NM_007078.3(LDB3):c.1606G>A (p.Val536Ile) AND Cardiovascular phenotype

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Oct 2, 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:: RCV002395564.2

Allele description [Variation Report for NM_007078.3(LDB3):c.1606G>A (p.Val536Ile)]

NM_007078.3(LDB3):c.1606G>A (p.Val536Ile)

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.1606G>A (p.Val536Ile)

HGVS:

NC_000010.11:g.86716701G>A
NG_008876.1:g.53138G>A
NM_001080114.2:c.1276G>A
NM_001171610.2:c.1621G>A
NM_001368064.1:c.1417G>A
NM_001368065.1:c.1417G>A
NM_001368066.1:c.1465G>A
NM_007078.3:c.1606G>AMANE SELECT
NP_001073583.1:p.Val426Ile
NP_001165081.1:p.Val541Ile
NP_001354993.1:p.Val473Ile
NP_001354994.1:p.Val473Ile
NP_001354995.1:p.Val489Ile
NP_009009.1:p.Val536Ile
LRG_385t1:c.1606G>A
LRG_385:g.53138G>A
NC_000010.10:g.88476458G>A
NM_007078.2:c.1606G>A

Protein change:

V426I

Links:

dbSNP: rs113817827

NCBI 1000 Genomes Browser:

rs113817827

Molecular consequence:

NM_001080114.2:c.1276G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001171610.2:c.1621G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001368064.1:c.1417G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001368065.1:c.1417G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001368066.1:c.1465G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_007078.3:c.1606G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Cardiovascular phenotype
Identifiers:: MedGen: CN230736

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002703669	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (Oct 2, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID] Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002703669

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(Oct 2, 2023)

germline

clinical testing

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

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

Genetic variants in Chinese patients with sporadic dilated cardiomyopathy: a cross-sectional study.

Shen C, Xu L, Sun X, Sun A, Ge J.

Ann Transl Med. 2022 Feb;10(3):129. doi: 10.21037/atm-21-6774.

PubMed [citation]

PMID:: 35284542
PMCID:: PMC8904992

Details of each submission

From Ambry Genetics, SCV002703669.2

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

Description

The p.V536I variant (also known as c.1606G>A), located in coding exon 9 of the LDB3 gene, results from a G to A substitution at nucleotide position 1606. The valine at codon 536 is replaced by isoleucine, an amino acid with highly similar properties. This alteration has been reported in a dilated cardiomyopathy (DCM) cohort; however, clinical details were limited (Shen C et al. Ann Transl Med, 2022 Feb;10:129). This amino acid position is not well conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. 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

ClinVar

Relating variation to medicine