NM_000546.6(TP53):c.288_291del (p.Val97fs) AND Li-Fraumeni syndrome

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jun 9, 2024
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:: RCV004802809.1

Allele description [Variation Report for NM_000546.6(TP53):c.288_291del (p.Val97fs)]

NM_000546.6(TP53):c.288_291del (p.Val97fs)

Gene:

TP53:tumor protein p53 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

17p13.1

Genomic location:

Preferred name:

NM_000546.6(TP53):c.288_291del (p.Val97fs)

HGVS:

NC_000017.11:g.7676080_7676083del
NG_017013.2:g.16470_16473del
NM_000546.6:c.288_291delMANE SELECT
NM_001126112.3:c.288_291del
NM_001126113.3:c.288_291del
NM_001126114.3:c.288_291del
NM_001126118.2:c.171_174del
NM_001276695.3:c.171_174del
NM_001276696.3:c.171_174del
NM_001276760.3:c.171_174del
NM_001276761.3:c.171_174del
NM_001407262.1:c.288_291del
NM_001407263.1:c.171_174del
NM_001407264.1:c.288_291del
NM_001407265.1:c.171_174del
NM_001407266.1:c.288_291del
NM_001407267.1:c.171_174del
NM_001407268.1:c.288_291del
NM_001407269.1:c.171_174del
NM_001407270.1:c.288_291del
NM_001407271.1:c.171_174del
NP_000537.3:p.Val97Leufs
NP_000537.3:p.Val97fs
NP_001119584.1:p.Val97Leufs
NP_001119584.1:p.Val97fs
NP_001119585.1:p.Val97Leufs
NP_001119585.1:p.Val97fs
NP_001119586.1:p.Val97Leufs
NP_001119586.1:p.Val97fs
NP_001119590.1:p.Val58Leufs
NP_001119590.1:p.Val58fs
NP_001263624.1:p.Val58fs
NP_001263625.1:p.Val58fs
NP_001263689.1:p.Val58fs
NP_001263690.1:p.Val58fs
NP_001394191.1:p.Val97fs
NP_001394192.1:p.Val58fs
NP_001394193.1:p.Val97fs
NP_001394194.1:p.Val58fs
NP_001394195.1:p.Val97fs
NP_001394196.1:p.Val58fs
NP_001394197.1:p.Val97fs
NP_001394198.1:p.Val58fs
NP_001394199.1:p.Val97fs
NP_001394200.1:p.Val58fs
LRG_321t1:c.286_289del
LRG_321t2:c.286_289del
LRG_321t3:c.286_289del
LRG_321t4:c.286_289del
LRG_321t8:c.169_172del
LRG_321:g.16470_16473del
LRG_321:p.Val97Leufs
LRG_321p1:p.Val97Leufs
LRG_321p3:p.Val97Leufs
LRG_321p4:p.Val97Leufs
LRG_321p8:p.Val58Leufs
NC_000017.10:g.7579398_7579401del
NM_000546.5:c.286_289delTCTG
NM_001126112.2:c.286_289delTCTG
NM_001126113.2:c.286_289delTCTG
NM_001126114.2:c.286_289delTCTG
NM_001126118.1:c.169_172delTCTG
NR_176326.1:n.430_433del

Protein change:

V58fs

Molecular consequence:

NM_000546.6:c.288_291del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001126112.3:c.288_291del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001126113.3:c.288_291del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001126114.3:c.288_291del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001126118.2:c.171_174del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001276695.3:c.171_174del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001276696.3:c.171_174del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001276760.3:c.171_174del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001276761.3:c.171_174del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407262.1:c.288_291del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407263.1:c.171_174del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407264.1:c.288_291del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407265.1:c.171_174del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407266.1:c.288_291del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407267.1:c.171_174del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407268.1:c.288_291del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407269.1:c.171_174del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407270.1:c.288_291del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407271.1:c.171_174del - frameshift variant - [Sequence Ontology: SO:0001589]
NR_176326.1:n.430_433del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Observations:

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
SCV005425743	All of Us Research Program, National Institutes of Health	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Jun 9, 2024)	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

SCV005425743

All of Us Research Program, National Institutes of Health

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Jun 9, 2024)

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	1	not provided	not provided	143475	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 All of Us Research Program, National Institutes of Health, SCV005425743.1

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

Description

This variant deletes 4 nucleotides in exon 4 of the TP53 gene, creating a frameshift and premature translation stop signal. This variant is expected to result in an absent or non-functional protein product. To our knowledge, this variant has not been reported in individuals affected with TP53-related disorders in the literature. This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Loss of TP53 function is a known mechanism of disease (clinicalgenome.org). Based on the available evidence, this variant is classified as Pathogenic.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	143475	not provided	not provided		1	not provided	not provided	not provided

Last Updated: Dec 22, 2024

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