NM_000546.6(TP53):c.905G>A (p.Gly302Glu) AND Hereditary cancer-predisposing syndrome

Germline classification:: Conflicting interpretations of pathogenicity (2 submissions)
Last evaluated:: Jun 18, 2022
Review status:: criteria provided, conflicting classifications

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:: RCV001018766.6

Allele description [Variation Report for NM_000546.6(TP53):c.905G>A (p.Gly302Glu)]

NM_000546.6(TP53):c.905G>A (p.Gly302Glu)

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.905G>A (p.Gly302Glu)

HGVS:

NC_000017.11:g.7673715C>T
NG_017013.2:g.18836G>A
NM_000546.6:c.905G>AMANE SELECT
NM_001126112.3:c.905G>A
NM_001126113.3:c.905G>A
NM_001126114.3:c.905G>A
NM_001126115.2:c.509G>A
NM_001126116.2:c.509G>A
NM_001126117.2:c.509G>A
NM_001126118.2:c.788G>A
NM_001276695.3:c.788G>A
NM_001276696.3:c.788G>A
NM_001276697.3:c.428G>A
NM_001276698.3:c.428G>A
NM_001276699.3:c.428G>A
NM_001276760.3:c.788G>A
NM_001276761.3:c.788G>A
NP_000537.3:p.Gly302Glu
NP_000537.3:p.Gly302Glu
NP_001119584.1:p.Gly302Glu
NP_001119585.1:p.Gly302Glu
NP_001119586.1:p.Gly302Glu
NP_001119587.1:p.Gly170Glu
NP_001119588.1:p.Gly170Glu
NP_001119589.1:p.Gly170Glu
NP_001119590.1:p.Gly263Glu
NP_001263624.1:p.Gly263Glu
NP_001263625.1:p.Gly263Glu
NP_001263626.1:p.Gly143Glu
NP_001263627.1:p.Gly143Glu
NP_001263628.1:p.Gly143Glu
NP_001263689.1:p.Gly263Glu
NP_001263690.1:p.Gly263Glu
LRG_321t1:c.905G>A
LRG_321:g.18836G>A
LRG_321p1:p.Gly302Glu
NC_000017.10:g.7577033C>T
NM_000546.4:c.905G>A
NM_000546.5:c.905G>A

Protein change:

G143E

Links:

dbSNP: rs1060501202

NCBI 1000 Genomes Browser:

rs1060501202

Molecular consequence:

NM_000546.6:c.905G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001126112.3:c.905G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001126113.3:c.905G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001126114.3:c.905G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001126115.2:c.509G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001126116.2:c.509G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001126117.2:c.509G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001126118.2:c.788G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001276695.3:c.788G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001276696.3:c.788G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001276697.3:c.428G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001276698.3:c.428G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001276699.3:c.428G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001276760.3:c.788G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001276761.3:c.788G>A - missense variant - [Sequence Ontology: SO:0001583]

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
SCV001180041	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Likely benign (Feb 16, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID] Citation Link,
SCV002581982	Genome-Nilou Lab	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (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

SCV001180041

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Likely benign
(Feb 16, 2021)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

Citation Link,

SCV002581982

Genome-Nilou Lab

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(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

High frequency of complex TP53 mutations in CNS metastases from breast cancer.

Lo Nigro C, Vivenza D, Monteverde M, Lattanzio L, Gojis O, Garrone O, Comino A, Merlano M, Quinlan PR, Syed N, Purdie CA, Thompson A, Palmieri C, Crook T.

Br J Cancer. 2012 Jan 17;106(2):397-404. doi: 10.1038/bjc.2011.464. Epub 2011 Dec 20.

PubMed [citation]

PMID:: 22187033
PMCID:: PMC3261685

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, SCV001180041.4

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

Description

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

#	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, SCV002581982.1

#	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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