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NM_000546.6(TP53):c.375+2_375+15del AND Li-Fraumeni syndrome

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Mar 27, 2020
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:
RCV001388867.7

Allele description [Variation Report for NM_000546.6(TP53):c.375+2_375+15del]

NM_000546.6(TP53):c.375+2_375+15del

Gene:
TP53:tumor protein p53 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
17p13.1
Genomic location:
Preferred name:
NM_000546.6(TP53):c.375+2_375+15del
HGVS:
  • NC_000017.11:g.7675980_7675993del
  • NG_017013.2:g.16559_16572del
  • NM_000546.6:c.375+2_375+15delMANE SELECT
  • NM_001126112.3:c.375+2_375+15del
  • NM_001126113.3:c.375+2_375+15del
  • NM_001126114.3:c.375+2_375+15del
  • NM_001126118.2:c.258+2_258+15del
  • NM_001276695.3:c.258+2_258+15del
  • NM_001276696.3:c.258+2_258+15del
  • NM_001276760.3:c.258+2_258+15del
  • NM_001276761.3:c.258+2_258+15del
  • LRG_321:g.16559_16572del
  • NC_000017.10:g.7579297_7579310del
  • NC_000017.10:g.7579298_7579311del
Links:
dbSNP: rs2151037977
NCBI 1000 Genomes Browser:
rs2151037977
Molecular consequence:
  • NM_000546.6:c.375+2_375+15del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001126112.3:c.375+2_375+15del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001126113.3:c.375+2_375+15del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001126114.3:c.375+2_375+15del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001126118.2:c.258+2_258+15del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001276695.3:c.258+2_258+15del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001276696.3:c.258+2_258+15del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001276760.3:c.258+2_258+15del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001276761.3:c.258+2_258+15del - splice donor variant - [Sequence Ontology: SO:0001575]

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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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001590017Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Mar 27, 2020) 		germlineclinical testing

PubMed (5)
[See all records that cite these PMIDs]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Splicing in action: assessing disease causing sequence changes.

Baralle D, Baralle M.

J Med Genet. 2005 Oct;42(10):737-48. Review.

PubMed [citation]
PMID:
16199547
PMCID:
PMC1735933

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
See all PubMed Citations (5)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001590017.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (5)

Description

For these reasons, this variant has been classified as Pathogenic. Donor and acceptor splice site variants typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in TP53 are known to be pathogenic (PMID: 20522432). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site, but this prediction has not been confirmed by published transcriptional studies. Disruption of this splice site has been observed in individual(s) with clinical features of Li-Fraumeni syndrome (PMID: 17224268, 7887414, Invitae). This variant is not present in population databases (ExAC no frequency). This sequence change affects a donor splice site in intron 4 of the TP53 gene. It is expected to disrupt RNA splicing and likely results in an absent or disrupted protein product.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Nov 10, 2024