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NM_000546.6(TP53):c.359A>T (p.Lys120Met) AND not specified

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Aug 28, 2020
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:
RCV001174845.2

Allele description [Variation Report for NM_000546.6(TP53):c.359A>T (p.Lys120Met)]

NM_000546.6(TP53):c.359A>T (p.Lys120Met)

Gene:
TP53:tumor protein p53 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
17p13.1
Genomic location:
Preferred name:
NM_000546.6(TP53):c.359A>T (p.Lys120Met)
HGVS:
  • NC_000017.11:g.7676010T>A
  • NG_017013.2:g.16541A>T
  • NM_000546.6:c.359A>TMANE SELECT
  • NM_001126112.3:c.359A>T
  • NM_001126113.3:c.359A>T
  • NM_001126114.3:c.359A>T
  • NM_001126118.2:c.242A>T
  • NM_001276695.3:c.242A>T
  • NM_001276696.3:c.242A>T
  • NM_001276760.3:c.242A>T
  • NM_001276761.3:c.242A>T
  • NP_000537.3:p.Lys120Met
  • NP_001119584.1:p.Lys120Met
  • NP_001119585.1:p.Lys120Met
  • NP_001119586.1:p.Lys120Met
  • NP_001119590.1:p.Lys81Met
  • NP_001263624.1:p.Lys81Met
  • NP_001263625.1:p.Lys81Met
  • NP_001263689.1:p.Lys81Met
  • NP_001263690.1:p.Lys81Met
  • LRG_321t1:c.359A>T
  • LRG_321:g.16541A>T
  • NC_000017.10:g.7579328T>A
  • NM_000546.5:c.359A>T
Protein change:
K120M
Links:
dbSNP: rs2073450819
NCBI 1000 Genomes Browser:
rs2073450819
Molecular consequence:
  • NM_000546.6:c.359A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001126112.3:c.359A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001126113.3:c.359A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001126114.3:c.359A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001126118.2:c.242A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001276695.3:c.242A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001276696.3:c.242A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001276760.3:c.242A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001276761.3:c.242A>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001338227Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)		Uncertain significance
(Aug 28, 2020) 		germlineclinical testing

PubMed (6)
[See all records that cite these PMIDs]

Citation Link

Help

Summary from all submissions

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

Citations

PubMed

Understanding the function-structure and function-mutation relationships of p53 tumor suppressor protein by high-resolution missense mutation analysis.

Kato S, Han SY, Liu W, Otsuka K, Shibata H, Kanamaru R, Ishioka C.

Proc Natl Acad Sci U S A. 2003 Jul 8;100(14):8424-9. Epub 2003 Jun 25.

PubMed [citation]
PMID:
12826609
PMCID:
PMC166245

Concomitant bifocal urothelial carcinoma and breast tumor: second primary cancer or metastatic spread to the breast?

Dumont C, Gauthier H, Vérine J, Lehmann-Che J, de Cremoux P, Pouessel D, Culine S.

Case Rep Oncol Med. 2014;2014:917581. doi: 10.1155/2014/917581. Epub 2014 Aug 4.

PubMed [citation]
PMID:
25161789
PMCID:
PMC4137750
See all PubMed Citations (6)

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV001338227.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (6)

Description

Variant summary: TP53 c.359A>T (p.Lys120Met) results in a non-conservative amino acid change located in the DNA-binding domain (IPR010991) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 251048 control chromosomes. To our knowledge, there are no reports of c.359A>T in individuals affected with Li-Fraumeni Syndrome. However, somatic occurrences of this variant have been reported in individuals affected with various cancer phenotypes (Examples- Zenz_2010, Dumont_2014, Malcikova_2015, Nikbakht_2016). At least one publication reports experimental evidence evaluating an impact on protein function. The most pronounced variant effect results in 10%-<30% of normal transcriptional activity in a yeast-based assay (Kato_2003). No other clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as VUS-possibly pathogenic.

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

Last Updated: Nov 5, 2022