NM_000546.6(TP53):c.159G>A (p.Trp53Ter) AND Hereditary cancer-predisposing syndrome

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Jun 18, 2022
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV001012297.5

Allele description [Variation Report for NM_000546.6(TP53):c.159G>A (p.Trp53Ter)]

NM_000546.6(TP53):c.159G>A (p.Trp53Ter)

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.159G>A (p.Trp53Ter)

HGVS:

NC_000017.11:g.7676210C>T
NG_017013.2:g.16341G>A
NM_000546.6:c.159G>AMANE SELECT
NM_001126112.3:c.159G>A
NM_001126113.3:c.159G>A
NM_001126114.3:c.159G>A
NM_001126118.2:c.42G>A
NM_001276695.3:c.42G>A
NM_001276696.3:c.42G>A
NM_001276760.3:c.42G>A
NM_001276761.3:c.42G>A
NP_000537.3:p.Trp53Ter
NP_000537.3:p.Trp53Ter
NP_001119584.1:p.Trp53Ter
NP_001119585.1:p.Trp53Ter
NP_001119586.1:p.Trp53Ter
NP_001119590.1:p.Trp14Ter
NP_001263624.1:p.Trp14Ter
NP_001263625.1:p.Trp14Ter
NP_001263689.1:p.Trp14Ter
NP_001263690.1:p.Trp14Ter
LRG_321t1:c.159G>A
LRG_321:g.16341G>A
LRG_321p1:p.Trp53Ter
NC_000017.10:g.7579528C>T
NM_000546.4:c.159G>A
NM_000546.5:c.159G>A

Protein change:

W14*

Links:

dbSNP: rs1064794618

NCBI 1000 Genomes Browser:

rs1064794618

Molecular consequence:

NM_000546.6:c.159G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001126112.3:c.159G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001126113.3:c.159G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001126114.3:c.159G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001126118.2:c.42G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001276695.3:c.42G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001276696.3:c.42G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001276760.3:c.42G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001276761.3:c.42G>A - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:: Hereditary cancer-predisposing syndrome
Synonyms:: Neoplastic Syndromes, Hereditary; Tumor predisposition; Cancer predisposition; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0015356; MeSH: D009386; MedGen: C0027672

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001172730	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Pathogenic (Dec 20, 2018)	germline	clinical testing	Citation Link,
SCV002582626	Genome-Nilou Lab	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Jun 18, 2022)	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

SCV001172730

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Pathogenic
(Dec 20, 2018)

germline

clinical testing

Citation Link,

SCV002582626

Genome-Nilou Lab

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Jun 18, 2022)

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
not provided	germline	no	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Ambry Genetics, SCV001172730.4

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

Description

The p.W53* pathogenic mutation (also known as c.159G>A), located in coding exon 3 of the TP53 gene, results from a G to A substitution at nucleotide position 159. This changes the amino acid from a tryptophan to a stop codon within coding exon 3. This alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. As such, this alteration is interpreted as a disease-causing mutation.

#	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

From Genome-Nilou Lab, SCV002582626.1

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	no	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Nov 10, 2024

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