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NM_000059.4(BRCA2):c.5614A>T (p.Lys1872Ter) AND not provided

Germline classification:
Pathogenic (3 submissions)
Last evaluated:
Jun 23, 2023
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:
RCV000212241.17

Allele description [Variation Report for NM_000059.4(BRCA2):c.5614A>T (p.Lys1872Ter)]

NM_000059.4(BRCA2):c.5614A>T (p.Lys1872Ter)

Gene:
BRCA2:BRCA2 DNA repair associated [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
13q13.1
Genomic location:
Preferred name:
NM_000059.4(BRCA2):c.5614A>T (p.Lys1872Ter)
Other names:
p.K1872X:AAA>TAA
HGVS:
  • NC_000013.11:g.32339969A>T
  • NG_012772.3:g.29490A>T
  • NM_000059.4:c.5614A>TMANE SELECT
  • NP_000050.2:p.Lys1872Ter
  • NP_000050.3:p.Lys1872Ter
  • LRG_293t1:c.5614A>T
  • LRG_293:g.29490A>T
  • LRG_293p1:p.Lys1872Ter
  • NC_000013.10:g.32914106A>T
  • NM_000059.3:c.5614A>T
  • U43746.1:n.5842A>T
  • p.K1872*
  • p.Lys1872X
Protein change:
K1872*
Links:
dbSNP: rs80358783
NCBI 1000 Genomes Browser:
rs80358783
Molecular consequence:
  • NM_000059.4:c.5614A>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:
none provided; RECLASSIFIED - ADRA2C POLYMORPHISM; RECLASSIFIED - ADRB1 POLYMORPHISM
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000210357GeneDx
criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)
Pathogenic
(Jun 23, 2023)
germlineclinical testing

Citation Link,

SCV001447151Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Oct 23, 2020)
germlineclinical testing

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

SCV001470434Quest Diagnostics Nichols Institute San Juan Capistrano
criteria provided, single submitter

(Quest Diagnostics criteria)
Pathogenic
(Jul 21, 2020)
unknownclinical testing

PubMed (6)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot provided1not providedclinical testing
not providedunknownunknownnot providednot providednot providednot providednot providedclinical 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

Prospective Evaluation of Germline Alterations in Patients With Exocrine Pancreatic Neoplasms.

Lowery MA, Wong W, Jordan EJ, Lee JW, Kemel Y, Vijai J, Mandelker D, Zehir A, Capanu M, Salo-Mullen E, Arnold AG, Yu KH, Varghese AM, Kelsen DP, Brenner R, Kaufmann E, Ravichandran V, Mukherjee S, Berger MF, Hyman DM, Klimstra DS, Abou-Alfa GK, et al.

J Natl Cancer Inst. 2018 Oct 1;110(10):1067-1074. doi: 10.1093/jnci/djy024.

PubMed [citation]
PMID:
29506128
PMCID:
PMC6186514
See all PubMed Citations (7)

Details of each submission

From GeneDx, SCV000210357.14

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

Description

Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Reported in individuals with personal or family history of BRCA2-related cancers (Meyer et al., 2003; Ramus et al., 2007; Tea et al., 2014; Annala et al., 2017; Mandelker et al., 2017; Lowery et al., 2018); Truncating variants in this gene are considered pathogenic by a well-established clinical consortium and/or database; Not observed at significant frequency in large population cohorts (gnomAD); Also known as 5842A>T; This variant is associated with the following publications: (PMID: 24156927, 17688236, 26681312, 12938098, 28259476, 25525159, 28873162, 29506128, 29446198, 30787465, 32377563, 20104584)

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

From Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen, SCV001447151.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyes1not providednot providednot providednot providednot providednot provided

From Quest Diagnostics Nichols Institute San Juan Capistrano, SCV001470434.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (6)

Description

The variant creates a premature nonsense codon, and is therefore predicted to result in the loss of a functional protein. Found in at least one patient with expected phenotype for this gene, and not found in general population data.

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

Last Updated: Jan 13, 2025