NM_000546.6(TP53):c.643del (p.Ser215fs) AND Hereditary cancer-predisposing syndrome

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Dec 28, 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:: RCV004518774.1

Allele description [Variation Report for NM_000546.6(TP53):c.643del (p.Ser215fs)]

NM_000546.6(TP53):c.643del (p.Ser215fs)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

17p13.1

Genomic location:

Preferred name:

NM_000546.6(TP53):c.643del (p.Ser215fs)

HGVS:

NC_000017.11:g.7674888del
NG_017013.2:g.17663del
NM_000546.6:c.643delMANE SELECT
NM_001126112.3:c.643del
NM_001126113.3:c.643del
NM_001126114.3:c.643del
NM_001126115.2:c.247del
NM_001126116.2:c.247del
NM_001126117.2:c.247del
NM_001126118.2:c.526del
NM_001276695.3:c.526del
NM_001276696.3:c.526del
NM_001276697.3:c.166del
NM_001276698.3:c.166del
NM_001276699.3:c.166del
NM_001276760.3:c.526del
NM_001276761.3:c.526del
NM_001407262.1:c.643del
NM_001407263.1:c.526del
NM_001407264.1:c.643del
NM_001407265.1:c.526del
NM_001407266.1:c.643del
NM_001407267.1:c.526del
NM_001407268.1:c.643del
NM_001407269.1:c.526del
NM_001407270.1:c.643del
NM_001407271.1:c.526del
NP_000537.3:p.Ser215Valfs
NP_000537.3:p.Ser215fs
NP_001119584.1:p.Ser215Valfs
NP_001119584.1:p.Ser215fs
NP_001119585.1:p.Ser215Valfs
NP_001119585.1:p.Ser215fs
NP_001119586.1:p.Ser215Valfs
NP_001119586.1:p.Ser215fs
NP_001119587.1:p.Ser83Valfs
NP_001119587.1:p.Ser83fs
NP_001119588.1:p.Ser83Valfs
NP_001119588.1:p.Ser83fs
NP_001119589.1:p.Ser83Valfs
NP_001119589.1:p.Ser83fs
NP_001119590.1:p.Ser176Valfs
NP_001119590.1:p.Ser176fs
NP_001263624.1:p.Ser176fs
NP_001263625.1:p.Ser176fs
NP_001263626.1:p.Ser56fs
NP_001263627.1:p.Ser56fs
NP_001263628.1:p.Ser56fs
NP_001263689.1:p.Ser176fs
NP_001263690.1:p.Ser176fs
NP_001394191.1:p.Ser215fs
NP_001394192.1:p.Ser176fs
NP_001394193.1:p.Ser215fs
NP_001394194.1:p.Ser176fs
NP_001394195.1:p.Ser215fs
NP_001394196.1:p.Ser176fs
NP_001394197.1:p.Ser215fs
NP_001394198.1:p.Ser176fs
NP_001394199.1:p.Ser215fs
NP_001394200.1:p.Ser176fs
LRG_321t1:c.643del
LRG_321t2:c.643del
LRG_321t3:c.643del
LRG_321t4:c.643del
LRG_321t5:c.247del
LRG_321t6:c.247del
LRG_321t7:c.247del
LRG_321t8:c.526del
LRG_321:g.17663del
LRG_321:p.Ser215Valfs
LRG_321p1:p.Ser215Valfs
LRG_321p3:p.Ser215Valfs
LRG_321p4:p.Ser215Valfs
LRG_321p5:p.Ser83Valfs
LRG_321p6:p.Ser83Valfs
LRG_321p7:p.Ser83Valfs
LRG_321p8:p.Ser176Valfs
NC_000017.10:g.7578206del
NM_000546.4:c.643delA
NM_000546.5:c.643delA
NM_001126112.2:c.643delA
NM_001126113.2:c.643delA
NM_001126114.2:c.643delA
NM_001126115.1:c.247delA
NM_001126116.1:c.247delA
NM_001126117.1:c.247delA
NM_001126118.1:c.526delA

Protein change:

S176fs

Molecular consequence:

NM_000546.6:c.643del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001126112.3:c.643del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001126113.3:c.643del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001126114.3:c.643del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001126115.2:c.247del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001126116.2:c.247del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001126117.2:c.247del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001126118.2:c.526del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001276695.3:c.526del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001276696.3:c.526del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001276697.3:c.166del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001276698.3:c.166del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001276699.3:c.166del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001276760.3:c.526del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001276761.3:c.526del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407262.1:c.643del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407263.1:c.526del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407264.1:c.643del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407265.1:c.526del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407266.1:c.643del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407267.1:c.526del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407268.1:c.643del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407269.1:c.526del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407270.1:c.643del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407271.1:c.526del - 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
SCV005036104	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Pathogenic (Dec 28, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV005036104

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Pathogenic
(Dec 28, 2023)

germline

clinical testing

Citation Link

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

Details of each submission

From Ambry Genetics, SCV005036104.1

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

Description

The c.643delA variant, located in coding exon 5 of the TP53 gene, results from a deletion of one nucleotide at nucleotide position 643, causing a translational frameshift with a predicted alternate stop codon (p.S215Vfs*32). This alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. As such, this alteration is interpreted as a disease-causing mutation.

#	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: May 7, 2024

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