NM_000546.6(TP53):c.175G>T (p.Gly59Cys) AND Li-Fraumeni syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Nov 8, 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:: RCV003622619.2

Allele description [Variation Report for NM_000546.6(TP53):c.175G>T (p.Gly59Cys)]

NM_000546.6(TP53):c.175G>T (p.Gly59Cys)

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.175G>T (p.Gly59Cys)

HGVS:

NC_000017.11:g.7676194C>A
NG_017013.2:g.16357G>T
NM_000546.6:c.175G>TMANE SELECT
NM_001126112.3:c.175G>T
NM_001126113.3:c.175G>T
NM_001126114.3:c.175G>T
NM_001126118.2:c.58G>T
NM_001276695.3:c.58G>T
NM_001276696.3:c.58G>T
NM_001276760.3:c.58G>T
NM_001276761.3:c.58G>T
NM_001407262.1:c.175G>T
NM_001407263.1:c.58G>T
NM_001407264.1:c.175G>T
NM_001407265.1:c.58G>T
NM_001407266.1:c.175G>T
NM_001407267.1:c.58G>T
NM_001407268.1:c.175G>T
NM_001407269.1:c.58G>T
NM_001407270.1:c.175G>T
NM_001407271.1:c.58G>T
NP_000537.3:p.Gly59Cys
NP_000537.3:p.Gly59Cys
NP_001119584.1:p.Gly59Cys
NP_001119584.1:p.Gly59Cys
NP_001119585.1:p.Gly59Cys
NP_001119585.1:p.Gly59Cys
NP_001119586.1:p.Gly59Cys
NP_001119586.1:p.Gly59Cys
NP_001119590.1:p.Gly20Cys
NP_001119590.1:p.Gly20Cys
NP_001263624.1:p.Gly20Cys
NP_001263625.1:p.Gly20Cys
NP_001263689.1:p.Gly20Cys
NP_001263690.1:p.Gly20Cys
NP_001394191.1:p.Gly59Cys
NP_001394192.1:p.Gly20Cys
NP_001394193.1:p.Gly59Cys
NP_001394194.1:p.Gly20Cys
NP_001394195.1:p.Gly59Cys
NP_001394196.1:p.Gly20Cys
NP_001394197.1:p.Gly59Cys
NP_001394198.1:p.Gly20Cys
NP_001394199.1:p.Gly59Cys
NP_001394200.1:p.Gly20Cys
LRG_321t1:c.175G>T
LRG_321t2:c.175G>T
LRG_321t3:c.175G>T
LRG_321t4:c.175G>T
LRG_321t8:c.58G>T
LRG_321:g.16357G>T
LRG_321:p.Gly59Cys
LRG_321p1:p.Gly59Cys
LRG_321p3:p.Gly59Cys
LRG_321p4:p.Gly59Cys
LRG_321p8:p.Gly20Cys
NC_000017.10:g.7579512C>A
NM_000546.5:c.175G>T
NM_001126112.2:c.175G>T
NM_001126113.2:c.175G>T
NM_001126114.2:c.175G>T
NM_001126118.1:c.58G>T
NR_176326.1:n.317G>T

Protein change:

G20C

Molecular consequence:

NM_000546.6:c.175G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001126112.3:c.175G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001126113.3:c.175G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001126114.3:c.175G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001126118.2:c.58G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001276695.3:c.58G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001276696.3:c.58G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001276760.3:c.58G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001276761.3:c.58G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407262.1:c.175G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407263.1:c.58G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407264.1:c.175G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407265.1:c.58G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407266.1:c.175G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407267.1:c.58G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407268.1:c.175G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407269.1:c.58G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407270.1:c.175G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407271.1:c.58G>T - missense variant - [Sequence Ontology: SO:0001583]
NR_176326.1:n.317G>T - 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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RecName: Full=E3 ubiquitin-protein ligase UHRF1; AltName: Full=RING-type E3 ubiq...
RecName: Full=E3 ubiquitin-protein ligase UHRF1; AltName: Full=RING-type E3 ubiquitin transferase UHRF1; AltName: Full=Ubiquitin-like PHD and RING finger domain-containing protein 1; AltName: Full=Ubiquitin-like-containing PHD and RING finger domains protein 1
gi|410591701|sp|E7EZF3.1|UHRF1_DANR

Protein
Chain B, 16-mer peptide from Nuclear receptor coactivator 1
Chain B, 16-mer peptide from Nuclear receptor coactivator 1
gi|1806061729|pdb|6KTN|B

Protein
Bromouracil
Bromouracil
5-Bromo-2,4(1H,3H)-pyrimidinedione. Brominated derivative of uracil that acts as an antimetabolite, substituting for thymine in DNA. It is used mainly as an experimental mutag...<br/>Year introduced: 1974(1971)

MeSH
Flucytosine
Flucytosine
A fluorinated cytosine analog that is used as an antifungal agent.<br/>Year introduced: 1987(1972)

MeSH
Amobarbital
Amobarbital
A barbiturate with hypnotic and sedative properties (but not antianxiety). Adverse effects are mainly a consequence of dose-related CNS depression and the risk of dependence w...<br/>

MeSH

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004413363	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Nov 8, 2022)	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

SCV004413363

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Nov 8, 2022)

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, SCV004413363.1

#	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. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. 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 present in population databases (no rsID available, gnomAD 0.01%). This sequence change replaces glycine, which is neutral and non-polar, with cysteine, which is neutral and slightly polar, at codon 59 of the TP53 protein (p.Gly59Cys).

#	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: Nov 10, 2024

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