NM_007078.3(LDB3):c.155T>C (p.Ile52Thr) AND Cardiovascular phenotype

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 7, 2019
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:: RCV002397952.1

Allele description [Variation Report for NM_007078.3(LDB3):c.155T>C (p.Ile52Thr)]

NM_007078.3(LDB3):c.155T>C (p.Ile52Thr)

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.155T>C (p.Ile52Thr)

HGVS:

NC_000010.11:g.86679428T>C
NG_008876.1:g.15865T>C
NM_001080114.2:c.155T>C
NM_001080115.2:c.155T>C
NM_001080116.1:c.155T>C
NM_001171610.2:c.155T>C
NM_001171611.2:c.155T>C
NM_001368063.1:c.155T>C
NM_001368064.1:c.155T>C
NM_001368065.1:c.155T>C
NM_001368066.1:c.155T>C
NM_001368067.1:c.155T>C
NM_001368068.1:c.155T>C
NM_007078.3:c.155T>CMANE SELECT
NP_001073583.1:p.Ile52Thr
NP_001073584.1:p.Ile52Thr
NP_001073585.1:p.Ile52Thr
NP_001165081.1:p.Ile52Thr
NP_001165082.1:p.Ile52Thr
NP_001354992.1:p.Ile52Thr
NP_001354993.1:p.Ile52Thr
NP_001354994.1:p.Ile52Thr
NP_001354995.1:p.Ile52Thr
NP_001354996.1:p.Ile52Thr
NP_001354997.1:p.Ile52Thr
NP_009009.1:p.Ile52Thr
LRG_385t1:c.155T>C
LRG_385t2:c.155T>C
LRG_385:g.15865T>C
LRG_385p2:p.Ile52Thr
NC_000010.10:g.88439185T>C
NM_001080116.1:c.155T>C
NM_007078.2:c.155T>C

Protein change:

I52T

Links:

dbSNP: rs1449865053

NCBI 1000 Genomes Browser:

rs1449865053

Molecular consequence:

NM_001080114.2:c.155T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001080115.2:c.155T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001080116.1:c.155T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001171610.2:c.155T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001171611.2:c.155T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001368063.1:c.155T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001368064.1:c.155T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001368065.1:c.155T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001368066.1:c.155T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001368067.1:c.155T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001368068.1:c.155T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_007078.3:c.155T>C - missense variant - [Sequence Ontology: SO:0001583]

Observations:

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
SCV002708885	Ambry Genetics	criteria provided, single submitter (Ambry General Variant Classification Scheme_2022)	Uncertain significance (Aug 7, 2019)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002708885

Ambry Genetics

criteria provided, single submitter

(Ambry General Variant Classification Scheme_2022)

Uncertain significance
(Aug 7, 2019)

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	1	not provided	not provided	1	not provided	clinical testing

Details of each submission

From Ambry Genetics, SCV002708885.1

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

Description

The p.I52T variant (also known as c.155T>C), located in coding exon 2 of the LDB3 gene, results from a T to C substitution at nucleotide position 155. The isoleucine at codon 52 is replaced by threonine, an amino acid with similar properties. This amino acid position is highly conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. 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	1	not provided	not provided		1	not provided	not provided	not provided

Last Updated: Feb 20, 2024

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