NM_000546.6(TP53):c.904G>A (p.Gly302Arg) AND Li-Fraumeni syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Mar 25, 2020
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:: RCV001352238.7

Allele description [Variation Report for NM_000546.6(TP53):c.904G>A (p.Gly302Arg)]

NM_000546.6(TP53):c.904G>A (p.Gly302Arg)

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.904G>A (p.Gly302Arg)

HGVS:

NC_000017.11:g.7673716C>T
NG_017013.2:g.18835G>A
NM_000546.6:c.904G>AMANE SELECT
NM_001126112.3:c.904G>A
NM_001126113.3:c.904G>A
NM_001126114.3:c.904G>A
NM_001126115.2:c.508G>A
NM_001126116.2:c.508G>A
NM_001126117.2:c.508G>A
NM_001126118.2:c.787G>A
NM_001276695.3:c.787G>A
NM_001276696.3:c.787G>A
NM_001276697.3:c.427G>A
NM_001276698.3:c.427G>A
NM_001276699.3:c.427G>A
NM_001276760.3:c.787G>A
NM_001276761.3:c.787G>A
NP_000537.3:p.Gly302Arg
NP_001119584.1:p.Gly302Arg
NP_001119585.1:p.Gly302Arg
NP_001119586.1:p.Gly302Arg
NP_001119587.1:p.Gly170Arg
NP_001119588.1:p.Gly170Arg
NP_001119589.1:p.Gly170Arg
NP_001119590.1:p.Gly263Arg
NP_001263624.1:p.Gly263Arg
NP_001263625.1:p.Gly263Arg
NP_001263626.1:p.Gly143Arg
NP_001263627.1:p.Gly143Arg
NP_001263628.1:p.Gly143Arg
NP_001263689.1:p.Gly263Arg
NP_001263690.1:p.Gly263Arg
LRG_321:g.18835G>A
NC_000017.10:g.7577034C>T
NM_000546.4:c.904G>A

Protein change:

G143R

Links:

dbSNP: rs863224686

NCBI 1000 Genomes Browser:

rs863224686

Molecular consequence:

NM_000546.6:c.904G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001126112.3:c.904G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001126113.3:c.904G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001126114.3:c.904G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001126115.2:c.508G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001126116.2:c.508G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001126117.2:c.508G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001126118.2:c.787G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001276695.3:c.787G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001276696.3:c.787G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001276697.3:c.427G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001276698.3:c.427G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001276699.3:c.427G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001276760.3:c.787G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001276761.3:c.787G>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

Recent activity

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Puccinia coronata f. sp. avenae isolate 12NC29 000067F_002, whole genome shotgun...
Puccinia coronata f. sp. avenae isolate 12NC29 000067F_002, whole genome shotgun sequence
gi|1321531756|gb|PGCJ01000839.1||gn :PGCJ01|000067F_002

Nucleotide
Puccinia coronata f. sp. avenae isolate 12NC29 000064F_002, whole genome shotgun...
Puccinia coronata f. sp. avenae isolate 12NC29 000064F_002, whole genome shotgun sequence
gi|1321529649|gb|PGCJ01000882.1||gn :PGCJ01|000064F_002

Nucleotide
Puccinia coronata f. sp. avenae isolate 12NC29 000021F_002, whole genome shotgun...
Puccinia coronata f. sp. avenae isolate 12NC29 000021F_002, whole genome shotgun sequence
gi|1321531878|gb|PGCJ01000837.1||gn :PGCJ01|000021F_002

Nucleotide
Puccinia coronata f. sp. avenae isolate 12NC29 000161F_001, whole genome shotgun...
Puccinia coronata f. sp. avenae isolate 12NC29 000161F_001, whole genome shotgun sequence
gi|1321530280|gb|PGCJ01000867.1||gn :PGCJ01|000161F_001

Nucleotide
dai42e05.x1 NICHD_XGC_Sp1 Xenopus laevis cDNA clone IMAGE:4964433 3' similar to ...
dai42e05.x1 NICHD_XGC_Sp1 Xenopus laevis cDNA clone IMAGE:4964433 3' similar to SW:NARY_MOUSE P70352 MEMBRANE-ASSOCIATED LYMPHOCYTE NAD(P)(+)--ARGININE ADP- RIBOSYLTRANSFERASE PRECURSOR, mRNA sequence
gi|17403420|gnl|dbEST|10489696|gb|B 49.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001546775	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Mar 25, 2020)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 12826609, 28369373, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001546775

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Mar 25, 2020)

germline

clinical testing

PubMed (3)
[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

Germline TP53 mutations result into a constitutive defect of p53 DNA binding and transcriptional response to DNA damage.

Zerdoumi Y, Lanos R, Raad S, Flaman JM, Bougeard G, Frebourg T, Tournier I.

Hum Mol Genet. 2017 Jul 15;26(14):2591-2602. doi: 10.1093/hmg/ddx106. Erratum in: Hum Mol Genet. 2017 Jul 15;26(14):2812. doi: 10.1093/hmg/ddx165.

PubMed [citation]

PMID:: 28369373
PMCID:: PMC5886078

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001546775.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

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. This variant has been reported not to substantially affect TP53 protein function (PMID: 12826609). This variant has been observed in individual(s) with breast cancer (PMID: 28369373). This variant is not present in population databases (ExAC no frequency). This sequence change replaces glycine with arginine at codon 302 of the TP53 protein (p.Gly302Arg). The glycine residue is moderately conserved and there is a moderate physicochemical difference between glycine and arginine.

#	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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