NM_000059.4(BRCA2):c.3010del (p.Ser1004fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jun 11, 2014
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:: RCV000160279.1

Allele description [Variation Report for NM_000059.4(BRCA2):c.3010del (p.Ser1004fs)]

NM_000059.4(BRCA2):c.3010del (p.Ser1004fs)

Gene:

BRCA2:BRCA2 DNA repair associated [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

13q13.1

Genomic location:

Preferred name:

NM_000059.4(BRCA2):c.3010del (p.Ser1004fs)

HGVS:

NC_000013.11:g.32337365del
NG_012772.3:g.26886del
NM_000059.4:c.3010delMANE SELECT
NP_000050.3:p.Ser1004fs
LRG_293:g.26886del
NC_000013.10:g.32911502del
NM_000059.3:c.3010delA
p.S1004VfsX39

Protein change:

S1004fs

Links:

dbSNP: rs730881604

NCBI 1000 Genomes Browser:

rs730881604

Molecular consequence:

NM_000059.4:c.3010del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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Rattus norvegicus TL0ACA35YM19 mRNA sequence
Rattus norvegicus TL0ACA35YM19 mRNA sequence
gi|298881408|emb|FQ217093.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000210732	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Pathogenic (Jun 11, 2014)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000210732

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Pathogenic
(Jun 11, 2014)

germline

clinical testing

Citation Link

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Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From GeneDx, SCV000210732.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

This deletion of one nucleotide is denoted BRCA2 c.3010delA at the cDNA level and p.Ser1004ValfsX39 (S1004VfsX39) at the protein level. The normal sequence, with the base that is deleted in brackets, is TCAC[A]GTTT. The deletion causes a frameshift, which changes a Serine to a Valine at codon 1004, and creates a premature stop codon at position 39 of the new reading frame. Although this variant has not, to our knowledge, been reported in the literature, it is predicted to cause loss of normal protein function through either protein truncation or nonsense-mediated mRNA decay. we consider this variant to be pathogenic.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 1, 2024

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