NM_000546.6(TP53):c.159G>A (p.Trp53Ter) AND Li-Fraumeni syndrome 1

Germline classification:: Pathogenic (3 submissions)
Last evaluated:: Feb 12, 2024
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:: RCV002289632.4

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:: Li-Fraumeni syndrome 1 (LFS)
Identifiers:: Gene: 553989; MedGen: C1835398; Orphanet: 524; OMIM: 151623

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002583187	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]
SCV003804719	Institute of Human Genetics, University of Leipzig Medical Center	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Jan 20, 2023)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004933904	Myriad Genetics, Inc.	criteria provided, single submitter (Myriad Autosomal Dominant, Autosomal Recessive and X-Linked Classification Criteria (2023))	Pathogenic (Feb 12, 2024)	unknown	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002583187

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]

SCV003804719

Institute of Human Genetics, University of Leipzig Medical Center

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Jan 20, 2023)

unknown

clinical testing

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

SCV004933904

Myriad Genetics, Inc.

criteria provided, single submitter

(Myriad Autosomal Dominant, Autosomal Recessive and X-Linked Classification Criteria (2023))

Pathogenic
(Feb 12, 2024)

unknown

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	unknown	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	unknown	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 Genome-Nilou Lab, SCV002583187.1

#	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

From Institute of Human Genetics, University of Leipzig Medical Center, SCV003804719.1

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

Description

_x000D_ Criteria applied: PVS1, PS4_MOD

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Myriad Genetics, Inc., SCV004933904.1

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

Description

This variant is considered pathogenic. This variant creates a termination codon and is predicted to result in premature protein truncation.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Nov 10, 2024

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