NM_000059.3(BRCA2):c.3199delA (p.Thr1067Leufs) AND not provided

Clinical significance:Pathogenic (Last evaluated: Mar 14, 2017)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:

Allele description

NM_000059.3(BRCA2):c.3199delA (p.Thr1067Leufs)

BRCA2:BRCA2, DNA repair associated [Gene - OMIM - HGNC]
Variant type:
Cytogenetic location:
Genomic location:
Preferred name:
NM_000059.3(BRCA2):c.3199delA (p.Thr1067Leufs)
  • NC_000013.11:g.32337554delA
  • NG_012772.3:g.27075delA
  • NM_000059.3:c.3199delA
  • NP_000050.2:p.Thr1067Leufs
  • LRG_293t1:c.3199delA
  • LRG_293:g.27075delA
  • LRG_293p1:p.Thr1067Leufs
  • NC_000013.10:g.32911691delA
  • NM_000059.3:c.3199del
  • U43746.1:n.3427delA
Nucleotide change:
Breast Cancer Information Core (BIC) (BRCA2): 3427&base_change=del A; dbSNP: rs80359377
NCBI 1000 Genomes Browser:
Molecular consequence:
  • NM_000059.3:c.3199delA - frameshift variant - [Sequence Ontology: SO:0001589]


MedGen: CN221809

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
SCV000565992GeneDxcriteria provided, single submitter
(Mar 14, 2017)
germlineclinical testing

Citation Link

Summary from all submissions

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

Details of each submission

From GeneDx, SCV000565992.1

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


This deletion of one nucleotide in BRCA2 is denoted c.3199delA at the cDNA level and p.Thr1067LeufsX10 (T1067LfsX10) at the protein level. Using alternate nomenclature, this variant would be defined as BRCA2 c.3427delA. The normal sequence, with the base that is deleted in brackets, is TAAT[A]CTGT. The deletion causes a frameshift, which changes a Threonine to a Leucine at codon 1067, and creates a premature stop codon at position 10 of the new reading frame. This variant is predicted to cause loss of normal protein function through either protein truncation or nonsense-mediated mRNA decay. BRCA2 c.3199delA has been observed in multiple families with hereditary breast and/or ovarian cancer (Gorski 2004, Lubinski 2004, Tea 2014, Couch 2015 ) as well as one individual with ampullary cancer (Villalona-Calero 2016). We consider this variant to be pathogenic.

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

Last Updated: Apr 27, 2017