NM_000546.6(TP53):c.324_335del (p.Arg110_Phe113del) AND Li-Fraumeni syndrome

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jul 14, 2023
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:: RCV001225317.8

Allele description [Variation Report for NM_000546.6(TP53):c.324_335del (p.Arg110_Phe113del)]

NM_000546.6(TP53):c.324_335del (p.Arg110_Phe113del)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

17p13.1

Genomic location:

Preferred name:

NM_000546.6(TP53):c.324_335del (p.Arg110_Phe113del)

HGVS:

NC_000017.11:g.7676036_7676047del
NG_017013.2:g.16506_16517del
NM_000546.6:c.324_335delMANE SELECT
NM_001126112.3:c.324_335del
NM_001126113.3:c.324_335del
NM_001126114.3:c.324_335del
NM_001126118.2:c.207_218del
NM_001276695.3:c.207_218del
NM_001276696.3:c.207_218del
NM_001276760.3:c.207_218del
NM_001276761.3:c.207_218del
NP_000537.3:p.Arg110_Phe113del
NP_001119584.1:p.Arg110_Phe113del
NP_001119585.1:p.Arg110_Phe113del
NP_001119586.1:p.Arg110_Phe113del
NP_001119590.1:p.Arg71_Phe74del
NP_001263624.1:p.Arg71_Phe74del
NP_001263625.1:p.Arg71_Phe74del
NP_001263689.1:p.Arg71_Phe74del
NP_001263690.1:p.Arg71_Phe74del
LRG_321t1:c.324_335del
LRG_321:g.16506_16517del
NC_000017.10:g.7579352_7579363del
NC_000017.10:g.7579354_7579365del
NM_000546.5:c.324_335del

Links:

dbSNP: rs2073454735

NCBI 1000 Genomes Browser:

rs2073454735

Molecular consequence:

NM_000546.6:c.324_335del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001126112.3:c.324_335del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001126113.3:c.324_335del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001126114.3:c.324_335del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001126118.2:c.207_218del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001276695.3:c.207_218del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001276696.3:c.207_218del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001276760.3:c.207_218del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001276761.3:c.207_218del - inframe_deletion - [Sequence Ontology: SO:0001822]

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
SCV001397593	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jul 14, 2023)	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

SCV001397593

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jul 14, 2023)

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	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

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, SCV001397593.5

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

Description

ClinVar contains an entry for this variant (Variation ID: 953078). For these reasons, this variant has been classified as Pathogenic. This variant disrupts a region of the TP53 protein in which other variant(s) (p.Phe113Leu) have been determined to be pathogenic (Invitae). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. This variant has been observed in individual(s) with clinical features of Li-Fraumeni syndrome (Invitae). This variant is not present in population databases (gnomAD no frequency). This variant, c.324_335del, results in the deletion of 4 amino acid(s) of the TP53 protein (p.Arg110_Phe113del), but otherwise preserves the integrity of the reading frame.

#	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

ClinVar

Relating variation to medicine