NM_007078.3(LDB3):c.1597del (p.Arg533fs) AND not specified

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Apr 4, 2023
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:: RCV003231027.1

Allele description [Variation Report for NM_007078.3(LDB3):c.1597del (p.Arg533fs)]

NM_007078.3(LDB3):c.1597del (p.Arg533fs)

Gene:

LDB3:LIM domain binding 3 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

10q23.2

Genomic location:

Preferred name:

NM_007078.3(LDB3):c.1597del (p.Arg533fs)

HGVS:

NC_000010.11:g.86716692del
NG_008876.1:g.53129del
NM_001080114.2:c.1267del
NM_001171610.2:c.1612del
NM_001368064.1:c.1408del
NM_001368065.1:c.1408del
NM_001368066.1:c.1456del
NM_007078.3:c.1597delMANE SELECT
NP_001073583.1:p.Arg423fs
NP_001165081.1:p.Arg538fs
NP_001354993.1:p.Arg470fs
NP_001354994.1:p.Arg470fs
NP_001354995.1:p.Arg486fs
NP_009009.1:p.Arg533Glyfs
NP_009009.1:p.Arg533fs
LRG_385t1:c.1597del
LRG_385:g.53129del
LRG_385p1:p.Arg533Glyfs
NC_000010.10:g.88476449del
NM_007078.2:c.1597delA

Protein change:

R423fs

Molecular consequence:

NM_001080114.2:c.1267del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001171610.2:c.1612del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001368064.1:c.1408del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001368065.1:c.1408del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001368066.1:c.1456del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_007078.3:c.1597del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003928323	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Uncertain significance (Apr 4, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003928323

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Uncertain significance
(Apr 4, 2023)

germline

clinical testing

Citation Link

Help

Summary from all submissions

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

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV003928323.1

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

Description

Variant summary: LDB3 c.1597delA (p.Arg533GlyfsX32) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay. No truncations downstream of this position have been classified as pathogenic by our laboratory or other ClinVar submitters. All truncating variants in ClinVar upstream or downstream of this position are classified as uncertain significance. Additionally, the LDB3 gene is classified as "limited association" with dilated cardiomyopathy and "disputed association" with arrhythmogenic right ventricular cardiomyopathy by ClinGen. Therefore, currently available evidence does not support that loss-of-function variants are pathogenic for Cardiomyopathy. The variant was absent in 250332 control chromosomes (gnomAD). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. To our knowledge, no occurrence of c.1597delA in individuals affected with Cardiomyopathy and no experimental evidence demonstrating its impact on protein function have been reported. No submitters have provided clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as uncertain significance.

#	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: Jun 10, 2023

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