NM_001368067.1(LDB3):c.346G>A (p.Ala116Thr) AND not provided

Germline classification:: Conflicting interpretations of pathogenicity (3 submissions)
Last evaluated:: Mar 31, 2023
Review status:: criteria provided, conflicting classifications

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:: RCV000171990.11

Allele description [Variation Report for NM_001368067.1(LDB3):c.346G>A (p.Ala116Thr)]

NM_001368067.1(LDB3):c.346G>A (p.Ala116Thr)

Genes:

LDB3:LIM domain binding 3 [Gene - OMIM - HGNC]
LOC110121486:VISTA enhancer hs2143 [Gene]

Variant type:

single nucleotide variant

Cytogenetic location:

10q23.2

Genomic location:

Preferred name:

NM_001368067.1(LDB3):c.346G>A (p.Ala116Thr)

Other names:

p.A231T:GCC>ACC

HGVS:

NC_000010.11:g.86687070G>A
NG_008876.1:g.23507G>A
NG_054099.1:g.3099G>A
NM_001080114.2:c.346G>A
NM_001080115.2:c.690-4826G>A
NM_001080116.1:c.346G>A
NM_001171610.2:c.691G>A
NM_001171611.2:c.691G>A
NM_001368063.1:c.690-4826G>A
NM_001368064.1:c.690-4826G>A
NM_001368065.1:c.690-4826G>A
NM_001368066.1:c.346G>A
NM_001368067.1:c.346G>A
NM_001368068.1:c.346G>A
NM_007078.3:c.690-4826G>AMANE SELECT
NP_001073583.1:p.Ala116Thr
NP_001073585.1:p.Ala116Thr
NP_001165081.1:p.Ala231Thr
NP_001165082.1:p.Ala231Thr
NP_001354995.1:p.Ala116Thr
NP_001354996.1:p.Ala116Thr
NP_001354997.1:p.Ala116Thr
LRG_385t1:c.690-4826G>A
LRG_385t2:c.346G>A
LRG_385:g.23507G>A
LRG_385p2:p.Ala116Thr
NC_000010.10:g.88446827G>A
NM_001080115.1:c.690-4826G>A
NM_001171610.1:c.691G>A
NM_007078.2:c.690-4826G>A

Protein change:

A116T

Links:

dbSNP: rs200458194

NCBI 1000 Genomes Browser:

rs200458194

Molecular consequence:

NM_001080115.2:c.690-4826G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001368063.1:c.690-4826G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001368064.1:c.690-4826G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001368065.1:c.690-4826G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_007078.3:c.690-4826G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001080114.2:c.346G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001080116.1:c.346G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001171610.2:c.691G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001171611.2:c.691G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001368066.1:c.346G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001368067.1:c.346G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001368068.1:c.346G>A - missense variant - [Sequence Ontology: SO:0001583]

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
SCV000050971	Biesecker Lab/Clinical Genomics Section, National Institutes of Health - ClinSeq	criteria provided, single submitter (Ng et al. (Circ Cardiovasc Genet. 2013))	Uncertain significance (Jun 24, 2013)	unknown	research	PubMed (1) [See all records that cite this PMID]
SCV000235993	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Likely benign (Jun 14, 2021)	germline	clinical testing	Citation Link,
SCV004236235	Revvity Omics, Revvity	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Mar 31, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000050971

Biesecker Lab/Clinical Genomics Section, National Institutes of Health - ClinSeq

criteria provided, single submitter

(Ng et al. (Circ Cardiovasc Genet. 2013))

Uncertain significance
(Jun 24, 2013)

unknown

research

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

SCV000235993

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Likely benign
(Jun 14, 2021)

germline

clinical testing

Citation Link,

SCV004236235

Revvity Omics, Revvity

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Mar 31, 2023)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	unknown	unknown	1	not provided	not provided	not provided	not provided	research
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Interpreting secondary cardiac disease variants in an exome cohort.

Ng D, Johnston JJ, Teer JK, Singh LN, Peller LC, Wynter JS, Lewis KL, Cooper DN, Stenson PD, Mullikin JC, Biesecker LG; NIH Intramural Sequencing Center (NISC) Comparative Sequencing Program..

Circ Cardiovasc Genet. 2013 Aug;6(4):337-46. doi: 10.1161/CIRCGENETICS.113.000039. Epub 2013 Jul 16.

PubMed [citation]

PMID:: 23861362
PMCID:: PMC3887521

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Biesecker Lab/Clinical Genomics Section, National Institutes of Health - ClinSeq, SCV000050971.1

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

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

From GeneDx, SCV000235993.11

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

#	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 Revvity Omics, Revvity, SCV004236235.1

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

#	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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