NM_000546.6(TP53):c.375G>A (p.Thr125=) AND Glioma susceptibility 1

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Feb 28, 2020
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV001530197.4

Allele description [Variation Report for NM_000546.6(TP53):c.375G>A (p.Thr125=)]

NM_000546.6(TP53):c.375G>A (p.Thr125=)

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.375G>A (p.Thr125=)

HGVS:

NC_000017.11:g.7675994C>T
NG_017013.2:g.16557G>A
NM_000546.6:c.375G>AMANE SELECT
NM_001126112.3:c.375G>A
NM_001126113.3:c.375G>A
NM_001126114.3:c.375G>A
NM_001126118.2:c.258G>A
NM_001276695.3:c.258G>A
NM_001276696.3:c.258G>A
NM_001276760.3:c.258G>A
NM_001276761.3:c.258G>A
NP_000537.3:p.Thr125=
NP_000537.3:p.Thr125=
NP_001119584.1:p.Thr125=
NP_001119585.1:p.Thr125=
NP_001119586.1:p.Thr125=
NP_001119590.1:p.Thr86=
NP_001263624.1:p.Thr86=
NP_001263625.1:p.Thr86=
NP_001263689.1:p.Thr86=
NP_001263690.1:p.Thr86=
LRG_321t1:c.375G>A
LRG_321:g.16557G>A
LRG_321p1:p.Thr125=
NC_000017.10:g.7579312C>T
NM_000546.4:c.375G>A
NM_000546.5:c.375G>A
p.Thr125Thr

Links:

dbSNP: rs55863639

NCBI 1000 Genomes Browser:

rs55863639

Molecular consequence:

NM_000546.6:c.375G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001126112.3:c.375G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001126113.3:c.375G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001126114.3:c.375G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001126118.2:c.258G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001276695.3:c.258G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001276696.3:c.258G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001276760.3:c.258G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001276761.3:c.258G>A - synonymous variant - [Sequence Ontology: SO:0001819]

Functional consequence:

sequence_variant_affecting_splicing [Sequence Ontology: SO:1000071] - Comment(s)

Observations:

Condition(s)

Name:: Glioma susceptibility 1 (GLM1)
Synonyms:: Glioblastoma, somatic
Identifiers:: MONDO: MONDO:0024498; MedGen: C2750850; OMIM: 137800

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001739492	Beijing Key Laboratry for Genetics of Birth Defects, Beijing Children's Hospital	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Feb 28, 2020)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001739492

Beijing Key Laboratry for Genetics of Birth Defects, Beijing Children's Hospital

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Feb 28, 2020)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
East asia	germline	yes	1	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

Details of each submission

From Beijing Key Laboratry for Genetics of Birth Defects, Beijing Children's Hospital, SCV001739492.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	East asia	1	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	yes	not provided	not provided	not provided		1	not provided	not provided	not provided

Last Updated: Nov 10, 2024

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