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NM_000546.6(TP53):c.869G>A (p.Arg290His) AND not provided

Germline classification:
Conflicting interpretations of pathogenicity (4 submissions)
Last evaluated:
Aug 1, 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:
RCV000760102.29

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]
Observations:
1

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000149649GeneDx
criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)
Benign
(Feb 21, 2020)
germlineclinical testing

Citation Link,

SCV000889884Quest Diagnostics Nichols Institute San Juan Capistrano
criteria provided, single submitter

(Quest Diagnostics criteria)
Uncertain significance
(Sep 21, 2020)
unknownclinical testing

PubMed (16)
[See all records that cite these PMIDs]

SCV002050056ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
criteria provided, single submitter

(ARUP Molecular Germline Variant Investigation Process 2021)
Likely benign
(Nov 14, 2020)
germlineclinical testing

Citation Link,

SCV004141812CeGaT Center for Human Genetics Tuebingen
criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)
Benign
(Aug 1, 2023)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot providednot providednot providedclinical testing
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

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

Biochemical and imaging surveillance in germline TP53 mutation carriers with Li-Fraumeni syndrome: a prospective observational study.

Villani A, Tabori U, Schiffman J, Shlien A, Beyene J, Druker H, Novokmet A, Finlay J, Malkin D.

Lancet Oncol. 2011 Jun;12(6):559-67. doi: 10.1016/S1470-2045(11)70119-X. Epub 2011 May 19.

PubMed [citation]
PMID:
21601526
See all PubMed Citations (16)

Details of each submission

From GeneDx, SCV000149649.11

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

In silico analysis supports that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 12610779, 28369373, 30309854, 30514802, 16437140, 24079673, 17606709, 22811390, 15580553, 17541742, 25925845, 21343334, 17318340, 19468865, 26332594, 24829203, 25637381, 10435620, 19643983, 27153395, 26086041, 28472496, 29979965, 28861920, 24076587, 12826609, 21601526, 30352134, 31016814, 30840781, 30374176, 30306255, 33300245)

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Quest Diagnostics Nichols Institute San Juan Capistrano, SCV000889884.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (16)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

From ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories, SCV002050056.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From CeGaT Center for Human Genetics Tuebingen, SCV004141812.10

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided

Description

TP53: PM5, BS3:Supporting, BS1, BS2

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided1not providednot providednot provided

Last Updated: Nov 3, 2024