very predictive of pathogenicity. The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) do not predict a difference in splicing. In summary, based on the above information, the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain significance.

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

Last Updated: Aug 11, 2021

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