NM_000546.6(TP53):c.26G>A (p.Ser9Asn) AND Li-Fraumeni syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Dec 27, 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:: RCV000534258.9

Allele description [Variation Report for NM_000546.6(TP53):c.26G>A (p.Ser9Asn)]

NM_000546.6(TP53):c.26G>A (p.Ser9Asn)

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.26G>A (p.Ser9Asn)

HGVS:

NC_000017.11:g.7676569C>T
NG_017013.2:g.15982G>A
NM_000546.6:c.26G>AMANE SELECT
NM_001126112.3:c.26G>A
NM_001126113.3:c.26G>A
NM_001126114.3:c.26G>A
NM_001126118.2:c.-209G>A
NM_001276695.3:c.-92G>A
NM_001276696.3:c.-92G>A
NM_001276760.3:c.-92G>A
NM_001276761.3:c.-92G>A
NP_000537.3:p.Ser9Asn
NP_000537.3:p.Ser9Asn
NP_001119584.1:p.Ser9Asn
NP_001119585.1:p.Ser9Asn
NP_001119586.1:p.Ser9Asn
LRG_321t1:c.26G>A
LRG_321:g.15982G>A
LRG_321p1:p.Ser9Asn
NC_000017.10:g.7579887C>T
NM_000546.5:c.26G>A

Protein change:

S9N

Links:

dbSNP: rs1555527015

NCBI 1000 Genomes Browser:

rs1555527015

Molecular consequence:

NM_001126118.2:c.-209G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001276695.3:c.-92G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001276696.3:c.-92G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001276760.3:c.-92G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001276761.3:c.-92G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_000546.6:c.26G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001126112.3:c.26G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001126113.3:c.26G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001126114.3:c.26G>A - 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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000629798	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Dec 27, 2021)	germline	clinical testing	PubMed (5) [See all records that cite these PMIDs] 12826609, 30224644, 33245408, 29522266, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000629798

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Dec 27, 2021)

germline

clinical testing

PubMed (5)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical 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 (5)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000629798.6

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (5)

Description

This sequence change replaces serine, which is neutral and polar, with asparagine, which is neutral and polar, at codon 9 of the TP53 protein (p.Ser9Asn). 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, 30224644, 33245408). 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. ClinVar contains an entry for this variant (Variation ID: 458531). This missense change has been observed in individual(s) with breast cancer (PMID: 29522266). This variant is not present in population databases (gnomAD no frequency).

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Nov 10, 2024

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