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NM_001126112.2(TP53):c.376-2dup AND not specified

Germline classification:
Uncertain significance (2 submissions)
Last evaluated:
Dec 15, 2016
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:
RCV000235779.3

Allele description

NM_001126112.2(TP53):c.376-2dup

Gene:
TP53:tumor protein p53 [Gene - OMIM - HGNC]
Variant type:
Duplication
Cytogenetic location:
17p13.1
Genomic location:
Preferred name:
NM_001126112.2(TP53):c.376-2dup
HGVS:
  • NC_000017.11:g.7675238dup
  • NG_017013.2:g.17313dup
  • NM_001126112.2:c.376-2dup
  • NM_001126113.2:c.376-2dup
  • NM_001126114.2:c.376-2dup
  • NM_001126115.1:c.-23dup
  • NM_001126116.1:c.-23dup
  • NM_001126117.1:c.-23dup
  • NM_001126118.1:c.259-2dup
  • NM_001276695.2:c.259-2dup
  • NM_001276696.2:c.259-2dup
  • NM_001276697.2:c.-104dup
  • NM_001276698.2:c.-104dup
  • NM_001276699.2:c.-104dup
  • NM_001276760.2:c.259-2dup
  • NM_001276761.2:c.259-2dup
  • LRG_321t1:c.376-2dup
  • LRG_321t2:c.376-2dup
  • LRG_321t3:c.376-2dup
  • LRG_321t4:c.376-2dup
  • LRG_321t5:c.-23dup
  • LRG_321t6:c.-23dup
  • LRG_321t7:c.-23dup
  • LRG_321t8:c.259-2dup
  • LRG_321:g.17313dup
  • NC_000017.10:g.7578556dup
  • NM_000546.4:c.376-2dupA
  • NM_000546.5:c.376-2dupA
Links:
dbSNP: rs751253294
NCBI 1000 Genomes Browser:
rs751253294
Molecular consequence:
  • NM_001126115.1:c.-23dup - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001126116.1:c.-23dup - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001126117.1:c.-23dup - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001276697.2:c.-104dup - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001276698.2:c.-104dup - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001276699.2:c.-104dup - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001126112.2:c.376-2dup - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001126113.2:c.376-2dup - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001126114.2:c.376-2dup - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001126118.1:c.259-2dup - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001276695.2:c.259-2dup - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001276696.2:c.259-2dup - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001276760.2:c.259-2dup - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001276761.2:c.259-2dup - splice acceptor variant - [Sequence Ontology: SO:0001574]

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000293780GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))
Uncertain significance
(Aug 29, 2016)
germlineclinical testing

Citation Link,

SCV000602270Quest Diagnostics Nichols Institute San Juan Capistrano
criteria provided, single submitter

(Quest pathogenicity assessment criteria)
Uncertain significance
(Dec 15, 2016)
germlineclinical testing

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

Summary from all submissions

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

Citations

PubMed

A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders.

Karbassi I, Maston GA, Love A, DiVincenzo C, Braastad CD, Elzinga CD, Bright AR, Previte D, Zhang K, Rowland CM, McCarthy M, Lapierre JL, Dubois F, Medeiros KA, Batish SD, Jones J, Liaquat K, Hoffman CA, Jaremko M, Wang Z, Sun W, Buller-Burckle A, et al.

Hum Mutat. 2016 Jan;37(1):127-34. doi: 10.1002/humu.22918. Epub 2015 Oct 29.

PubMed [citation]
PMID:
26467025
PMCID:
PMC4737317

Details of each submission

From GeneDx, SCV000293780.7

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

Description

This variant is denoted TP53 c.376-2dupA or IVS4-2dupA and consists of a duplication of one nucleotide at the -2 position in intron 4 of the T53 gene. The normal sequence, with the base that is duplicated in braces, is ctac{a}gTAC, where the capital letters are exonic and lowercase are intronic. The adenine (A) nucleotide that is duplicated is conserved across species and is part of the canonical splice acceptor site. Multiple in silico models predict this variant to cause a reduction in use of this natural splice acceptor site, and to possibly cause abnormal gene splicing. However, in the absence of RNA or functional studies, the actual effect of this variant is unknown. TP53 c.376-2dupA was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. This variant has not, to our knowledge, been published in the literature as pathogenic or benign. Based on currently available information, we consider TP53 c.376-2dupA to be a variant of uncertain significance.

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

From Quest Diagnostics Nichols Institute San Juan Capistrano, SCV000602270.1

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

Last Updated: Nov 2, 2019