NM_007078.3(LDB3):c.1603_1605delinsTGCCACTCA (p.Thr535delinsCysHisSer) AND Cardiovascular phenotype

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Sep 7, 2022
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:: RCV002397697.2

Allele description [Variation Report for NM_007078.3(LDB3):c.1603_1605delinsTGCCACTCA (p.Thr535delinsCysHisSer)]

NM_007078.3(LDB3):c.1603_1605delinsTGCCACTCA (p.Thr535delinsCysHisSer)

Gene:

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

Variant type:

Indel

Cytogenetic location:

10q23.2

Genomic location:

Preferred name:

NM_007078.3(LDB3):c.1603_1605delinsTGCCACTCA (p.Thr535delinsCysHisSer)

HGVS:

NC_000010.11:g.86716698_86716700delinsTGCCACTCA
NG_008876.1:g.53135_53137delinsTGCCACTCA
NM_001080114.2:c.1273_1275delinsTGCCACTCA
NM_001171610.2:c.1618_1620delinsTGCCACTCA
NM_001368064.1:c.1414_1416delinsTGCCACTCA
NM_001368065.1:c.1414_1416delinsTGCCACTCA
NM_001368066.1:c.1462_1464delinsTGCCACTCA
NM_007078.3:c.1603_1605delinsTGCCACTCAMANE SELECT
NP_001073583.1:p.Thr425delinsCysHisSer
NP_001165081.1:p.Thr540delinsCysHisSer
NP_001354993.1:p.Thr472delinsCysHisSer
NP_001354994.1:p.Thr472delinsCysHisSer
NP_001354995.1:p.Thr488delinsCysHisSer
NP_009009.1:p.Thr535delinsCysHisSer
LRG_385t1:c.1603_1605delinsTGCCACTCA
LRG_385:g.53135_53137delinsTGCCACTCA
NC_000010.10:g.88476455_88476457delinsTGCCACTCA
NM_007078.2:c.1603_1605delACCinsTGCCACTCA
NM_007078.2:c.1603_1605delinsTGCCACTCA

Links:

dbSNP: rs1589675306

NCBI 1000 Genomes Browser:

rs1589675306

Molecular consequence:

NM_001080114.2:c.1273_1275delinsTGCCACTCA - inframe_indel - [Sequence Ontology: SO:0001820]
NM_001171610.2:c.1618_1620delinsTGCCACTCA - inframe_indel - [Sequence Ontology: SO:0001820]
NM_001368064.1:c.1414_1416delinsTGCCACTCA - inframe_indel - [Sequence Ontology: SO:0001820]
NM_001368065.1:c.1414_1416delinsTGCCACTCA - inframe_indel - [Sequence Ontology: SO:0001820]
NM_001368066.1:c.1462_1464delinsTGCCACTCA - inframe_indel - [Sequence Ontology: SO:0001820]
NM_007078.3:c.1603_1605delinsTGCCACTCA - inframe_indel - [Sequence Ontology: SO:0001820]

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
SCV002706397	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (Sep 7, 2022)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002706397

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(Sep 7, 2022)

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 Ambry Genetics, SCV002706397.2

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

Description

The c.1603_1605delACCinsTGCCACTCA variant, located in coding exon 9 of the LDB3 gene, results from an in-frame deletion of ACC and insertion of TGCCACTCA at nucleotide positions 1603 to 1605. This results in the substitution of the threonine residue for a residue at codon 535, an amino acid with highly similar properties. This amino acid position is not well conserved in available vertebrate species. 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: Sep 29, 2024

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