NM_000546.6(TP53):c.86del (p.Asn29fs) AND Li-Fraumeni syndrome

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Sep 18, 2017
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:: RCV000633338.5

Allele description [Variation Report for NM_000546.6(TP53):c.86del (p.Asn29fs)]

NM_000546.6(TP53):c.86del (p.Asn29fs)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

17p13.1

Genomic location:

Preferred name:

NM_000546.6(TP53):c.86del (p.Asn29fs)

HGVS:

NC_000017.10:g.7579710del
NC_000017.11:g.7676395del
NG_017013.2:g.16159del
NM_000546.6:c.86delMANE SELECT
NM_001126112.3:c.86del
NM_001126113.3:c.86del
NM_001126114.3:c.86del
NM_001126118.2:c.-32del
NM_001276695.3:c.-32del
NM_001276696.3:c.-32del
NM_001276760.3:c.-32del
NM_001276761.3:c.-32del
NP_000537.3:p.Asn29fs
NP_001119584.1:p.Asn29fs
NP_001119585.1:p.Asn29fs
NP_001119586.1:p.Asn29fs
LRG_321:g.16159del
NC_000017.10:g.7579710del
NC_000017.10:g.7579710delT
NC_000017.10:g.7579713del
NM_000546.5:c.86delA

Protein change:

N29fs

Links:

dbSNP: rs1555526931

NCBI 1000 Genomes Browser:

rs1555526931

Molecular consequence:

NM_001126118.2:c.-32del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001276695.3:c.-32del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001276696.3:c.-32del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001276760.3:c.-32del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001276761.3:c.-32del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_000546.6:c.86del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001126112.3:c.86del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001126113.3:c.86del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001126114.3:c.86del - frameshift variant - [Sequence Ontology: SO:0001589]

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
SCV000754560	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Sep 18, 2017)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 20522432, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000754560

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Sep 18, 2017)

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

TP53 germline mutation testing in 180 families suspected of Li-Fraumeni syndrome: mutation detection rate and relative frequency of cancers in different familial phenotypes.

Ruijs MW, Verhoef S, Rookus MA, Pruntel R, van der Hout AH, Hogervorst FB, Kluijt I, Sijmons RH, Aalfs CM, Wagner A, Ausems MG, Hoogerbrugge N, van Asperen CJ, Gomez Garcia EB, Meijers-Heijboer H, Ten Kate LP, Menko FH, van 't Veer LJ.

J Med Genet. 2010 Jun;47(6):421-8. doi: 10.1136/jmg.2009.073429.

PubMed [citation]

PMID:: 20522432

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, SCV000754560.4

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

Description

This variant is not present in population databases (ExAC no frequency). This sequence change creates a premature translational stop signal (p.Asn29Thrfs*15) in the TP53 gene. It is expected to result in an absent or disrupted protein product. This variant has not been reported in the literature in individuals with TP53-related disease. For these reasons, this variant has been classified as Pathogenic. Loss-of-function variants in TP53 are known to be pathogenic (PMID: 20522432).

#	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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