Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

ClinVar Genomic variation as it relates to human health

Advanced search

NM_007078.3(LDB3):c.1697T>G (p.Met566Arg)

Help
Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(2);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
3 (Most recent: Jan 7, 2021)
Last evaluated:
Oct 6, 2020
Accession:
VCV000228795.3
Variation ID:
228795
Description:
single nucleotide variant
Help

NM_007078.3(LDB3):c.1697T>G (p.Met566Arg)

Allele ID
229950
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
10q23.2
Genomic location
10: 86717984 (GRCh38) GRCh38 UCSC
10: 88477741 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000010.10:g.88477741T>G
NC_000010.11:g.86717984T>G
NM_007078.3:c.1697T>G MANE Select NP_009009.1:p.Met566Arg missense
... more HGVS
Protein change
M566R, M571R, M503R, M519R, M456R
Other names
-
Canonical SPDI
NC_000010.11:86717983:T:G
Functional consequence
-
Global minor allele frequency (GMAF)
0.00020 (G)

Allele frequency
1000 Genomes Project 0.00020
Trans-Omics for Precision Medicine (TOPMed) 0.00016
The Genome Aggregation Database (gnomAD), exomes 0.00018
The Genome Aggregation Database (gnomAD) 0.00006
Exome Aggregation Consortium (ExAC) 0.00012
Links
ClinGen: CA5585218
dbSNP: rs566463138
Varsome
Help

Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 1 criteria provided, single submitter May 7, 2015 RCV000221610.1
Likely benign 1 criteria provided, single submitter Aug 3, 2018 RCV000552722.2
Likely benign 1 criteria provided, single submitter Oct 6, 2020 RCV001428629.1
Help
Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
LDB3 - - GRCh38
GRCh37
645 763

Submitted interpretations and evidence

Help
Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(May 07, 2015)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine
Accession: SCV000271911.2
Submitted: (Mar 21, 2019)
Evidence details
Comment:
Variant classified as Uncertain Significance - Favor Benign. The p.Met556Arg var iant in LDB3 has not been previously reported in individuals with cardiomyopathy , but … (more)
Likely benign
(Aug 03, 2018)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV000638661.2
Submitted: (Mar 14, 2019)
Evidence details
Likely benign
(Oct 06, 2020)
criteria provided, single submitter
Method: clinical testing
Myofibrillar myopathy, ZASP-related
Allele origin: germline
Invitae
Accession: SCV001631331.1
Submitted: (Jan 07, 2021)
Evidence details

Functional evidence

Help
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

Help
There are no citations in ClinVar for this variation. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for rs566463138...

Help
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 Jul 07, 2021