NM_000546.6(TP53):c.166G>A (p.Glu56Lys) AND Hereditary cancer-predisposing syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Nov 20, 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:: RCV004518766.1

Allele description [Variation Report for NM_000546.6(TP53):c.166G>A (p.Glu56Lys)]

NM_000546.6(TP53):c.166G>A (p.Glu56Lys)

Gene:

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

Variant type:

single nucleotide variant

Cytogenetic location:

17p13.1

Genomic location:

Preferred name:

NM_000546.6(TP53):c.166G>A (p.Glu56Lys)

HGVS:

NC_000017.11:g.7676203C>T
NG_017013.2:g.16348G>A
NM_000546.6:c.166G>AMANE SELECT
NM_001126112.3:c.166G>A
NM_001126113.3:c.166G>A
NM_001126114.3:c.166G>A
NM_001126118.2:c.49G>A
NM_001276695.3:c.49G>A
NM_001276696.3:c.49G>A
NM_001276760.3:c.49G>A
NM_001276761.3:c.49G>A
NM_001407262.1:c.166G>A
NM_001407263.1:c.49G>A
NM_001407264.1:c.166G>A
NM_001407265.1:c.49G>A
NM_001407266.1:c.166G>A
NM_001407267.1:c.49G>A
NM_001407268.1:c.166G>A
NM_001407269.1:c.49G>A
NM_001407270.1:c.166G>A
NM_001407271.1:c.49G>A
NP_000537.3:p.Glu56Lys
NP_000537.3:p.Glu56Lys
NP_001119584.1:p.Glu56Lys
NP_001119584.1:p.Glu56Lys
NP_001119585.1:p.Glu56Lys
NP_001119585.1:p.Glu56Lys
NP_001119586.1:p.Glu56Lys
NP_001119586.1:p.Glu56Lys
NP_001119590.1:p.Glu17Lys
NP_001119590.1:p.Glu17Lys
NP_001263624.1:p.Glu17Lys
NP_001263625.1:p.Glu17Lys
NP_001263689.1:p.Glu17Lys
NP_001263690.1:p.Glu17Lys
NP_001394191.1:p.Glu56Lys
NP_001394192.1:p.Glu17Lys
NP_001394193.1:p.Glu56Lys
NP_001394194.1:p.Glu17Lys
NP_001394195.1:p.Glu56Lys
NP_001394196.1:p.Glu17Lys
NP_001394197.1:p.Glu56Lys
NP_001394198.1:p.Glu17Lys
NP_001394199.1:p.Glu56Lys
NP_001394200.1:p.Glu17Lys
LRG_321t1:c.166G>A
LRG_321t2:c.166G>A
LRG_321t3:c.166G>A
LRG_321t4:c.166G>A
LRG_321t8:c.49G>A
LRG_321:g.16348G>A
LRG_321:p.Glu56Lys
LRG_321p1:p.Glu56Lys
LRG_321p3:p.Glu56Lys
LRG_321p4:p.Glu56Lys
LRG_321p8:p.Glu17Lys
NC_000017.10:g.7579521C>T
NM_000546.4:c.166G>A
NM_000546.5:c.166G>A
NM_001126112.2:c.166G>A
NM_001126113.2:c.166G>A
NM_001126114.2:c.166G>A
NM_001126118.1:c.49G>A
NR_176326.1:n.308G>A

Protein change:

E17K

Molecular consequence:

NM_000546.6:c.166G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001126112.3:c.166G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001126113.3:c.166G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001126114.3:c.166G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001126118.2:c.49G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001276695.3:c.49G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001276696.3:c.49G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001276760.3:c.49G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001276761.3:c.49G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407262.1:c.166G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407263.1:c.49G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407264.1:c.166G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407265.1:c.49G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407266.1:c.166G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407267.1:c.49G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407268.1:c.166G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407269.1:c.49G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407270.1:c.166G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407271.1:c.49G>A - missense variant - [Sequence Ontology: SO:0001583]
NR_176326.1:n.308G>A - 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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Nucleotide
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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV005036214	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (Nov 20, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV005036214

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(Nov 20, 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, SCV005036214.1

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

Description

The p.E56K variant (also known as c.166G>A), located in coding exon 3 of the TP53 gene, results from a G to A substitution at nucleotide position 166. The glutamic acid at codon 56 is replaced by lysine, an amino acid with similar properties. This variant is reported to have partially functional transactivation in yeast based assays (Kato S et al. Proc. Natl. Acad. Sci. USA. 2003 Jul;100:8424-9). Studies conducted in human cell lines indicate this alteration is proficient at growth suppression and has no dominant negative effect (Giacomelli AO et al. Nat. Genet. 2018 Oct;50:1381-1387). This amino acid position is well conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

#	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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