NM_000546.6(TP53):c.484_487delinsGG (p.Ile162fs) AND Hereditary cancer-predisposing syndrome

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jul 12, 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:: RCV003339029.2

Allele description [Variation Report for NM_000546.6(TP53):c.484_487delinsGG (p.Ile162fs)]

NM_000546.6(TP53):c.484_487delinsGG (p.Ile162fs)

Gene:

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

Variant type:

Indel

Cytogenetic location:

17p13.1

Genomic location:

Preferred name:

NM_000546.6(TP53):c.484_487delinsGG (p.Ile162fs)

HGVS:

NC_000017.11:g.7675125_7675128delinsCC
NG_017013.2:g.17423_17426delinsGG
NM_000546.6:c.484_487delinsGGMANE SELECT
NM_001126112.3:c.484_487delinsGG
NM_001126113.3:c.484_487delinsGG
NM_001126114.3:c.484_487delinsGG
NM_001126115.2:c.88_91delinsGG
NM_001126116.2:c.88_91delinsGG
NM_001126117.2:c.88_91delinsGG
NM_001126118.2:c.367_370delinsGG
NM_001276695.3:c.367_370delinsGG
NM_001276696.3:c.367_370delinsGG
NM_001276697.3:c.7_10delinsGG
NM_001276698.3:c.7_10delinsGG
NM_001276699.3:c.7_10delinsGG
NM_001276760.3:c.367_370delinsGG
NM_001276761.3:c.367_370delinsGG
NM_001407262.1:c.484_487delinsGG
NM_001407263.1:c.367_370delinsGG
NM_001407264.1:c.484_487delinsGG
NM_001407265.1:c.367_370delinsGG
NM_001407266.1:c.484_487delinsGG
NM_001407267.1:c.367_370delinsGG
NM_001407268.1:c.484_487delinsGG
NM_001407269.1:c.367_370delinsGG
NM_001407270.1:c.484_487delinsGG
NM_001407271.1:c.367_370delinsGG
NP_000537.3:p.Ile162Glyfs
NP_000537.3:p.Ile162fs
NP_001119584.1:p.Ile162Glyfs
NP_001119584.1:p.Ile162fs
NP_001119585.1:p.Ile162Glyfs
NP_001119585.1:p.Ile162fs
NP_001119586.1:p.Ile162Glyfs
NP_001119586.1:p.Ile162fs
NP_001119587.1:p.Ile30Glyfs
NP_001119587.1:p.Ile30fs
NP_001119588.1:p.Ile30Glyfs
NP_001119588.1:p.Ile30fs
NP_001119589.1:p.Ile30Glyfs
NP_001119589.1:p.Ile30fs
NP_001119590.1:p.Ile123Glyfs
NP_001119590.1:p.Ile123fs
NP_001263624.1:p.Ile123fs
NP_001263625.1:p.Ile123fs
NP_001263626.1:p.Ile3fs
NP_001263627.1:p.Ile3fs
NP_001263628.1:p.Ile3fs
NP_001263689.1:p.Ile123fs
NP_001263690.1:p.Ile123fs
NP_001394191.1:p.Ile162fs
NP_001394192.1:p.Ile123fs
NP_001394193.1:p.Ile162fs
NP_001394194.1:p.Ile123fs
NP_001394195.1:p.Ile162fs
NP_001394196.1:p.Ile123fs
NP_001394197.1:p.Ile162fs
NP_001394198.1:p.Ile123fs
NP_001394199.1:p.Ile162fs
NP_001394200.1:p.Ile123fs
LRG_321t1:c.484_487delATCTinsGG
LRG_321t2:c.484_487delATCTinsGG
LRG_321t3:c.484_487delATCTinsGG
LRG_321t4:c.484_487delATCTinsGG
LRG_321t5:c.88_91delATCTinsGG
LRG_321t6:c.88_91delATCTinsGG
LRG_321t7:c.88_91delATCTinsGG
LRG_321t8:c.367_370delATCTinsGG
LRG_321:g.17423_17426delinsGG
LRG_321:p.Ile162Glyfs
LRG_321p1:p.Ile162Glyfs
LRG_321p3:p.Ile162Glyfs
LRG_321p4:p.Ile162Glyfs
LRG_321p5:p.Ile30Glyfs
LRG_321p6:p.Ile30Glyfs
LRG_321p7:p.Ile30Glyfs
LRG_321p8:p.Ile123Glyfs
NC_000017.10:g.7578443_7578446delinsCC
NM_000546.4:c.484_487delATCTinsGG
NM_000546.5:c.484_487delATCTinsGG
NM_001126112.2:c.484_487delATCTinsGG
NM_001126113.2:c.484_487delATCTinsGG
NM_001126114.2:c.484_487delATCTinsGG
NM_001126115.1:c.88_91delATCTinsGG
NM_001126116.1:c.88_91delATCTinsGG
NM_001126117.1:c.88_91delATCTinsGG
NM_001126118.1:c.367_370delATCTinsGG
NR_176326.1:n.626_629delinsGG

Protein change:

I123fs

Molecular consequence:

NM_000546.6:c.484_487delinsGG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001126112.3:c.484_487delinsGG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001126113.3:c.484_487delinsGG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001126114.3:c.484_487delinsGG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001126115.2:c.88_91delinsGG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001126116.2:c.88_91delinsGG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001126117.2:c.88_91delinsGG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001126118.2:c.367_370delinsGG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001276695.3:c.367_370delinsGG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001276696.3:c.367_370delinsGG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001276697.3:c.7_10delinsGG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001276698.3:c.7_10delinsGG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001276699.3:c.7_10delinsGG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001276760.3:c.367_370delinsGG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001276761.3:c.367_370delinsGG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407262.1:c.484_487delinsGG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407263.1:c.367_370delinsGG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407264.1:c.484_487delinsGG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407265.1:c.367_370delinsGG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407266.1:c.484_487delinsGG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407267.1:c.367_370delinsGG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407268.1:c.484_487delinsGG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407269.1:c.367_370delinsGG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407270.1:c.484_487delinsGG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407271.1:c.367_370delinsGG - frameshift variant - [Sequence Ontology: SO:0001589]
NR_176326.1:n.626_629delinsGG - non-coding transcript variant - [Sequence Ontology: SO:0001619]

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
SCV004058530	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Pathogenic (Jul 12, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004058530

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Pathogenic
(Jul 12, 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, SCV004058530.2

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

Description

The c.484_487delATCTinsGG pathogenic mutation, located in coding exon 4 of the TP53 gene, results from the deletion of 4 nucleotides and insertion of two nucleotides causing a translational frameshift with a predicted alternate stop codon (p.I162Gfs*18). This alteration has been observed in at least one individual with a personal and/or family history that is consistent with TP53-related disease (Ambry internal data). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). 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 1, 2024

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