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NM_007078.3(LDB3):c.690-4826G>A

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(1);Uncertain significance(2)

Review status:
criteria provided, conflicting interpretations
Submissions:
3 (Most recent: Sep 29, 2021)
Last evaluated:
Jun 14, 2021
Accession:
VCV000191696.4
Variation ID:
191696
Description:
single nucleotide variant
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NM_007078.3(LDB3):c.690-4826G>A

Allele ID
189874
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
10q23.2
Genomic location
10: 86687070 (GRCh38) GRCh38 UCSC
10: 88446827 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_385:g.23507G>A
LRG_385t2:c.346G>A LRG_385p2:p.Ala116Thr
LRG_385t1:c.690-4826G>A
... more HGVS
Protein change
A116T, A231T
Other names
p.A231T:GCC>ACC
Canonical SPDI
NC_000010.11:86687069:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00040 (A)

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00002
The Genome Aggregation Database (gnomAD) 0.00006
Exome Aggregation Consortium (ExAC) 0.00009
1000 Genomes Project 0.00040
The Genome Aggregation Database (gnomAD), exomes 0.00009
Links
ClinGen: CA302363
dbSNP: rs200458194
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 1 criteria provided, single submitter Jul 20, 2020 RCV001324560.1
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Jun 14, 2021 RCV000171990.5
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
LDB3 - - GRCh38
GRCh37
656 776
LOC110121486 - - - GRCh38 - 93

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Jun 24, 2013)
criteria provided, single submitter
Method: research
Not provided
Allele origin: unknown
Biesecker Lab/Clinical Genomics Section,National Institutes of Health
Study: ClinSeq
Accession: SCV000050971.1
Submitted: (Mar 10, 2015)
Comments (2):
The study set was not selected for affection status in relation to any cancer. Pathogenicity categories were based on literature curation. See Pubmed ID:23861362 for … (more)
Medical sequencing
Evidence details
Uncertain significance
(Jul 20, 2020)
criteria provided, single submitter
Method: clinical testing
Myofibrillar myopathy, ZASP-related
Allele origin: germline
Invitae
Accession: SCV001515517.1
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (2)
Comment:
This sequence change replaces alanine with threonine at codon 116 of the LDB3 protein (p.Ala116Thr). The alanine residue is weakly conserved and there is a … (more)
Likely benign
(Jun 14, 2021)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000235993.10
Submitted: (Sep 29, 2021)
Evidence details

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Pathogenic variant burden in the ExAC database: an empirical approach to evaluating population data for clinical variant interpretation. Kobayashi Y Genome medicine 2017 PMID: 28166811
LOVD v.2.0: the next generation in gene variant databases. Fokkema IF Human mutation 2011 PMID: 21520333

Text-mined citations for rs200458194...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Oct 06, 2021