NM_000546.6(TP53):c.773A>C (p.Glu258Ala) AND Li-Fraumeni syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Sep 22, 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:: RCV000551157.8

Allele description [Variation Report for NM_000546.6(TP53):c.773A>C (p.Glu258Ala)]

NM_000546.6(TP53):c.773A>C (p.Glu258Ala)

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.773A>C (p.Glu258Ala)

HGVS:

NC_000017.11:g.7674190T>G
NG_017013.2:g.18361A>C
NM_000546.6:c.773A>CMANE SELECT
NM_001126112.3:c.773A>C
NM_001126113.3:c.773A>C
NM_001126114.3:c.773A>C
NM_001126115.2:c.377A>C
NM_001126116.2:c.377A>C
NM_001126117.2:c.377A>C
NM_001126118.2:c.656A>C
NM_001276695.3:c.656A>C
NM_001276696.3:c.656A>C
NM_001276697.3:c.296A>C
NM_001276698.3:c.296A>C
NM_001276699.3:c.296A>C
NM_001276760.3:c.656A>C
NM_001276761.3:c.656A>C
NP_000537.3:p.Glu258Ala
NP_000537.3:p.Glu258Ala
NP_001119584.1:p.Glu258Ala
NP_001119585.1:p.Glu258Ala
NP_001119586.1:p.Glu258Ala
NP_001119587.1:p.Glu126Ala
NP_001119588.1:p.Glu126Ala
NP_001119589.1:p.Glu126Ala
NP_001119590.1:p.Glu219Ala
NP_001263624.1:p.Glu219Ala
NP_001263625.1:p.Glu219Ala
NP_001263626.1:p.Glu99Ala
NP_001263627.1:p.Glu99Ala
NP_001263628.1:p.Glu99Ala
NP_001263689.1:p.Glu219Ala
NP_001263690.1:p.Glu219Ala
LRG_321t1:c.773A>C
LRG_321:g.18361A>C
LRG_321p1:p.Glu258Ala
NC_000017.10:g.7577508T>G
NM_000546.5:c.773A>C

Protein change:

E126A

Links:

dbSNP: rs1060501201

NCBI 1000 Genomes Browser:

rs1060501201

Molecular consequence:

NM_000546.6:c.773A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001126112.3:c.773A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001126113.3:c.773A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001126114.3:c.773A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001126115.2:c.377A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001126116.2:c.377A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001126117.2:c.377A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001126118.2:c.656A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001276695.3:c.656A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001276696.3:c.656A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001276697.3:c.296A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001276698.3:c.296A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001276699.3:c.296A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001276760.3:c.656A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001276761.3:c.656A>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

Recent activity

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PREDICTED: Homo sapiens uncharacterized LOC105378066 (LOC105378066), transcript ...
PREDICTED: Homo sapiens uncharacterized LOC105378066 (LOC105378066), transcript variant X3, ncRNA
gi|1034653589|ref|XR_943129.2|

Nucleotide
Trypanosoma conorhini uncharacterized protein (Tco025E_00886), partial mRNA
Trypanosoma conorhini uncharacterized protein (Tco025E_00886), partial mRNA
gi|1673129991|ref|XM_029367825.1|

Nucleotide
Trypanosoma conorhini uncharacterized protein (Tco025E_00829), partial mRNA
Trypanosoma conorhini uncharacterized protein (Tco025E_00829), partial mRNA
gi|1673129941|ref|XM_029367769.1|

Nucleotide
Trypanosoma conorhini uncharacterized protein (Tco025E_00765), partial mRNA
Trypanosoma conorhini uncharacterized protein (Tco025E_00765), partial mRNA
gi|1673129813|ref|XM_029367705.1|

Nucleotide
Trypanosoma conorhini putative inosine-guanine nucleoside hydrolase (Tco025E_008...
Trypanosoma conorhini putative inosine-guanine nucleoside hydrolase (Tco025E_00814), partial mRNA
gi|1673129911|ref|XM_029367754.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000629868	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Sep 22, 2022)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 12826609, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000629868

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Sep 22, 2022)

germline

clinical testing

PubMed (2)
[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

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000629868.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

Experimental studies have shown that this missense change affects TP53 function (PMID: 12826609). 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. 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 expected to disrupt TP53 protein function. ClinVar contains an entry for this variant (Variation ID: 458563). This variant has not been reported in the literature in individuals affected with TP53-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces glutamic acid, which is acidic and polar, with alanine, which is neutral and non-polar, at codon 258 of the TP53 protein (p.Glu258Ala).

#	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: Sep 29, 2024

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