NM_000059.3(BRCA2):c.4889C>G (p.Ser1630Ter) AND not provided

This record was updated by the submitter. Please see the current version.

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Nov 1, 2017
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:: RCV000255089.2

Allele description

NM_000059.3(BRCA2):c.4889C>G (p.Ser1630Ter)

Gene:

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

Variant type:

single nucleotide variant

Cytogenetic location:

13q13.1

Genomic location:

Preferred name:

NM_000059.3(BRCA2):c.4889C>G (p.Ser1630Ter)

HGVS:

NC_000013.11:g.32339244C>G
NG_012772.3:g.28765C>G
NM_000059.3:c.4889C>G
NP_000050.2:p.Ser1630Ter
LRG_293t1:c.4889C>G
LRG_293:g.28765C>G
LRG_293p1:p.Ser1630Ter
NC_000013.10:g.32913381C>G
U43746.1:n.5117C>G
p.S1630*
p.Ser1630*
p.Ser1630X

Nucleotide change:

5117C>G

Protein change:

S1630*

Links:

dbSNP: rs80358711

NCBI 1000 Genomes Browser:

rs80358711

Allele Frequency:

0.00002(G)

Molecular consequence:

NM_000059.3:c.4889C>G - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Identifiers:: MedGen: CN517202

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000321464	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Pathogenic (Jan 5, 2017)	germline	clinical testing	Citation Link,
SCV000693568	GeneKor MSA,	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Nov 1, 2017)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000321464

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Pathogenic
(Jan 5, 2017)

germline

clinical testing

Citation Link,

SCV000693568

GeneKor MSA,

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Nov 1, 2017)

germline

clinical testing

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

Help

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
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical 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

Details of each submission

From GeneDx, SCV000321464.6

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

Description

This pathogenic variant is denoted BRCA2 c.4889C>G at the cDNA level and p.Ser1630Ter (S1630X) at the protein level. The substitution creates a nonsense variant, which changes a Serine to a premature stop codon (TCA>TGA), and is predicted to cause loss of normal protein function through either protein truncation or nonsense-mediated mRNA decay. This variant, also known as BRCA2 5117C>G using alternate nomenclature, has been reported in individuals and families with breast and/or ovarian cancer (Ozcelik 2003, Claus 2005, Malone 2006, Rodriguez 2012, Castera 2014, Zugazagoitia 2014, Pellegrino 2016). 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

From GeneKor MSA,, SCV000693568.1

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

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

Last Updated: Dec 9, 2018

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