NM_007078.3(LDB3):c.548del (p.Pro183fs) AND Cardiovascular phenotype

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Mar 30, 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:: RCV000617200.4

Allele description [Variation Report for NM_007078.3(LDB3):c.548del (p.Pro183fs)]

NM_007078.3(LDB3):c.548del (p.Pro183fs)

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.548del (p.Pro183fs)

HGVS:

NC_000010.11:g.86681662del
NG_008876.1:g.18099del
NM_001080114.2:c.321+1505del
NM_001080115.2:c.548del
NM_001080116.1:c.321+1505del
NM_001171610.2:c.548del
NM_001171611.2:c.548del
NM_001368063.1:c.548del
NM_001368064.1:c.548del
NM_001368065.1:c.548del
NM_001368066.1:c.321+1505del
NM_001368067.1:c.321+1505del
NM_001368068.1:c.321+1505del
NM_007078.3:c.548delMANE SELECT
NP_001073584.1:p.Pro183fs
NP_001165081.1:p.Pro183fs
NP_001165082.1:p.Pro183fs
NP_001354992.1:p.Pro183fs
NP_001354993.1:p.Pro183fs
NP_001354994.1:p.Pro183fs
NP_009009.1:p.Pro183fs
LRG_385t1:c.548del
LRG_385t2:c.321+1505del
LRG_385:g.18099del
NC_000010.10:g.88441417del
NC_000010.10:g.88441419del
NM_007078.2:c.548del
NM_007078.2:c.548delC

Protein change:

P183fs

Links:

dbSNP: rs1285270306

NCBI 1000 Genomes Browser:

rs1285270306

Molecular consequence:

NM_001080115.2:c.548del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001171610.2:c.548del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001171611.2:c.548del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001368063.1:c.548del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001368064.1:c.548del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001368065.1:c.548del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_007078.3:c.548del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001080114.2:c.321+1505del - intron variant - [Sequence Ontology: SO:0001627]
NM_001080116.1:c.321+1505del - intron variant - [Sequence Ontology: SO:0001627]
NM_001368066.1:c.321+1505del - intron variant - [Sequence Ontology: SO:0001627]
NM_001368067.1:c.321+1505del - intron variant - [Sequence Ontology: SO:0001627]
NM_001368068.1:c.321+1505del - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:: Cardiovascular phenotype
Identifiers:: MedGen: CN230736

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000736224	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (Mar 30, 2023)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 11696561, 19028670 Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000736224

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(Mar 30, 2023)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

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

Citations

PubMed

Ablation of Cypher, a PDZ-LIM domain Z-line protein, causes a severe form of congenital myopathy.

Zhou Q, Chu PH, Huang C, Cheng CF, Martone ME, Knoll G, Shelton GD, Evans S, Chen J.

J Cell Biol. 2001 Nov 12;155(4):605-12. Epub 2001 Nov 5.

PubMed [citation]

PMID:: 11696561
PMCID:: PMC2198871

Cardiac-specific ablation of Cypher leads to a severe form of dilated cardiomyopathy with premature death.

Zheng M, Cheng H, Li X, Zhang J, Cui L, Ouyang K, Han L, Zhao T, Gu Y, Dalton ND, Bang ML, Peterson KL, Chen J.

Hum Mol Genet. 2009 Feb 15;18(4):701-13. doi: 10.1093/hmg/ddn400. Epub 2008 Nov 21.

PubMed [citation]

PMID:: 19028670
PMCID:: PMC2722217

Details of each submission

From Ambry Genetics, SCV000736224.6

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

The c.548delC variant, located in coding exon 4 of the LDB3 gene, results from a deletion of one nucleotide at nucleotide position 548, causing a translational frameshift with a predicted alternate stop codon (p.P183Qfs*25). This alteration is expected to result in protein truncation or nonsense-mediated mRNA decay. However, loss of function of LDB3 has not been established as a mechanism of disease. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

#	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: May 1, 2024

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