NM_000546.6(TP53):c.199C>T (p.Pro67Ser) AND Li-Fraumeni syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Feb 7, 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:: RCV001036060.9

Allele description [Variation Report for NM_000546.6(TP53):c.199C>T (p.Pro67Ser)]

NM_000546.6(TP53):c.199C>T (p.Pro67Ser)

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.199C>T (p.Pro67Ser)

HGVS:

NC_000017.11:g.7676170G>A
NG_017013.2:g.16381C>T
NM_000546.6:c.199C>TMANE SELECT
NM_001126112.3:c.199C>T
NM_001126113.3:c.199C>T
NM_001126114.3:c.199C>T
NM_001126118.2:c.82C>T
NM_001276695.3:c.82C>T
NM_001276696.3:c.82C>T
NM_001276760.3:c.82C>T
NM_001276761.3:c.82C>T
NP_000537.3:p.Pro67Ser
NP_001119584.1:p.Pro67Ser
NP_001119585.1:p.Pro67Ser
NP_001119586.1:p.Pro67Ser
NP_001119590.1:p.Pro28Ser
NP_001263624.1:p.Pro28Ser
NP_001263625.1:p.Pro28Ser
NP_001263689.1:p.Pro28Ser
NP_001263690.1:p.Pro28Ser
LRG_321t1:c.199C>T
LRG_321:g.16381C>T
NC_000017.10:g.7579488G>A
NM_000546.5:c.199C>T

Protein change:

P28S

Links:

dbSNP: rs2073476832

NCBI 1000 Genomes Browser:

rs2073476832

Molecular consequence:

NM_000546.6:c.199C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001126112.3:c.199C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001126113.3:c.199C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001126114.3:c.199C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001126118.2:c.82C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001276695.3:c.82C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001276696.3:c.82C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001276760.3:c.82C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001276761.3:c.82C>T - 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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001199407	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Feb 7, 2020)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001199407

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Feb 7, 2020)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

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

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001199407.5

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

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. An experimental study in yeast has shown that this variant does not impair the transcriptional transactivation activity of the TP53 protein (PMID:¬†12826609). 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 proline with serine at codon 67 of the TP53 protein (p.Pro67Ser). The proline residue is moderately conserved and there is a moderate physicochemical difference between proline and serine.

#	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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