NM_007078.3(LDB3):c.1502C>T (p.Ala501Val) AND not provided

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Sep 1, 2022
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000489670.10

Allele description [Variation Report for NM_007078.3(LDB3):c.1502C>T (p.Ala501Val)]

NM_007078.3(LDB3):c.1502C>T (p.Ala501Val)

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.1502C>T (p.Ala501Val)

HGVS:

NC_000010.11:g.86716597C>T
NG_008876.1:g.53034C>T
NM_001080114.2:c.1172C>T
NM_001171610.2:c.1517C>T
NM_001368064.1:c.1313C>T
NM_001368065.1:c.1313C>T
NM_001368066.1:c.1361C>T
NM_007078.3:c.1502C>TMANE SELECT
NP_001073583.1:p.Ala391Val
NP_001165081.1:p.Ala506Val
NP_001354993.1:p.Ala438Val
NP_001354994.1:p.Ala438Val
NP_001354995.1:p.Ala454Val
NP_009009.1:p.Ala501Val
LRG_385t1:c.1502C>T
LRG_385:g.53034C>T
NC_000010.10:g.88476354C>T
NM_007078.2:c.1502C>T

Protein change:

A391V

Links:

dbSNP: rs755362259

NCBI 1000 Genomes Browser:

rs755362259

Molecular consequence:

NM_001080114.2:c.1172C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001171610.2:c.1517C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001368064.1:c.1313C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001368065.1:c.1313C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001368066.1:c.1361C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_007078.3:c.1502C>T - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000577562	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Uncertain significance (Jul 17, 2018)	germline	clinical testing	Citation Link,
SCV002585235	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Uncertain significance (Sep 1, 2022)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000577562

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Uncertain significance
(Jul 17, 2018)

germline

clinical testing

Citation Link,

SCV002585235

CeGaT Center for Human Genetics Tuebingen

criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)

Uncertain significance
(Sep 1, 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	yes	2	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From GeneDx, SCV000577562.3

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

Description

A variant of uncertain significance has been identified in the LDB3 gene. The A501V variant has not been published as pathogenic or been reported as benign to our knowledge. This variant is not observed at a significant frequency in large population cohorts (Lek et al., 2016). However, the A501V variant is a conservative amino acid substitution, which is not likely to impact secondary protein structure as these residues share similar properties. Finally, in-silico analyses, including protein predictors and evolutionary conservation, support that this variant does not alter protein structure/function. Therefore, based on the currently available information, it is unclear whether this variant is pathogenic or rare benign.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From CeGaT Center for Human Genetics Tuebingen, SCV002585235.9

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

Description

LDB3: PM2, BP4

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		2	not provided	not provided	not provided

Last Updated: May 1, 2024

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