NM_000546.6(TP53):c.869G>A (p.Arg290His) AND Hereditary cancer-predisposing syndrome

Germline classification:: Benign/Likely benign (4 submissions)
Last evaluated:: Apr 23, 2021
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000115740.24

Allele description [Variation Report for NM_000546.6(TP53):c.869G>A (p.Arg290His)]

NM_000546.6(TP53):c.869G>A (p.Arg290His)

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.869G>A (p.Arg290His)

Other names:

p.R290H:CGC>CAC

HGVS:

NC_000017.11:g.7673751C>T
NG_017013.2:g.18800G>A
NM_000546.6:c.869G>AMANE SELECT
NM_001126112.3:c.869G>A
NM_001126113.3:c.869G>A
NM_001126114.3:c.869G>A
NM_001126115.1:c.473G>A
NM_001126115.2:c.473G>A
NM_001126116.2:c.473G>A
NM_001126117.2:c.473G>A
NM_001126118.2:c.752G>A
NM_001276695.3:c.752G>A
NM_001276696.3:c.752G>A
NM_001276697.3:c.392G>A
NM_001276698.3:c.392G>A
NM_001276699.3:c.392G>A
NM_001276760.3:c.752G>A
NM_001276761.3:c.752G>A
NP_000537.3:p.Arg290His
NP_000537.3:p.Arg290His
NP_001119584.1:p.Arg290His
NP_001119585.1:p.Arg290His
NP_001119586.1:p.Arg290His
NP_001119587.1:p.Arg158His
NP_001119588.1:p.Arg158His
NP_001119589.1:p.Arg158His
NP_001119590.1:p.Arg251His
NP_001263624.1:p.Arg251His
NP_001263625.1:p.Arg251His
NP_001263626.1:p.Arg131His
NP_001263627.1:p.Arg131His
NP_001263628.1:p.Arg131His
NP_001263689.1:p.Arg251His
NP_001263690.1:p.Arg251His
LRG_321t1:c.869G>A
LRG_321:g.18800G>A
LRG_321p1:p.Arg290His
NC_000017.10:g.7577069C>T
NM_000546.4:c.869G>A
NM_000546.5(TP53):c.869G>A
NM_000546.5:c.869G>A
P04637:p.Arg290His
p.R290H

Protein change:

R131H

Links:

UniProtKB: P04637#VAR_045411; dbSNP: rs55819519

NCBI 1000 Genomes Browser:

rs55819519

Molecular consequence:

NM_000546.6:c.869G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001126112.3:c.869G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001126113.3:c.869G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001126114.3:c.869G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001126115.2:c.473G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001126116.2:c.473G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001126117.2:c.473G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001126118.2:c.752G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001276695.3:c.752G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001276696.3:c.752G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001276697.3:c.392G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001276698.3:c.392G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001276699.3:c.392G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001276760.3:c.752G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001276761.3:c.752G>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
SCV000187277	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Benign (Feb 8, 2021)	germline	clinical testing	PubMed (10) [See all records that cite these PMIDs] 12826609, 16437140, 19468865, 21601526, 22811390, 24076587, 28472496, 30374176, 30840781, 31016814 Citation Link,
SCV000805309	True Health Diagnostics	no assertion criteria provided	Uncertain significance (Mar 19, 2018)	germline	clinical testing
SCV000910675	Color Diagnostics, LLC DBA Color Health	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely benign (May 20, 2020)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002532717	Sema4, Sema4	criteria provided, single submitter (Sema4 Curation Guidelines)	Likely benign (Apr 23, 2021)	germline	curation	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, curation

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

Acute myelogenous leukemia in a patient with Li-Fraumeni syndrome treated with valproic acid, theophyllamine and all-trans retinoic acid: a case report.

Anensen N, Skavland J, Stapnes C, Ryningen A, Børresen-Dale AL, Gjertsen BT, Bruserud Ø.

Leukemia. 2006 Apr;20(4):734-6. No abstract available.

PubMed [citation]

PMID:: 16437140

See all PubMed Citations (11)

Details of each submission

From Ambry Genetics, SCV000187277.9

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (10)

Description

This alteration is classified as 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 True Health Diagnostics, SCV000805309.1

#	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

From Color Diagnostics, LLC DBA Color Health, SCV000910675.2

#	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	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Sema4, Sema4, SCV002532717.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	curation	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 3, 2024

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