NM_000546.6(TP53):c.375+1G>T AND Li-Fraumeni syndrome

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Aug 16, 2022
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:: RCV000804919.7

Allele description [Variation Report for NM_000546.6(TP53):c.375+1G>T]

NM_000546.6(TP53):c.375+1G>T

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.375+1G>T

HGVS:

NC_000017.11:g.7675993C>A
NG_017013.2:g.16558G>T
NM_000546.6:c.375+1G>TMANE SELECT
NM_001126112.3:c.375+1G>T
NM_001126113.3:c.375+1G>T
NM_001126114.3:c.375+1G>T
NM_001126118.2:c.258+1G>T
NM_001276695.3:c.258+1G>T
NM_001276696.3:c.258+1G>T
NM_001276760.3:c.258+1G>T
NM_001276761.3:c.258+1G>T
NM_001407262.1:c.375+1G>T
NM_001407263.1:c.258+1G>T
NM_001407264.1:c.375+1G>T
NM_001407265.1:c.258+1G>T
NM_001407266.1:c.375+1G>T
NM_001407267.1:c.258+1G>T
NM_001407268.1:c.375+1G>T
NM_001407269.1:c.258+1G>T
NM_001407270.1:c.375+1G>T
NM_001407271.1:c.258+1G>T
LRG_321t1:c.375+1G>T
LRG_321:g.16558G>T
NC_000017.10:g.7579311C>A
NM_000546.4:c.375+1G>T
NM_000546.5:c.375+1G>T

Links:

dbSNP: rs1567555445

NCBI 1000 Genomes Browser:

rs1567555445

Molecular consequence:

NM_000546.6:c.375+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001126112.3:c.375+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001126113.3:c.375+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001126114.3:c.375+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001126118.2:c.258+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001276695.3:c.258+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001276696.3:c.258+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001276760.3:c.258+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001276761.3:c.258+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001407262.1:c.375+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001407263.1:c.258+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001407264.1:c.375+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001407265.1:c.258+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001407266.1:c.375+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001407267.1:c.258+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001407268.1:c.375+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001407269.1:c.258+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001407270.1:c.375+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001407271.1:c.258+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]

Functional consequence:

sequence_variant_affecting_splicing [Sequence Ontology: SO:1000071] - Comment(s)

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
SCV000944857	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Aug 16, 2022)	germline	clinical testing	PubMed (5) [See all records that cite these PMIDs] 7887414, 17224268, 16199547, 20522432, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000944857

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Aug 16, 2022)

germline

clinical testing

PubMed (5)
[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

Germ-line p53 mutations in 15 families with Li-Fraumeni syndrome.

Frebourg T, Barbier N, Yan YX, Garber JE, Dreyfus M, Fraumeni J Jr, Li FP, Friend SH.

Am J Hum Genet. 1995 Mar;56(3):608-15.

PubMed [citation]

PMID:: 7887414
PMCID:: PMC1801151

Germline mutations of TP53 and BRCA2 genes in breast cancer/sarcoma families.

Manoukian S, Peissel B, Pensotti V, Barile M, Cortesi L, Stacchiotti S, Terenziani M, Barbera F, Pasquini G, Frigerio S, Pierotti MA, Radice P, Della-Torre G.

Eur J Cancer. 2007 Feb;43(3):601-6. Epub 2007 Jan 16.

PubMed [citation]

PMID:: 17224268

See all PubMed Citations (5)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000944857.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (5)

Description

For these reasons, this variant has been classified as Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. ClinVar contains an entry for this variant (Variation ID: 635393). Disruption of this splice site has been observed in individuals with clinical features of Li-Fraumeni syndrome (PMID: 7887414, 17224268; Invitae). This variant is not present in population databases (gnomAD no frequency). This sequence change affects a donor splice site in intron 4 of the TP53 gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and 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: Nov 10, 2024

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