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NM_000546.6(TP53):c.170A>C (p.Asp57Ala) AND Li-Fraumeni syndrome

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Sep 12, 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:
RCV001926617.4

Allele description [Variation Report for NM_000546.6(TP53):c.170A>C (p.Asp57Ala)]

NM_000546.6(TP53):c.170A>C (p.Asp57Ala)

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.170A>C (p.Asp57Ala)
HGVS:
  • NC_000017.11:g.7676199T>G
  • NG_017013.2:g.16352A>C
  • NM_000546.4:c.170A>C
  • NM_000546.6:c.170A>CMANE SELECT
  • NM_001126112.3:c.170A>C
  • NM_001126113.3:c.170A>C
  • NM_001126114.3:c.170A>C
  • NM_001126118.2:c.53A>C
  • NM_001276695.3:c.53A>C
  • NM_001276696.3:c.53A>C
  • NM_001276760.3:c.53A>C
  • NM_001276761.3:c.53A>C
  • NP_000537.3:p.Asp57Ala
  • NP_001119584.1:p.Asp57Ala
  • NP_001119585.1:p.Asp57Ala
  • NP_001119586.1:p.Asp57Ala
  • NP_001119590.1:p.Asp18Ala
  • NP_001263624.1:p.Asp18Ala
  • NP_001263625.1:p.Asp18Ala
  • NP_001263689.1:p.Asp18Ala
  • NP_001263690.1:p.Asp18Ala
  • LRG_321:g.16352A>C
  • NC_000017.10:g.7579517T>G
Protein change:
D18A
Links:
dbSNP: rs1442824382
NCBI 1000 Genomes Browser:
rs1442824382
Molecular consequence:
  • NM_000546.6:c.170A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001126112.3:c.170A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001126113.3:c.170A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001126114.3:c.170A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001126118.2:c.53A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001276695.3:c.53A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001276696.3:c.53A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001276760.3:c.53A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001276761.3:c.53A>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Li-Fraumeni syndrome (LFS)
Synonyms:
Sarcoma family syndrome of Li and Fraumeni
Identifiers:
MONDO: MONDO:0018875; MedGen: C0085390; OMIM: PS151623

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002204549Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Sep 12, 2021) 		germlineclinical testing

PubMed (3)
[See all records that cite these PMIDs]

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

Mutational processes shape the landscape of TP53 mutations in human cancer.

Giacomelli AO, Yang X, Lintner RE, McFarland JM, Duby M, Kim J, Howard TP, Takeda DY, Ly SH, Kim E, Gannon HS, Hurhula B, Sharpe T, Goodale A, Fritchman B, Steelman S, Vazquez F, Tsherniak A, Aguirre AJ, Doench JG, Piccioni F, Roberts CWM, et al.

Nat Genet. 2018 Oct;50(10):1381-1387. doi: 10.1038/s41588-018-0204-y. Epub 2018 Sep 17.

PubMed [citation]
PMID:
30224644
PMCID:
PMC6168352
See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002204549.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

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. Experimental studies are conflicting or provide insufficient evidence to determine the effect of this variant on TP53 function (PMID: 12826609, 30224644). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt TP53 protein function. This variant has not been reported in the literature in individuals affected with TP53-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change replaces aspartic acid with alanine at codon 57 of the TP53 protein (p.Asp57Ala). The aspartic acid residue is weakly conserved and there is a moderate physicochemical difference between aspartic acid and alanine.

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

Last Updated: Nov 10, 2024