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NM_000546.6(TP53):c.79C>T (p.Pro27Ser) AND Li-Fraumeni syndrome

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Aug 31, 2022
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:
RCV000633393.10

Allele description [Variation Report for NM_000546.6(TP53):c.79C>T (p.Pro27Ser)]

NM_000546.6(TP53):c.79C>T (p.Pro27Ser)

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.79C>T (p.Pro27Ser)
HGVS:
  • NC_000017.11:g.7676399G>A
  • NG_017013.2:g.16152C>T
  • NM_000546.6:c.79C>TMANE SELECT
  • NM_001126112.3:c.79C>T
  • NM_001126113.3:c.79C>T
  • NM_001126114.3:c.79C>T
  • NM_001126118.2:c.-39C>T
  • NM_001276695.3:c.-39C>T
  • NM_001276696.3:c.-39C>T
  • NM_001276760.3:c.-39C>T
  • NM_001276761.3:c.-39C>T
  • NP_000537.3:p.Pro27Ser
  • NP_000537.3:p.Pro27Ser
  • NP_001119584.1:p.Pro27Ser
  • NP_001119585.1:p.Pro27Ser
  • NP_001119586.1:p.Pro27Ser
  • LRG_321t1:c.79C>T
  • LRG_321:g.16152C>T
  • LRG_321p1:p.Pro27Ser
  • NC_000017.10:g.7579717G>A
  • NM_000546.4:c.79C>T
  • NM_000546.5:c.79C>T
Protein change:
P27S
Links:
dbSNP: rs922736614
NCBI 1000 Genomes Browser:
rs922736614
Molecular consequence:
  • NM_001126118.2:c.-39C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001276695.3:c.-39C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001276696.3:c.-39C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001276760.3:c.-39C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001276761.3:c.-39C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_000546.6:c.79C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001126112.3:c.79C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001126113.3:c.79C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001126114.3:c.79C>T - 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
SCV000754615Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Aug 31, 2022) 		germlineclinical testing

PubMed (4)
[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

A Systematic p53 Mutation Library Links Differential Functional Impact to Cancer Mutation Pattern and Evolutionary Conservation.

Kotler E, Shani O, Goldfeld G, Lotan-Pompan M, Tarcic O, Gershoni A, Hopf TA, Marks DS, Oren M, Segal E.

Mol Cell. 2018 Jul 5;71(1):178-190.e8. doi: 10.1016/j.molcel.2018.06.012. Erratum in: Mol Cell. 2018 Sep 6;71(5):873. doi: 10.1016/j.molcel.2018.08.013.

PubMed [citation]
PMID:
29979965
See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000754615.7

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (4)

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 have shown that this missense change does not substantially affect TP53 function (PMID: 12826609, 29979965, 30224644). Advanced modeling of experimental studies (such as gene expression, population dynamics, functional pathways, and cell-cycle effects in cell culture) performed at Invitae indicates that this missense variant is not expected to disrupt TP53 protein function. ClinVar contains an entry for this variant (Variation ID: 528271). This variant has not been reported in the literature in individuals affected with TP53-related conditions. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This sequence change replaces proline, which is neutral and non-polar, with serine, which is neutral and polar, at codon 27 of the TP53 protein (p.Pro27Ser).

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

Last Updated: Sep 29, 2024