NM_000546.6(TP53):c.894G>C (p.Glu298Asp) AND Li-Fraumeni syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jun 26, 2023
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:: RCV003623445.2

Allele description [Variation Report for NM_000546.6(TP53):c.894G>C (p.Glu298Asp)]

NM_000546.6(TP53):c.894G>C (p.Glu298Asp)

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.894G>C (p.Glu298Asp)

HGVS:

NC_000017.11:g.7673726C>G
NG_017013.2:g.18825G>C
NM_000546.6:c.894G>CMANE SELECT
NM_001126112.3:c.894G>C
NM_001126113.3:c.894G>C
NM_001126114.3:c.894G>C
NM_001126115.2:c.498G>C
NM_001126116.2:c.498G>C
NM_001126117.2:c.498G>C
NM_001126118.2:c.777G>C
NM_001276695.3:c.777G>C
NM_001276696.3:c.777G>C
NM_001276697.3:c.417G>C
NM_001276698.3:c.417G>C
NM_001276699.3:c.417G>C
NM_001276760.3:c.777G>C
NM_001276761.3:c.777G>C
NM_001407262.1:c.894G>C
NM_001407263.1:c.777G>C
NM_001407264.1:c.894G>C
NM_001407265.1:c.777G>C
NM_001407266.1:c.894G>C
NM_001407267.1:c.777G>C
NM_001407268.1:c.894G>C
NM_001407269.1:c.777G>C
NM_001407270.1:c.894G>C
NM_001407271.1:c.777G>C
NP_000537.3:p.Glu298Asp
NP_000537.3:p.Glu298Asp
NP_001119584.1:p.Glu298Asp
NP_001119584.1:p.Glu298Asp
NP_001119585.1:p.Glu298Asp
NP_001119585.1:p.Glu298Asp
NP_001119586.1:p.Glu298Asp
NP_001119586.1:p.Glu298Asp
NP_001119587.1:p.Glu166Asp
NP_001119587.1:p.Glu166Asp
NP_001119588.1:p.Glu166Asp
NP_001119588.1:p.Glu166Asp
NP_001119589.1:p.Glu166Asp
NP_001119589.1:p.Glu166Asp
NP_001119590.1:p.Glu259Asp
NP_001119590.1:p.Glu259Asp
NP_001263624.1:p.Glu259Asp
NP_001263625.1:p.Glu259Asp
NP_001263626.1:p.Glu139Asp
NP_001263627.1:p.Glu139Asp
NP_001263628.1:p.Glu139Asp
NP_001263689.1:p.Glu259Asp
NP_001263690.1:p.Glu259Asp
NP_001394191.1:p.Glu298Asp
NP_001394192.1:p.Glu259Asp
NP_001394193.1:p.Glu298Asp
NP_001394194.1:p.Glu259Asp
NP_001394195.1:p.Glu298Asp
NP_001394196.1:p.Glu259Asp
NP_001394197.1:p.Glu298Asp
NP_001394198.1:p.Glu259Asp
NP_001394199.1:p.Glu298Asp
NP_001394200.1:p.Glu259Asp
LRG_321t1:c.894G>C
LRG_321t2:c.894G>C
LRG_321t3:c.894G>C
LRG_321t4:c.894G>C
LRG_321t5:c.498G>C
LRG_321t6:c.498G>C
LRG_321t7:c.498G>C
LRG_321t8:c.777G>C
LRG_321:g.18825G>C
LRG_321:p.Glu298Asp
LRG_321p1:p.Glu298Asp
LRG_321p3:p.Glu298Asp
LRG_321p4:p.Glu298Asp
LRG_321p5:p.Glu166Asp
LRG_321p6:p.Glu166Asp
LRG_321p7:p.Glu166Asp
LRG_321p8:p.Glu259Asp
NC_000017.10:g.7577044C>G
NM_000546.5:c.894G>C
NM_001126112.2:c.894G>C
NM_001126113.2:c.894G>C
NM_001126114.2:c.894G>C
NM_001126115.1:c.498G>C
NM_001126116.1:c.498G>C
NM_001126117.1:c.498G>C
NM_001126118.1:c.777G>C
NR_176326.1:n.923G>C

Protein change:

E139D

Molecular consequence:

NM_000546.6:c.894G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001126112.3:c.894G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001126113.3:c.894G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001126114.3:c.894G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001126115.2:c.498G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001126116.2:c.498G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001126117.2:c.498G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001126118.2:c.777G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001276695.3:c.777G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001276696.3:c.777G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001276697.3:c.417G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001276698.3:c.417G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001276699.3:c.417G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001276760.3:c.777G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001276761.3:c.777G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001407262.1:c.894G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001407263.1:c.777G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001407264.1:c.894G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001407265.1:c.777G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001407266.1:c.894G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001407267.1:c.777G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001407268.1:c.894G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001407269.1:c.777G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001407270.1:c.894G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001407271.1:c.777G>C - missense variant - [Sequence Ontology: SO:0001583]
NR_176326.1:n.923G>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]

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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Mus musculus CLOCK interacting protein, circadian (Cipc), transcript variant 1, ...
Mus musculus CLOCK interacting protein, circadian (Cipc), transcript variant 1, mRNA
gi|295424170|ref|NM_173735.3|

Nucleotide
Puccinia coronata f. sp. avenae isolate 12SD80 000119F_001, whole genome shotgun...
Puccinia coronata f. sp. avenae isolate 12SD80 000119F_001, whole genome shotgun sequence
gi|1321519599|gb|PGCI01001192.1||gn :PGCI01|000119F_001

Nucleotide
JGI_XZT9327.fwd NIH_XGC_tropTad5 Xenopus tropicalis cDNA clone IMAGE:7587653 5',...
JGI_XZT9327.fwd NIH_XGC_tropTad5 Xenopus tropicalis cDNA clone IMAGE:7587653 5', mRNA sequence
gi|57042428|gnl|dbEST|26935473|gb|C 09.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004466765	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jun 26, 2023)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 12826609, 29979965, 30224644, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004466765

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jun 26, 2023)

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

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, SCV004466765.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical 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. Advanced modeling performed at Invitae incorporating data from internal and/or published experimental studies (PMID: 12826609, 29979965, 30224644) indicates that this missense variant is not expected to disrupt TP53 function. 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 aspartic acid, which is acidic and polar, at codon 298 of the TP53 protein (p.Glu298Asp).

#	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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