NM_000546.6(TP53):c.31G>C (p.Glu11Gln) AND Hereditary cancer-predisposing syndrome

Germline classification:: Likely benign (3 submissions)
Last evaluated:: Feb 10, 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:: RCV000161016.13

Allele description [Variation Report for NM_000546.6(TP53):c.31G>C (p.Glu11Gln)]

NM_000546.6(TP53):c.31G>C (p.Glu11Gln)

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.31G>C (p.Glu11Gln)

Other names:

p.E11Q:GAG>CAG

HGVS:

NC_000017.11:g.7676564C>G
NG_017013.2:g.15987G>C
NM_000546.6:c.31G>CMANE SELECT
NM_001126112.3:c.31G>C
NM_001126113.3:c.31G>C
NM_001126114.3:c.31G>C
NM_001126118.2:c.-204G>C
NM_001276695.3:c.-87G>C
NM_001276696.3:c.-87G>C
NM_001276760.3:c.-87G>C
NM_001276761.3:c.-87G>C
NP_000537.3:p.Glu11Gln
NP_000537.3:p.Glu11Gln
NP_001119584.1:p.Glu11Gln
NP_001119585.1:p.Glu11Gln
NP_001119586.1:p.Glu11Gln
LRG_321t1:c.31G>C
LRG_321:g.15987G>C
LRG_321p1:p.Glu11Gln
NC_000017.10:g.7579882C>G
NM_000546.4:c.31G>C
NM_000546.5:c.31G>C
P04637:p.Glu11Gln
p.E11Q

Protein change:

E11Q

Links:

UniProtKB: P04637#VAR_044548; dbSNP: rs201382018

NCBI 1000 Genomes Browser:

rs201382018

Molecular consequence:

NM_001126118.2:c.-204G>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001276695.3:c.-87G>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001276696.3:c.-87G>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001276760.3:c.-87G>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001276761.3:c.-87G>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_000546.6:c.31G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001126112.3:c.31G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001126113.3:c.31G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001126114.3:c.31G>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

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2-oxoglutarate and iron-dependent oxygenase domain-containing protein 3 isoform ...
2-oxoglutarate and iron-dependent oxygenase domain-containing protein 3 isoform 2 [Homo sapiens]
gi|285397288|ref|NP_787098.3|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000214035	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Likely benign (Feb 1, 2019)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 22571758, 24724063 Citation Link,
SCV000910740	Color Diagnostics, LLC DBA Color Health	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely benign (Jun 7, 2016)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002530447	Sema4, Sema4	criteria provided, single submitter (Sema4 Curation Guidelines)	Likely benign (Feb 10, 2021)	germline	curation	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000214035

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Likely benign
(Feb 1, 2019)

germline

clinical testing

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

Citation Link,

SCV000910740

Color Diagnostics, LLC DBA Color Health

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely benign
(Jun 7, 2016)

germline

clinical testing

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

SCV002530447

Sema4, Sema4

criteria provided, single submitter

(Sema4 Curation Guidelines)

Likely benign
(Feb 10, 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

De novo childhood myelodysplastic/myeloproliferative disease with unique molecular characteristics.

Ismael O, Shimada A, Hama A, Elshazley M, Muramatsu H, Goto A, Sakaguchi H, Tanaka M, Takahashi Y, Yinyan X, Fukuda M, Miyajima Y, Yamashita Y, Horibe K, Hanada R, Ito M, Kojima S.

Br J Haematol. 2012 Jul;158(1):129-37. doi: 10.1111/j.1365-2141.2012.09140.x. Epub 2012 May 10.

PubMed [citation]

PMID:: 22571758

Characteristics of hematologic malignancies with coexisting t(9;22) and inv(16) chromosomal abnormalities.

Han E, Lee H, Kim M, Kim Y, Han K, Lee SE, Kim HJ, Kim DW.

Blood Res. 2014 Mar;49(1):22-8. doi: 10.5045/br.2014.49.1.22. Epub 2014 Mar 24.

PubMed [citation]

PMID:: 24724063
PMCID:: PMC3974952

See all PubMed Citations (3)

Details of each submission

From Ambry Genetics, SCV000214035.7

#	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

From Color Diagnostics, LLC DBA Color Health, SCV000910740.1

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

From Sema4, Sema4, SCV002530447.1

#	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: Oct 8, 2024

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