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NM_000546.6(TP53):c.1015G>T (p.Glu339Ter) AND Li-Fraumeni syndrome

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Feb 14, 2018
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:
RCV000689964.8

Allele description [Variation Report for NM_000546.6(TP53):c.1015G>T (p.Glu339Ter)]

NM_000546.6(TP53):c.1015G>T (p.Glu339Ter)

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.1015G>T (p.Glu339Ter)
HGVS:
  • NC_000017.11:g.7670694C>A
  • NG_017013.2:g.21857G>T
  • NM_000546.6:c.1015G>TMANE SELECT
  • NM_001126112.3:c.1015G>T
  • NM_001126113.3:c.*34G>T
  • NM_001126114.3:c.*122G>T
  • NM_001126115.2:c.619G>T
  • NM_001126116.2:c.*122G>T
  • NM_001126117.2:c.*34G>T
  • NM_001126118.2:c.898G>T
  • NM_001276695.3:c.*34G>T
  • NM_001276696.3:c.*122G>T
  • NM_001276697.3:c.538G>T
  • NM_001276698.3:c.*122G>T
  • NM_001276699.3:c.*34G>T
  • NM_001276760.3:c.898G>T
  • NM_001276761.3:c.898G>T
  • NP_000537.3:p.Glu339Ter
  • NP_000537.3:p.Glu339Ter
  • NP_001119584.1:p.Glu339Ter
  • NP_001119587.1:p.Glu207Ter
  • NP_001119590.1:p.Glu300Ter
  • NP_001263626.1:p.Glu180Ter
  • NP_001263689.1:p.Glu300Ter
  • NP_001263690.1:p.Glu300Ter
  • LRG_321t1:c.1015G>T
  • LRG_321t8:c.898G>T
  • LRG_321:g.21857G>T
  • LRG_321p1:p.Glu339Ter
  • NC_000017.10:g.7574012C>A
  • NM_000546.4:c.1015G>T
  • NM_000546.5:c.1015G>T
Protein change:
E180*
Links:
dbSNP: rs17882252
NCBI 1000 Genomes Browser:
rs17882252
Molecular consequence:
  • NM_001126113.3:c.*34G>T - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001126114.3:c.*122G>T - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001126116.2:c.*122G>T - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001126117.2:c.*34G>T - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001276695.3:c.*34G>T - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001276696.3:c.*122G>T - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001276698.3:c.*122G>T - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001276699.3:c.*34G>T - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_000546.6:c.1015G>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001126112.3:c.1015G>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001126115.2:c.619G>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001126118.2:c.898G>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001276697.3:c.538G>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001276760.3:c.898G>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001276761.3:c.898G>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:
Li-Fraumeni syndrome (LFS)
Synonyms:
Sarcoma family syndrome of Li and Fraumeni
Identifiers:
MONDO: MONDO:0018875; MedGen: C0085390; OMIM: PS151623

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000817637Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Feb 14, 2018) 		germlineclinical testing

PubMed (5)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

TP53 germline mutation testing in 180 families suspected of Li-Fraumeni syndrome: mutation detection rate and relative frequency of cancers in different familial phenotypes.

Ruijs MW, Verhoef S, Rookus MA, Pruntel R, van der Hout AH, Hogervorst FB, Kluijt I, Sijmons RH, Aalfs CM, Wagner A, Ausems MG, Hoogerbrugge N, van Asperen CJ, Gomez Garcia EB, Meijers-Heijboer H, Ten Kate LP, Menko FH, van 't Veer LJ.

J Med Genet. 2010 Jun;47(6):421-8. doi: 10.1136/jmg.2009.073429.

PubMed [citation]
PMID:
20522432

Comprehensive mutational scanning of the p53 coding region by two-dimensional gene scanning.

Rines RD, van Orsouw NJ, Sigalas I, Li FP, Eng C, Vijg J.

Carcinogenesis. 1998 Jun;19(6):979-84.

PubMed [citation]
PMID:
9667734
See all PubMed Citations (5)

Details of each submission

From Invitae, SCV000817637.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (5)

Description

For these reasons, this variant has been classified as Pathogenic. Loss-of-function variants in TP53 are known to be pathogenic (PMID: 20522432). This variant has been reported in individuals affected with Li-Fraumeni syndrome (PMID: 9667734, 21552135), and in an individual affected with early-onset breast cancer (PMID: 26641009). ClinVar contains an entry for this variant (Variation ID: 438708). This variant is not present in population databases (ExAC no frequency). This sequence change creates a premature translational stop signal (p.Glu339*) in the TP53 gene. It is expected to result in an absent or disrupted protein product.

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

Last Updated: Sep 16, 2024