NM_000546.6(TP53):c.865C>A (p.Leu289Ile) AND Li-Fraumeni syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jan 25, 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:: RCV001958047.6

Allele description [Variation Report for NM_000546.6(TP53):c.865C>A (p.Leu289Ile)]

NM_000546.6(TP53):c.865C>A (p.Leu289Ile)

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.865C>A (p.Leu289Ile)

HGVS:

NC_000017.11:g.7673755G>T
NG_017013.2:g.18796C>A
NM_000546.6:c.865C>AMANE SELECT
NM_001126112.3:c.865C>A
NM_001126113.3:c.865C>A
NM_001126114.3:c.865C>A
NM_001126115.2:c.469C>A
NM_001126116.2:c.469C>A
NM_001126117.2:c.469C>A
NM_001126118.2:c.748C>A
NM_001276695.3:c.748C>A
NM_001276696.3:c.748C>A
NM_001276697.3:c.388C>A
NM_001276698.3:c.388C>A
NM_001276699.3:c.388C>A
NM_001276760.3:c.748C>A
NM_001276761.3:c.748C>A
NP_000537.3:p.Leu289Ile
NP_001119584.1:p.Leu289Ile
NP_001119585.1:p.Leu289Ile
NP_001119586.1:p.Leu289Ile
NP_001119587.1:p.Leu157Ile
NP_001119588.1:p.Leu157Ile
NP_001119589.1:p.Leu157Ile
NP_001119590.1:p.Leu250Ile
NP_001263624.1:p.Leu250Ile
NP_001263625.1:p.Leu250Ile
NP_001263626.1:p.Leu130Ile
NP_001263627.1:p.Leu130Ile
NP_001263628.1:p.Leu130Ile
NP_001263689.1:p.Leu250Ile
NP_001263690.1:p.Leu250Ile
LRG_321:g.18796C>A
NC_000017.10:g.7577073G>T

Protein change:

L130I

Links:

dbSNP: rs1555525154

NCBI 1000 Genomes Browser:

rs1555525154

Molecular consequence:

NM_000546.6:c.865C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001126112.3:c.865C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001126113.3:c.865C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001126114.3:c.865C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001126115.2:c.469C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001126116.2:c.469C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001126117.2:c.469C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001126118.2:c.748C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001276695.3:c.748C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001276696.3:c.748C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001276697.3:c.388C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001276698.3:c.388C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001276699.3:c.388C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001276760.3:c.748C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001276761.3:c.748C>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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Aspergillus kawachii IFO 4308 DNA, contig: scaffold00025, whole genome shotgun s...
Aspergillus kawachii IFO 4308 DNA, contig: scaffold00025, whole genome shotgun sequence
gi|358373340|dbj|DF126471.1|

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JGI_XZT10121.fwd NIH_XGC_tropTad5 Xenopus tropicalis cDNA clone IMAGE:7588141 5'...
JGI_XZT10121.fwd NIH_XGC_tropTad5 Xenopus tropicalis cDNA clone IMAGE:7588141 5', mRNA sequence
gi|57045904|gnl|dbEST|26936718|gb|C 54.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002209023	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jan 25, 2021)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 12826609, 30224644, 29979965, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002209023

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jan 25, 2021)

germline

clinical testing

PubMed (4)
[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 (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002209023.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

Experimental studies have shown that this variant does not substantially affect TP53 protein function (PMID: 12826609, 30224644, 29979965). This variant has not been reported in the literature in individuals with TP53-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change replaces leucine with isoleucine at codon 289 of the TP53 protein (p.Leu289Ile). The leucine residue is weakly conserved and there is a small physicochemical difference between leucine and isoleucine. 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.

#	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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