NM_000546.6(TP53):c.1066G>C (p.Gly356Arg) AND Hereditary cancer-predisposing syndrome

Germline classification:: Conflicting interpretations of pathogenicity (3 submissions)
Last evaluated:: Jul 26, 2023
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:: RCV000213405.14

Allele description [Variation Report for NM_000546.6(TP53):c.1066G>C (p.Gly356Arg)]

NM_000546.6(TP53):c.1066G>C (p.Gly356Arg)

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.1066G>C (p.Gly356Arg)

Other names:

NM_000546.5(TP53):c.1066G>C; p.Gly356Arg

HGVS:

NC_000017.11:g.7670643C>G
NG_017013.2:g.21908G>C
NM_000546.6:c.1066G>CMANE SELECT
NM_001126112.3:c.1066G>C
NM_001126113.3:c.*85G>C
NM_001126114.3:c.*173G>C
NM_001126115.2:c.670G>C
NM_001126116.2:c.*173G>C
NM_001126117.2:c.*85G>C
NM_001126118.2:c.949G>C
NM_001276695.3:c.*85G>C
NM_001276696.3:c.*173G>C
NM_001276697.3:c.589G>C
NM_001276698.3:c.*173G>C
NM_001276699.3:c.*85G>C
NM_001276760.3:c.949G>C
NM_001276761.3:c.949G>C
NP_000537.3:p.Gly356Arg
NP_000537.3:p.Gly356Arg
NP_001119584.1:p.Gly356Arg
NP_001119587.1:p.Gly224Arg
NP_001119590.1:p.Gly317Arg
NP_001263626.1:p.Gly197Arg
NP_001263689.1:p.Gly317Arg
NP_001263690.1:p.Gly317Arg
LRG_321t1:c.1066G>C
LRG_321:g.21908G>C
LRG_321p1:p.Gly356Arg
NC_000017.10:g.7573961C>G
NM_000546.4:c.1066G>C
NM_000546.5:c.1066G>C

Protein change:

G197R

Links:

dbSNP: rs766786605

NCBI 1000 Genomes Browser:

rs766786605

Molecular consequence:

NM_001126113.3:c.*85G>C - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001126114.3:c.*173G>C - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001126116.2:c.*173G>C - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001126117.2:c.*85G>C - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001276695.3:c.*85G>C - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001276696.3:c.*173G>C - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001276698.3:c.*173G>C - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001276699.3:c.*85G>C - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_000546.6:c.1066G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001126112.3:c.1066G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001126115.2:c.670G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001126118.2:c.949G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001276697.3:c.589G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001276760.3:c.949G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001276761.3:c.949G>C - 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

Recent activity

Clear Turn Off Turn On

dickkopf-like protein 1 [Mus musculus]
dickkopf-like protein 1 [Mus musculus]
gi|385398328|gb|AFI61654.1|

Protein
Streptococcus salivarius strain DFI.4.50 LFGFHOCO_3, whole genome shotgun sequen...
Streptococcus salivarius strain DFI.4.50 LFGFHOCO_3, whole genome shotgun sequence
gi|2124840623|ref|NZ_JAJCHE01000000 gnl|WGS:NZ_JAJCHE01|LFGFHOCO_3

Nucleotide
Streptococcus parasanguinis strain CF8_Ac2-4, whole genome shotgun sequencing pr...
Streptococcus parasanguinis strain CF8_Ac2-4, whole genome shotgun sequencing project
gi|2273334230|gb|JANCOR000000000.1| R010000000

Nucleotide
oocyte zinc finger protein XlCOF6.1 [Fundulus heteroclitus]
oocyte zinc finger protein XlCOF6.1 [Fundulus heteroclitus]
gi|1900292982|ref|XP_012737156.2|

Protein
MIGS Cultured Bacterial/Archaeal sample from Streptococcus parasanguinis
MIGS Cultured Bacterial/Archaeal sample from Streptococcus parasanguinis

biosample

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000278550	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Likely benign (Jun 8, 2021)	germline	clinical testing	Citation Link,
SCV000691572	Color Diagnostics, LLC DBA Color Health	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Jul 26, 2023)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 12826609, 30224644, 25741868
SCV000788222	True Health Diagnostics	no assertion criteria provided	Uncertain significance (Aug 22, 2017)	germline	clinical testing

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000278550

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Likely benign
(Jun 8, 2021)

germline

clinical testing

Citation Link,

SCV000691572

Color Diagnostics, LLC DBA Color Health

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Jul 26, 2023)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

SCV000788222

True Health Diagnostics

no assertion criteria provided

Uncertain significance
(Aug 22, 2017)

germline

clinical testing

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

Citations

PubMed

Understanding the function-structure and function-mutation relationships of p53 tumor suppressor protein by high-resolution missense mutation analysis.

Kato S, Han SY, Liu W, Otsuka K, Shibata H, Kanamaru R, Ishioka C.

Proc Natl Acad Sci U S A. 2003 Jul 8;100(14):8424-9. Epub 2003 Jun 25.

PubMed [citation]

PMID:: 12826609
PMCID:: PMC166245

Mutational processes shape the landscape of TP53 mutations in human cancer.

Giacomelli AO, Yang X, Lintner RE, McFarland JM, Duby M, Kim J, Howard TP, Takeda DY, Ly SH, Kim E, Gannon HS, Hurhula B, Sharpe T, Goodale A, Fritchman B, Steelman S, Vazquez F, Tsherniak A, Aguirre AJ, Doench JG, Piccioni F, Roberts CWM, et al.

Nat Genet. 2018 Oct;50(10):1381-1387. doi: 10.1038/s41588-018-0204-y. Epub 2018 Sep 17.

PubMed [citation]

PMID:: 30224644
PMCID:: PMC6168352

See all PubMed Citations (3)

Details of each submission

From Ambry Genetics, SCV000278550.7

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

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 Color Diagnostics, LLC DBA Color Health, SCV000691572.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

This missense variant replaces glycine with arginine at codon 356 of the TP53 protein. Computational prediction suggests that this variant may not impact protein structure and function (internally defined REVEL score threshold <= 0.5, PMID: 27666373). Functional studies have shown that this variant is functional in yeast transcriptional activation assays and human cell growth suppression assays (PMID: 12826609, 30224644). To our knowledge, this variant has not been reported in individuals affected with TP53-related disorders in the literature. This variant has been identified in 1/245622 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.

#	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 True Health Diagnostics, SCV000788222.1

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

#	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: Nov 10, 2024

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