NM_004281.4(BAG3):c.699C>A (p.Tyr233Ter) AND not provided

Clinical significance:Pathogenic (Last evaluated: Jun 1, 2020)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV000223884.2

Allele description [Variation Report for NM_004281.4(BAG3):c.699C>A (p.Tyr233Ter)]

NM_004281.4(BAG3):c.699C>A (p.Tyr233Ter)

Gene:
BAG3:BAG cochaperone 3 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
10q26.11
Genomic location:
Preferred name:
NM_004281.4(BAG3):c.699C>A (p.Tyr233Ter)
HGVS:
  • NC_000010.11:g.119672446C>A
  • NG_016125.1:g.26077C>A
  • NM_004281.3:c.699C>A
  • NM_004281.4:c.699C>AMANE SELECT
  • NP_004272.2:p.Tyr233Ter
  • NP_004272.2:p.Tyr233Ter
  • LRG_742t1:c.699C>A
  • LRG_742:g.26077C>A
  • LRG_742p1:p.Tyr233Ter
  • NC_000010.10:g.121431958C>A
Protein change:
Y233*
Links:
dbSNP: rs876661342
NCBI 1000 Genomes Browser:
rs876661342
Molecular consequence:
  • NM_004281.3:c.699C>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_004281.4:c.699C>A - nonsense - [Sequence Ontology: SO:0001587]
Observations:
2

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000280054Stanford Center for Inherited Cardiovascular Disease, Stanford Universityno assertion criteria providedLikely pathogenic
(Jul 22, 2015)
germlineclinical testing

SCV000564689GeneDxcriteria provided, single submitter
Pathogenic
(Jun 1, 2020)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlinenot provided2not providednot providednot providednot providedclinical testing

Details of each submission

From Stanford Center for Inherited Cardiovascular Disease, Stanford University, SCV000280054.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided2not providednot providedclinical testingnot provided

Description

Note this variant was found in clinical genetic testing performed by one or more labs who may also submit to ClinVar. Thus any internal case data may overlap with the internal case data of other labs. The interpretation reviewed below is that of the Stanford Center for Inherited Cardiovascular Disease. Given the data supporting pathogenicity of nonsense BAG3 variants, the case data, and the absence in patients unselected for cardiomyopathy, we consider this variant likely disease causing. This specific variant (p.Tyr233Ter) is novel. However, it has been seen in one of the families reported in an initial publication on BAG3 (Norton et al 2011). That family had two brothers with DCM and both had this variant and p.Ala262Thr in BAG3. No phase data is available. The variant is not listed in the Exome Aggregation Consortium dataset (http://exac.broadinstitute.org/), which currently includes variant calls on ~64,000 individuals of European, African, Latino and Asian descent (as of July 14th, 2015).

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot provided2not providednot providednot provided

From GeneDx, SCV000564689.3

#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; Not observed in large population cohorts (Lek et al., 2016); Reported in ClinVar (ClinVar Variant ID# 234982; Landrum et al., 2016); This variant is associated with the following publications: (PMID: 31514951)

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

Last Updated: Oct 25, 2021

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