NM_007078.3(LDB3):c.794G>A (p.Arg265His) AND Primary dilated cardiomyopathy

Clinical significance:Uncertain significance (Last evaluated: Feb 26, 2021)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV001375640.1

Allele description [Variation Report for NM_007078.3(LDB3):c.794G>A (p.Arg265His)]

NM_007078.3(LDB3):c.794G>A (p.Arg265His)

Gene:
LDB3:LIM domain binding 3 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
10q23.2
Genomic location:
Preferred name:
NM_007078.3(LDB3):c.794G>A (p.Arg265His)
Other names:
p.R265H:CGC>CAC
HGVS:
  • NC_000010.11:g.86692000G>A
  • NG_008876.1:g.28437G>A
  • NM_001080114.2:c.653G>A
  • NM_001080115.2:c.794G>A
  • NM_001080116.1:c.653G>A
  • NM_001171610.2:c.998G>A
  • NM_001171611.2:c.998G>A
  • NM_001368063.1:c.794G>A
  • NM_001368064.1:c.794G>A
  • NM_001368065.1:c.794G>A
  • NM_001368066.1:c.653G>A
  • NM_001368067.1:c.653G>A
  • NM_001368068.1:c.653G>A
  • NM_007078.3:c.794G>AMANE SELECT
  • NP_001073583.1:p.Arg218His
  • NP_001073584.1:p.Arg265His
  • NP_001073585.1:p.Arg218His
  • NP_001165081.1:p.Arg333His
  • NP_001165082.1:p.Arg333His
  • NP_001354992.1:p.Arg265His
  • NP_001354993.1:p.Arg265His
  • NP_001354994.1:p.Arg265His
  • NP_001354995.1:p.Arg218His
  • NP_001354996.1:p.Arg218His
  • NP_001354997.1:p.Arg218His
  • NP_009009.1:p.Arg265His
  • LRG_385t1:c.794G>A
  • LRG_385t2:c.653G>A
  • LRG_385:g.28437G>A
  • LRG_385p2:p.Arg218His
  • NC_000010.10:g.88451757G>A
  • NM_007078.2:c.794G>A
Protein change:
R218H
Links:
dbSNP: rs45458895
NCBI 1000 Genomes Browser:
rs45458895
Molecular consequence:
  • NM_001080114.2:c.653G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001080115.2:c.794G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001080116.1:c.653G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001171610.2:c.998G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001171611.2:c.998G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001368063.1:c.794G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001368064.1:c.794G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001368065.1:c.794G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001368066.1:c.653G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001368067.1:c.653G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001368068.1:c.653G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_007078.3:c.794G>A - missense variant - [Sequence Ontology: SO:0001583]
Observations:
1

Condition(s)

Name:
Primary dilated cardiomyopathy (DCM)
Synonyms:
Congestive cardiomyopathy; Dilated Cardiomyopathy
Identifiers:
EFO: EFO_0000407; MONDO: MONDO:0005021; MeSH: D002311; MedGen: C0007193; Human Phenotype Ontology: HP:0001644

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001572565Loeys Lab,Universiteit Antwerpencriteria provided, single submitter
Uncertain significance
(Feb 26, 2021)
somaticclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedsomaticyes11not provided1not 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

Details of each submission

From Loeys Lab,Universiteit Antwerpen, SCV001572565.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednoclinical testing PubMed (1)

Description

This sequence change results in a missense variant in the LDB3 gene (p.(Arg333His)). This variant is present in population databases with a prevalence of 36/282804 in GnomAD (BS1) . This variant has not been reported in the literature and no functional data are available. Prediction programs show conflicting results (Align GVGD: C0; Polyphen-2-HumDiv: possibly damaging ; Polyphen-2-HumVar: benign; SIFT: tolerated; MutationTaster: disease causing). The variant affects a highly conserved nucleotide and a moderately conserved amino acid. We identified this variant in a patients with DCM. In conclusion this variant was classified as a variant of unknown significance according to ACMG-guidelines (insufficient data, criteria for other classification are not met: BS1).

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1somaticyes1Bloodnot provided1not provided1not provided

Last Updated: Jul 29, 2021

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