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NM_000546.6(TP53):c.772G>A (p.Glu258Lys) AND Li-Fraumeni syndrome 1

Germline classification:
Likely pathogenic (2 submissions)
Last evaluated:
Jun 18, 2022
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:
RCV000013141.28

Allele description [Variation Report for NM_000546.6(TP53):c.772G>A (p.Glu258Lys)]

NM_000546.6(TP53):c.772G>A (p.Glu258Lys)

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.772G>A (p.Glu258Lys)
Other names:
p.E258K:GAA>AAA
HGVS:
  • NC_000017.11:g.7674191C>T
  • NG_017013.2:g.18360G>A
  • NM_000546.6:c.772G>AMANE SELECT
  • NM_001126112.3:c.772G>A
  • NM_001126113.3:c.772G>A
  • NM_001126114.3:c.772G>A
  • NM_001126115.2:c.376G>A
  • NM_001126116.2:c.376G>A
  • NM_001126117.2:c.376G>A
  • NM_001126118.2:c.655G>A
  • NM_001276695.3:c.655G>A
  • NM_001276696.3:c.655G>A
  • NM_001276697.3:c.295G>A
  • NM_001276698.3:c.295G>A
  • NM_001276699.3:c.295G>A
  • NM_001276760.3:c.655G>A
  • NM_001276761.3:c.655G>A
  • NP_000537.3:p.Glu258Lys
  • NP_000537.3:p.Glu258Lys
  • NP_001119584.1:p.Glu258Lys
  • NP_001119585.1:p.Glu258Lys
  • NP_001119586.1:p.Glu258Lys
  • NP_001119587.1:p.Glu126Lys
  • NP_001119588.1:p.Glu126Lys
  • NP_001119589.1:p.Glu126Lys
  • NP_001119590.1:p.Glu219Lys
  • NP_001263624.1:p.Glu219Lys
  • NP_001263625.1:p.Glu219Lys
  • NP_001263626.1:p.Glu99Lys
  • NP_001263627.1:p.Glu99Lys
  • NP_001263628.1:p.Glu99Lys
  • NP_001263689.1:p.Glu219Lys
  • NP_001263690.1:p.Glu219Lys
  • LRG_321t1:c.772G>A
  • LRG_321:g.18360G>A
  • LRG_321p1:p.Glu258Lys
  • NC_000017.10:g.7577509C>T
  • NM_000546.4:c.772G>A
  • NM_000546.5:c.772G>A
  • P04637:p.Glu258Lys
Protein change:
E126K; GLU258LYS
Links:
UniProtKB: P04637#VAR_005991; OMIM: 191170.0002; dbSNP: rs121912652
NCBI 1000 Genomes Browser:
rs121912652
Molecular consequence:
  • NM_000546.6:c.772G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001126112.3:c.772G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001126113.3:c.772G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001126114.3:c.772G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001126115.2:c.376G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001126116.2:c.376G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001126117.2:c.376G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001126118.2:c.655G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001276695.3:c.655G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001276696.3:c.655G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001276697.3:c.295G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001276698.3:c.295G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001276699.3:c.295G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001276760.3:c.655G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001276761.3:c.655G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Li-Fraumeni syndrome 1 (LFS)
Identifiers:
Gene: 553989; MedGen: C1835398; Orphanet: 524; OMIM: 151623

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000033388OMIM
no assertion criteria provided
Pathogenic
(Aug 27, 2020) 		germlineliterature only

Malkin, D., Li, F. P., Strong, L. C., Fraumeni, J. F., Jr., Nelson, C. E., Kim, D. H., Kassel, J., Gryka, M. A., Bischoff, F. Z., Tainsky, M. A., Friend, S. H. Germ line p53 mutations in a familial syndrome of breast cancer, sarcomas, and other neoplasms. Science 250: 1233-1238, 1990. Note: Erratum: Science 259: 878 only, 1993.,

SCV002583018Genome-Nilou Lab
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely pathogenic
(Jun 18, 2022) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenonot providednot providednot providednot providednot providedclinical testing
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only

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 OMIM, SCV000033388.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature onlynot provided

Description

In a family with the Li-Fraumeni syndrome-1 (151623), Malkin et al. (1990) identified a G-to-A mutation at the first nucleotide of codon 258, resulting in substitution of lysine for glutamic acid (E258K).

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

From Genome-Nilou Lab, SCV002583018.1

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

Last Updated: Nov 10, 2024