NM_000546.6(TP53):c.700_702del (p.Tyr234del) AND Hereditary cancer-predisposing syndrome

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Feb 8, 2024
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:: RCV004518776.1

Allele description [Variation Report for NM_000546.6(TP53):c.700_702del (p.Tyr234del)]

NM_000546.6(TP53):c.700_702del (p.Tyr234del)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

17p13.1

Genomic location:

Preferred name:

NM_000546.6(TP53):c.700_702del (p.Tyr234del)

HGVS:

NC_000017.11:g.7674263_7674265del
NG_017013.2:g.18288_18290del
NM_000546.6:c.700_702delMANE SELECT
NM_001126112.3:c.700_702del
NM_001126113.3:c.700_702del
NM_001126114.3:c.700_702del
NM_001126115.2:c.304_306del
NM_001126116.2:c.304_306del
NM_001126117.2:c.304_306del
NM_001126118.2:c.583_585del
NM_001276695.3:c.583_585del
NM_001276696.3:c.583_585del
NM_001276697.3:c.223_225del
NM_001276698.3:c.223_225del
NM_001276699.3:c.223_225del
NM_001276760.3:c.583_585del
NM_001276761.3:c.583_585del
NM_001407262.1:c.700_702del
NM_001407263.1:c.583_585del
NM_001407264.1:c.700_702del
NM_001407265.1:c.583_585del
NM_001407266.1:c.700_702del
NM_001407267.1:c.583_585del
NM_001407268.1:c.700_702del
NM_001407269.1:c.583_585del
NM_001407270.1:c.700_702del
NM_001407271.1:c.583_585del
NP_000537.3:p.Tyr234del
NP_000537.3:p.Tyr234del
NP_001119584.1:p.Tyr234del
NP_001119584.1:p.Tyr234del
NP_001119585.1:p.Tyr234del
NP_001119585.1:p.Tyr234del
NP_001119586.1:p.Tyr234del
NP_001119586.1:p.Tyr234del
NP_001119587.1:p.Tyr102del
NP_001119587.1:p.Tyr102del
NP_001119588.1:p.Tyr102del
NP_001119588.1:p.Tyr102del
NP_001119589.1:p.Tyr102del
NP_001119589.1:p.Tyr102del
NP_001119590.1:p.Tyr195del
NP_001119590.1:p.Tyr195del
NP_001263624.1:p.Tyr195del
NP_001263625.1:p.Tyr195del
NP_001263626.1:p.Tyr75del
NP_001263627.1:p.Tyr75del
NP_001263628.1:p.Tyr75del
NP_001263689.1:p.Tyr195del
NP_001263690.1:p.Tyr195del
NP_001394191.1:p.Tyr234del
NP_001394192.1:p.Tyr195del
NP_001394193.1:p.Tyr234del
NP_001394194.1:p.Tyr195del
NP_001394195.1:p.Tyr234del
NP_001394196.1:p.Tyr195del
NP_001394197.1:p.Tyr234del
NP_001394198.1:p.Tyr195del
NP_001394199.1:p.Tyr234del
NP_001394200.1:p.Tyr195del
LRG_321t1:c.698_700del
LRG_321t2:c.698_700del
LRG_321t3:c.698_700del
LRG_321t4:c.698_700del
LRG_321t5:c.302_304del
LRG_321t6:c.302_304del
LRG_321t7:c.302_304del
LRG_321t8:c.581_583del
LRG_321:g.18288_18290del
LRG_321:p.Tyr234del
LRG_321p1:p.Tyr234del
LRG_321p3:p.Tyr234del
LRG_321p4:p.Tyr234del
LRG_321p5:p.Tyr102del
LRG_321p6:p.Tyr102del
LRG_321p7:p.Tyr102del
LRG_321p8:p.Tyr195del
NC_000017.10:g.7577581_7577583del
NM_000546.4:c.700_702delTAC
NM_000546.5:c.698_700delACT
NM_001126112.2:c.698_700delACT
NM_001126113.2:c.698_700delACT
NM_001126114.2:c.698_700delACT
NM_001126115.1:c.302_304delACT
NM_001126116.1:c.302_304delACT
NM_001126117.1:c.302_304delACT
NM_001126118.1:c.581_583delACT
NR_176326.1:n.729_731del

Protein change:

Y102del

Molecular consequence:

NM_000546.6:c.700_702del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001126112.3:c.700_702del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001126113.3:c.700_702del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001126114.3:c.700_702del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001126115.2:c.304_306del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001126116.2:c.304_306del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001126117.2:c.304_306del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001126118.2:c.583_585del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001276695.3:c.583_585del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001276696.3:c.583_585del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001276697.3:c.223_225del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001276698.3:c.223_225del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001276699.3:c.223_225del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001276760.3:c.583_585del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001276761.3:c.583_585del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001407262.1:c.700_702del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001407263.1:c.583_585del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001407264.1:c.700_702del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001407265.1:c.583_585del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001407266.1:c.700_702del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001407267.1:c.583_585del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001407268.1:c.700_702del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001407269.1:c.583_585del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001407270.1:c.700_702del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001407271.1:c.583_585del - inframe_deletion - [Sequence Ontology: SO:0001822]
NR_176326.1:n.729_731del - 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
SCV005036106	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Likely pathogenic (Feb 8, 2024)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV005036106

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Likely pathogenic
(Feb 8, 2024)

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, SCV005036106.1

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

Description

The c.700_702delTAC variant (also known as p.Y234del) is located in coding exon 6 of the TP53 gene. This variant results from an in-frame TAC deletion at nucleotide positions 700 to 702. This results in the in-frame deletion of a tyrosine at codon 234. This amino acid position is well conserved in available vertebrate species and the impacted region is critical for protein function (Ambry internal data). In addition, this alteration is predicted to be deleterious by in silico analysis (Choi Y et al. PLoS ONE. 2012; 7(10):e46688). Based on the majority of available evidence to date, this variant is likely to be 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: May 7, 2024

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