NM_000546.6(TP53):c.862A>G (p.Asn288Asp) AND Li-Fraumeni syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Mar 14, 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:: RCV001325049.7

Allele description [Variation Report for NM_000546.6(TP53):c.862A>G (p.Asn288Asp)]

NM_000546.6(TP53):c.862A>G (p.Asn288Asp)

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.862A>G (p.Asn288Asp)

HGVS:

NC_000017.11:g.7673758T>C
NG_017013.2:g.18793A>G
NM_000546.6:c.862A>GMANE SELECT
NM_001126112.3:c.862A>G
NM_001126113.3:c.862A>G
NM_001126114.3:c.862A>G
NM_001126115.2:c.466A>G
NM_001126116.2:c.466A>G
NM_001126117.2:c.466A>G
NM_001126118.2:c.745A>G
NM_001276695.3:c.745A>G
NM_001276696.3:c.745A>G
NM_001276697.3:c.385A>G
NM_001276698.3:c.385A>G
NM_001276699.3:c.385A>G
NM_001276760.3:c.745A>G
NM_001276761.3:c.745A>G
NP_000537.3:p.Asn288Asp
NP_001119584.1:p.Asn288Asp
NP_001119585.1:p.Asn288Asp
NP_001119586.1:p.Asn288Asp
NP_001119587.1:p.Asn156Asp
NP_001119588.1:p.Asn156Asp
NP_001119589.1:p.Asn156Asp
NP_001119590.1:p.Asn249Asp
NP_001263624.1:p.Asn249Asp
NP_001263625.1:p.Asn249Asp
NP_001263626.1:p.Asn129Asp
NP_001263627.1:p.Asn129Asp
NP_001263628.1:p.Asn129Asp
NP_001263689.1:p.Asn249Asp
NP_001263690.1:p.Asn249Asp
LRG_321:g.18793A>G
NC_000017.10:g.7577076T>C

Protein change:

N129D

Links:

dbSNP: rs2073184850

NCBI 1000 Genomes Browser:

rs2073184850

Molecular consequence:

NM_000546.6:c.862A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001126112.3:c.862A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001126113.3:c.862A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001126114.3:c.862A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001126115.2:c.466A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001126116.2:c.466A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001126117.2:c.466A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001126118.2:c.745A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001276695.3:c.745A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001276696.3:c.745A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001276697.3:c.385A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001276698.3:c.385A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001276699.3:c.385A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001276760.3:c.745A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001276761.3:c.745A>G - 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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leucine-rich repeat neuronal protein 1-like [Gadus morhua]
leucine-rich repeat neuronal protein 1-like [Gadus morhua]
gi|1721956665|ref|XP_030231294.1|

Protein
uncharacterized protein LOC115532525 isoform X1 [Gadus morhua]
uncharacterized protein LOC115532525 isoform X1 [Gadus morhua]
gi|1721985405|ref|XP_030198215.1|

Protein
PREDICTED: Gadus morhua metalloproteinase inhibitor 2-like (LOC115556743), trans...
PREDICTED: Gadus morhua metalloproteinase inhibitor 2-like (LOC115556743), transcript variant X1, mRNA
gi|1721879274|ref|XM_030374023.1|

Nucleotide
Lymphoid-restricted membrane protein [Mus musculus]
Lymphoid-restricted membrane protein [Mus musculus]
gi|31127122|gb|AAH52909.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001516022	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Mar 14, 2022)	germline	clinical testing	PubMed (5) [See all records that cite these PMIDs] 12826609, 12909720, 29979965, 30224644, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001516022

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Mar 14, 2022)

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

Functional mutants of the sequence-specific transcription factor p53 and implications for master genes of diversity.

Resnick MA, Inga A.

Proc Natl Acad Sci U S A. 2003 Aug 19;100(17):9934-9. Epub 2003 Aug 8.

PubMed [citation]

PMID:: 12909720
PMCID:: PMC187891

See all PubMed Citations (5)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001516022.4

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

Description

Experimental studies are conflicting or provide insufficient evidence to determine the effect of this variant on TP53 function (PMID: 12826609, 12909720, 29979965, 30224644). 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: 1024822). 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 asparagine, which is neutral and polar, with aspartic acid, which is acidic and polar, at codon 288 of the TP53 protein (p.Asn288Asp).

#	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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