NM_000546.6(TP53):c.908G>A (p.Ser303Asn) AND Li-Fraumeni syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Oct 21, 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:: RCV000700080.6

Allele description [Variation Report for NM_000546.6(TP53):c.908G>A (p.Ser303Asn)]

NM_000546.6(TP53):c.908G>A (p.Ser303Asn)

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.908G>A (p.Ser303Asn)

HGVS:

NC_000017.11:g.7673712C>T
NG_017013.2:g.18839G>A
NM_000546.6:c.908G>AMANE SELECT
NM_001126112.3:c.908G>A
NM_001126113.3:c.908G>A
NM_001126114.3:c.908G>A
NM_001126115.2:c.512G>A
NM_001126116.2:c.512G>A
NM_001126117.2:c.512G>A
NM_001126118.2:c.791G>A
NM_001276695.3:c.791G>A
NM_001276696.3:c.791G>A
NM_001276697.3:c.431G>A
NM_001276698.3:c.431G>A
NM_001276699.3:c.431G>A
NM_001276760.3:c.791G>A
NM_001276761.3:c.791G>A
NP_000537.3:p.Ser303Asn
NP_000537.3:p.Ser303Asn
NP_001119584.1:p.Ser303Asn
NP_001119585.1:p.Ser303Asn
NP_001119586.1:p.Ser303Asn
NP_001119587.1:p.Ser171Asn
NP_001119588.1:p.Ser171Asn
NP_001119589.1:p.Ser171Asn
NP_001119590.1:p.Ser264Asn
NP_001263624.1:p.Ser264Asn
NP_001263625.1:p.Ser264Asn
NP_001263626.1:p.Ser144Asn
NP_001263627.1:p.Ser144Asn
NP_001263628.1:p.Ser144Asn
NP_001263689.1:p.Ser264Asn
NP_001263690.1:p.Ser264Asn
LRG_321t1:c.908G>A
LRG_321:g.18839G>A
LRG_321p1:p.Ser303Asn
NC_000017.10:g.7577030C>T
NM_000546.4:c.908G>A
NM_000546.5:c.908G>A
P04637:p.Ser303Asn

Protein change:

S144N

Links:

UniProtKB: P04637#VAR_045465; dbSNP: rs876658714

NCBI 1000 Genomes Browser:

rs876658714

Molecular consequence:

NM_000546.6:c.908G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001126112.3:c.908G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001126113.3:c.908G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001126114.3:c.908G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001126115.2:c.512G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001126116.2:c.512G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001126117.2:c.512G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001126118.2:c.791G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001276695.3:c.791G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001276696.3:c.791G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001276697.3:c.431G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001276698.3:c.431G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001276699.3:c.431G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001276760.3:c.791G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001276761.3:c.791G>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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LOC100547274 [Meleagris gallopavo]
LOC100547274 [Meleagris gallopavo]
Gene ID:100547274

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000828820	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Oct 21, 2021)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 12826609, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000828820

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Oct 21, 2021)

germline

clinical testing

PubMed (2)
[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

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, SCV000828820.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

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. Experimental studies have shown that this missense change does not substantially affect TP53 protein function (PMID: 12826609). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The asparagine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. ClinVar contains an entry for this variant (Variation ID: 230695). This variant has not been reported in the literature in individuals affected with TP53-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change replaces serine with asparagine at codon 303 of the TP53 protein (p.Ser303Asn). The serine residue is moderately conserved and there is a small physicochemical difference between serine and asparagine.

#	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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