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NM_000546.6(TP53):c.478A>G (p.Met160Val) AND not provided

Germline classification:
Uncertain significance (2 submissions)
Last evaluated:
Aug 10, 2017
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:
RCV000513585.29

Allele description [Variation Report for NM_000546.6(TP53):c.478A>G (p.Met160Val)]

NM_000546.6(TP53):c.478A>G (p.Met160Val)

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.478A>G (p.Met160Val)
HGVS:
  • NC_000017.11:g.7675134T>C
  • NG_017013.2:g.17417A>G
  • NM_000546.6:c.478A>GMANE SELECT
  • NM_001126112.3:c.478A>G
  • NM_001126113.3:c.478A>G
  • NM_001126114.3:c.478A>G
  • NM_001126115.2:c.82A>G
  • NM_001126116.2:c.82A>G
  • NM_001126117.2:c.82A>G
  • NM_001126118.2:c.361A>G
  • NM_001276695.3:c.361A>G
  • NM_001276696.3:c.361A>G
  • NM_001276697.3:c.1A>G
  • NM_001276698.3:c.1A>G
  • NM_001276699.3:c.1A>G
  • NM_001276760.3:c.361A>G
  • NM_001276761.3:c.361A>G
  • NP_000537.3:p.Met160Val
  • NP_000537.3:p.Met160Val
  • NP_001119584.1:p.Met160Val
  • NP_001119585.1:p.Met160Val
  • NP_001119586.1:p.Met160Val
  • NP_001119587.1:p.Met28Val
  • NP_001119587.1:p.Met28Val
  • NP_001119588.1:p.Met28Val
  • NP_001119589.1:p.Met28Val
  • NP_001119590.1:p.Met121Val
  • NP_001263624.1:p.Met121Val
  • NP_001263625.1:p.Met121Val
  • NP_001263626.1:p.Met1Val
  • NP_001263627.1:p.Met1Val
  • NP_001263628.1:p.Met1Val
  • NP_001263689.1:p.Met121Val
  • NP_001263690.1:p.Met121Val
  • LRG_321t1:c.478A>G
  • LRG_321t5:c.82A>G
  • LRG_321:g.17417A>G
  • LRG_321p1:p.Met160Val
  • LRG_321p5:p.Met28Val
  • NC_000017.10:g.7578452T>C
  • NM_000546.4:c.478A>G
  • NM_000546.5:c.478A>G
  • NM_001126115.1:c.82A>G
Protein change:
M121V
Links:
dbSNP: rs377274728
NCBI 1000 Genomes Browser:
rs377274728
Molecular consequence:
  • NM_001276697.3:c.1A>G - initiator_codon_variant - [Sequence Ontology: SO:0001582]
  • NM_001276698.3:c.1A>G - initiator_codon_variant - [Sequence Ontology: SO:0001582]
  • NM_001276699.3:c.1A>G - initiator_codon_variant - [Sequence Ontology: SO:0001582]
  • NM_000546.6:c.478A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001126112.3:c.478A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001126113.3:c.478A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001126114.3:c.478A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001126115.2:c.82A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001126116.2:c.82A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001126117.2:c.82A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001126118.2:c.361A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001276695.3:c.361A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001276696.3:c.361A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001276697.3:c.1A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001276698.3:c.1A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001276699.3:c.1A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001276760.3:c.361A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001276761.3:c.361A>G - missense variant - [Sequence Ontology: SO:0001583]
Observations:
2

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
SCV000608803CeGaT Center for Human Genetics Tuebingen
criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)
Uncertain significance
(Jun 1, 2017)
germlineclinical testing

Citation Link,

SCV000884717ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
criteria provided, single submitter

(ARUP Molecular Germline Variant Investigation Process)
Uncertain significance
(Aug 10, 2017)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes2not providednot providednot providednot providedclinical testing
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From CeGaT Center for Human Genetics Tuebingen, SCV000608803.32

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided2not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided2not providednot providednot provided

From ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories, SCV000884717.2

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

Description

The TP53 c.478A>G;p.Met160Val variant has not been described in the medical literature as a germline variant occurring in an individual with Li-Fraumeni syndrome. The variant has been described as a somatic variant occurring in multiple different tumors (Glebov 1994, Powell 2000, Yokoyama 1998). The variant is not listed in the ClinVar database, but is listed in the dbSNP variant database (rs377274728) with an allele frequency of 0.0004063 percent (1/246128 alleles) in the Genome Aggregation Database. The amino acid at this position is moderately conserved across species, is reported to occur in a DNA binding domain, and has been reported to not function normally in at least one assay (Shiraishi 2004). However, computational algorithms (AlignGVGD, PolyPhen2, SIFT) predict this variant is tolerated. Considering available information, there is not enough evidence to classify this variant with certainty. References: Glebov OK et al. Frequent p53 gene mutations and novel alleles in familial breast cancer. Cancer Res. 1994 Jul 15;54(14):3703-9. Powell B et al. Prognostic significance of mutations to different structural and functional regions of the p53 gene in breast cancer. Clin Cancer Res. 2000 Feb;6(2):443-51. Shi XB et al. A modified yeast assay used on archival samples of localized prostate cancer tissue improves the detection of p53 abnormalities and increases their predictive value. BJU Int. 2004 Nov;94(7):996-1002. Shiraishi K et al. Isolation of temperature-sensitive p53 mutations from a comprehensive missense mutation library. J Biol Chem. 2004 Jan 2;279(1):348-55. Yokoyama N et al. Mutations of p53 in gallbladder carcinomas in high-incidence areas of Japan and Chile. Cancer Epidemiol Biomarkers Prev. 1998 Apr;7(4):297-301.

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

Last Updated: Oct 20, 2024