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

Germline classification:: Conflicting interpretations of pathogenicity (2 submissions)
Last evaluated:: Dec 18, 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:: RCV003585848.2

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

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

HGVS:

NC_000017.11:g.7670643C>T
NG_017013.2:g.21908G>A
NM_000546.6:c.1066G>AMANE SELECT
NM_001126112.3:c.1066G>A
NM_001126113.3:c.*85G>A
NM_001126114.3:c.*173G>A
NM_001126115.2:c.670G>A
NM_001126116.2:c.*173G>A
NM_001126117.2:c.*85G>A
NM_001126118.2:c.949G>A
NM_001276695.3:c.*85G>A
NM_001276696.3:c.*173G>A
NM_001276697.3:c.589G>A
NM_001276698.3:c.*173G>A
NM_001276699.3:c.*85G>A
NM_001276760.3:c.949G>A
NM_001276761.3:c.949G>A
NM_001407262.1:c.1066G>A
NM_001407263.1:c.949G>A
NM_001407264.1:c.1066G>A
NM_001407265.1:c.949G>A
NM_001407266.1:c.1066G>A
NM_001407267.1:c.949G>A
NM_001407268.1:c.*173G>A
NM_001407269.1:c.*173G>A
NM_001407270.1:c.*173G>A
NM_001407271.1:c.*173G>A
NP_000537.3:p.Gly356Arg
NP_000537.3:p.Gly356Arg
NP_001119584.1:p.Gly356Arg
NP_001119584.1:p.Gly356Arg
NP_001119587.1:p.Gly224Arg
NP_001119587.1:p.Gly224Arg
NP_001119590.1:p.Gly317Arg
NP_001119590.1:p.Gly317Arg
NP_001263626.1:p.Gly197Arg
NP_001263689.1:p.Gly317Arg
NP_001263690.1:p.Gly317Arg
NP_001394191.1:p.Gly356Arg
NP_001394192.1:p.Gly317Arg
NP_001394193.1:p.Gly356Arg
NP_001394194.1:p.Gly317Arg
NP_001394195.1:p.Gly356Arg
NP_001394196.1:p.Gly317Arg
LRG_321t1:c.1066G>A
LRG_321t2:c.1066G>A
LRG_321t3:c.*173G>A
LRG_321t4:c.*85G>A
LRG_321t5:c.670G>A
LRG_321t6:c.*173G>A
LRG_321t7:c.*85G>A
LRG_321t8:c.949G>A
LRG_321:g.21908G>A
LRG_321:p.Gly356Arg
LRG_321p1:p.Gly356Arg
LRG_321p5:p.Gly224Arg
LRG_321p8:p.Gly317Arg
NC_000017.10:g.7573961C>T
NM_000546.4:c.1066G>A
NM_000546.5:c.1066G>A
NM_001126112.2:c.1066G>A
NM_001126113.2:c.*85G>A
NM_001126114.2:c.*173G>A
NM_001126115.1:c.670G>A
NM_001126116.1:c.*173G>A
NM_001126117.1:c.*85G>A
NM_001126118.1:c.949G>A
NR_176326.1:n.1095G>A

Protein change:

G197R

Molecular consequence:

NM_001126113.3:c.*85G>A - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001126114.3:c.*173G>A - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001126116.2:c.*173G>A - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001126117.2:c.*85G>A - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001276695.3:c.*85G>A - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001276696.3:c.*173G>A - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001276698.3:c.*173G>A - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001276699.3:c.*85G>A - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001407268.1:c.*173G>A - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001407269.1:c.*173G>A - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001407270.1:c.*173G>A - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001407271.1:c.*173G>A - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_000546.6:c.1066G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001126112.3:c.1066G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001126115.2:c.670G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001126118.2:c.949G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001276697.3:c.589G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001276760.3:c.949G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001276761.3:c.949G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407262.1:c.1066G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407263.1:c.949G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407264.1:c.1066G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407265.1:c.949G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407266.1:c.1066G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407267.1:c.949G>A - missense variant - [Sequence Ontology: SO:0001583]
NR_176326.1:n.1095G>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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Mus musculus cDNA clone IMAGE:6491940, containing frame-shift errors
Mus musculus cDNA clone IMAGE:6491940, containing frame-shift errors
gi|32484355|gb|BC054454.1|

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004359970	Color Diagnostics, LLC DBA Color Health	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Jun 13, 2023)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 12826609, 30224644, 25741868
SCV005036211	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Likely benign (Dec 18, 2023)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 12826609, 30224644 Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004359970

Color Diagnostics, LLC DBA Color Health

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Jun 13, 2023)

germline

clinical testing

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

SCV005036211

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Likely benign
(Dec 18, 2023)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

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

Citations

PubMed

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

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

See all PubMed Citations (3)

Details of each submission

From Color Diagnostics, LLC DBA Color Health, SCV004359970.1

#	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). Experimental studies have shown that this variant did not impact function in yeast transactivation assays (PMID: 12826609) and human cell growth suppression assays (PMID: 30224644). To our knowledge, this variant has not been reported in individuals affected with TP53-related disorders in the literature. This variant has not been identified 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 Ambry Genetics, SCV005036211.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

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

Last Updated: May 7, 2024

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