NM_000546.6(TP53):c.651_666del (p.Val218fs) AND Hereditary cancer-predisposing syndrome

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Jun 18, 2022
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000165061.5

Allele description [Variation Report for NM_000546.6(TP53):c.651_666del (p.Val218fs)]

NM_000546.6(TP53):c.651_666del (p.Val218fs)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

17p13.1

Genomic location:

Preferred name:

NM_000546.6(TP53):c.651_666del (p.Val218fs)

HGVS:

NC_000017.11:g.7674865_7674880del
NG_017013.2:g.17671_17686del
NM_000546.6:c.651_666delMANE SELECT
NM_001126112.3:c.651_666del
NM_001126113.3:c.651_666del
NM_001126114.3:c.651_666del
NM_001126115.2:c.255_270del
NM_001126116.2:c.255_270del
NM_001126117.2:c.255_270del
NM_001126118.2:c.534_549del
NM_001276695.3:c.534_549del
NM_001276696.3:c.534_549del
NM_001276697.3:c.174_189del
NM_001276698.3:c.174_189del
NM_001276699.3:c.174_189del
NM_001276760.3:c.534_549del
NM_001276761.3:c.534_549del
NP_000537.3:p.Val218fs
NP_001119584.1:p.Val218fs
NP_001119585.1:p.Val218fs
NP_001119586.1:p.Val218fs
NP_001119587.1:p.Val86fs
NP_001119588.1:p.Val86fs
NP_001119589.1:p.Val86fs
NP_001119590.1:p.Val179fs
NP_001263624.1:p.Val179fs
NP_001263625.1:p.Val179fs
NP_001263626.1:p.Val59fs
NP_001263627.1:p.Val59fs
NP_001263628.1:p.Val59fs
NP_001263689.1:p.Val179fs
NP_001263690.1:p.Val179fs
LRG_321:g.17671_17686del
NC_000017.10:g.7578183_7578198del
NM_000546.4:c.651_666del16
p.V217VFS*25

Protein change:

V179fs

Links:

dbSNP: rs786202315

NCBI 1000 Genomes Browser:

rs786202315

Molecular consequence:

NM_000546.6:c.651_666del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001126112.3:c.651_666del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001126113.3:c.651_666del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001126114.3:c.651_666del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001126115.2:c.255_270del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001126116.2:c.255_270del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001126117.2:c.255_270del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001126118.2:c.534_549del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001276695.3:c.534_549del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001276696.3:c.534_549del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001276697.3:c.174_189del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001276698.3:c.174_189del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001276699.3:c.174_189del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001276760.3:c.534_549del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001276761.3:c.534_549del - 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

Recent activity

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PREDICTED: Mus musculus sorting nexin 14 (Snx14), transcript variant X1, mRNA
PREDICTED: Mus musculus sorting nexin 14 (Snx14), transcript variant X1, mRNA
gi|1907197968|ref|XM_036155012.1|

Nucleotide
K0420F05-3 NIA Mouse Mesenchymal Stem Cell cDNA Library (Long) Mus musculus cDNA...
K0420F05-3 NIA Mouse Mesenchymal Stem Cell cDNA Library (Long) Mus musculus cDNA clone NIA:K0420F05 IMAGE:30061024 3', mRNA sequence
gi|31492389|gnl|dbEST|18571481|gb|B 54.2|

Nucleotide
Mus musculus 10 day old male pancreas cDNA, RIKEN full-length enriched library, ...
Mus musculus 10 day old male pancreas cDNA, RIKEN full-length enriched library, clone:1810034K20 product:Mus musculus magnesium-dependent phosphatase-1 (Mdp1) mRNA, complete cds, full insert sequence
gi|12841401|dbj|AK007694.1|

Nucleotide
Drepanium fastigiatum isolate B1228 NADH dehydrogenase subunit 5 (nad5) gene, pa...
Drepanium fastigiatum isolate B1228 NADH dehydrogenase subunit 5 (nad5) gene, partial cds; mitochondrial
gi|1547039926|gb|MK211965.1|

Nucleotide
RNA-seq of human uninfected Caco-2 cells treated with a nutraceutical formula (S...
RNA-seq of human uninfected Caco-2 cells treated with a nutraceutical formula (Solution-3), or vehicle-(saline solution)- control
RNA-seq of human uninfected Caco-2 cells treated with a nutraceutical formula (Solution-3), or vehicle-(saline solution)- control

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000215762	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Pathogenic (Jul 9, 2014)	germline	clinical testing	Citation Link,
SCV002582477	Genome-Nilou Lab	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Jun 18, 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

SCV000215762

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Pathogenic
(Jul 9, 2014)

germline

clinical testing

Citation Link,

SCV002582477

Genome-Nilou Lab

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Jun 18, 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	no	not provided	not provided	not provided	not provided	not provided	clinical testing
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 Ambry Genetics, SCV000215762.7

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

Description

The c.651_666del16 pathogenic mutation, located in coding exon 5 of the TP53 gene, results from a deletion of 16 nucleotides at positions 651 to 666, causing a translational frameshift with a predicted alternate stop codon. Since frameshifts are typically deleterious in nature, this alteration is interpreted as a disease-causing mutation (ACMG Recommendations for Standards for Interpretation and Reporting of Sequence Variations. Revision 2007. Genet Med. 2008;10:294).

#	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

From Genome-Nilou Lab, SCV002582477.1

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	no	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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