NM_000546.6(TP53):c.968_986del (p.Leu323fs) AND Hereditary cancer-predisposing syndrome

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Mar 11, 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:: RCV000772929.3

Allele description [Variation Report for NM_000546.6(TP53):c.968_986del (p.Leu323fs)]

NM_000546.6(TP53):c.968_986del (p.Leu323fs)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

17p13.1

Genomic location:

Preferred name:

NM_000546.6(TP53):c.968_986del (p.Leu323fs)

HGVS:

NC_000017.11:g.7673545_7673563del
NG_017013.2:g.18991_19009del
NM_000546.6:c.968_986delMANE SELECT
NM_001126112.3:c.968_986del
NM_001126113.3:c.968_986del
NM_001126114.3:c.968_986del
NM_001126115.2:c.572_590del
NM_001126116.2:c.572_590del
NM_001126117.2:c.572_590del
NM_001126118.2:c.851_869del
NM_001276695.3:c.851_869del
NM_001276696.3:c.851_869del
NM_001276697.3:c.491_509del
NM_001276698.3:c.491_509del
NM_001276699.3:c.491_509del
NM_001276760.3:c.851_869del
NM_001276761.3:c.851_869del
NP_000537.3:p.Leu323fs
NP_001119584.1:p.Leu323fs
NP_001119585.1:p.Leu323fs
NP_001119586.1:p.Leu323fs
NP_001119587.1:p.Leu191fs
NP_001119588.1:p.Leu191fs
NP_001119589.1:p.Leu191fs
NP_001119590.1:p.Leu284fs
NP_001263624.1:p.Leu284fs
NP_001263625.1:p.Leu284fs
NP_001263626.1:p.Leu164fs
NP_001263627.1:p.Leu164fs
NP_001263628.1:p.Leu164fs
NP_001263689.1:p.Leu284fs
NP_001263690.1:p.Leu284fs
LRG_321:g.18991_19009del
NC_000017.10:g.7576863_7576881del

Protein change:

L164fs

Links:

dbSNP: rs1567545918

NCBI 1000 Genomes Browser:

rs1567545918

Molecular consequence:

NM_000546.6:c.968_986del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001126112.3:c.968_986del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001126113.3:c.968_986del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001126114.3:c.968_986del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001126115.2:c.572_590del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001126116.2:c.572_590del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001126117.2:c.572_590del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001126118.2:c.851_869del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001276695.3:c.851_869del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001276696.3:c.851_869del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001276697.3:c.491_509del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001276698.3:c.491_509del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001276699.3:c.491_509del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001276760.3:c.851_869del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001276761.3:c.851_869del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:: Hereditary cancer-predisposing syndrome
Synonyms:: Neoplastic Syndromes, Hereditary; Tumor predisposition; Cancer predisposition; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0015356; MeSH: D009386; MedGen: C0027672

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000906311	Color Diagnostics, LLC DBA Color Health	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Mar 11, 2022)	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

SCV000906311

Color Diagnostics, LLC DBA Color Health

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Mar 11, 2022)

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

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 Color Diagnostics, LLC DBA Color Health, SCV000906311.2

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

Description

This variant deletes 19 nucleotides in exon 9 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 hereditary cancer 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	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Feb 20, 2024

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