NM_007078.3(LDB3):c.1697T>G (p.Met566Arg) AND not specified

Clinical significance:Uncertain significance (Last evaluated: May 7, 2015)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000221610.1

Allele description [Variation Report for NM_007078.3(LDB3):c.1697T>G (p.Met566Arg)]

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

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.1697T>G (p.Met566Arg)
HGVS:
  • NC_000010.11:g.86717984T>G
  • NG_008876.1:g.54421T>G
  • NM_001080114.2:c.1367T>G
  • NM_001080116.1:c.*18610T>G
  • NM_001171610.2:c.1712T>G
  • NM_001368064.1:c.1508T>G
  • NM_001368065.1:c.1508T>G
  • NM_001368066.1:c.1556T>G
  • NM_007078.3:c.1697T>GMANE SELECT
  • NP_001073583.1:p.Met456Arg
  • NP_001165081.1:p.Met571Arg
  • NP_001354993.1:p.Met503Arg
  • NP_001354994.1:p.Met503Arg
  • NP_001354995.1:p.Met519Arg
  • NP_009009.1:p.Met566Arg
  • LRG_385t1:c.1697T>G
  • LRG_385t2:c.*18610T>G
  • LRG_385:g.54421T>G
  • NC_000010.10:g.88477741T>G
  • NM_007078.2:c.1697T>G
Protein change:
M456R
Links:
dbSNP: rs566463138
NCBI 1000 Genomes Browser:
rs566463138
Molecular consequence:
  • NM_001080116.1:c.*18610T>G - genic downstream transcript variant - [Sequence Ontology: SO:0002152]
  • NM_001080114.2:c.1367T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001171610.2:c.1712T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001368064.1:c.1508T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001368065.1:c.1508T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001368066.1:c.1556T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_007078.3:c.1697T>G - missense variant - [Sequence Ontology: SO:0001583]
Observations:
1

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000271911Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicinecriteria provided, single submitter
Uncertain significance
(May 7, 2015)
germlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot provided11not providednot providednot providedclinical testing

Citations

PubMed

A systematic approach to assessing the clinical significance of genetic variants.

Duzkale H, Shen J, McLaughlin H, Alfares A, Kelly MA, Pugh TJ, Funke BH, Rehm HL, Lebo MS.

Clin Genet. 2013 Nov;84(5):453-63. doi: 10.1111/cge.12257.

PubMed [citation]
PMID:
24033266
PMCID:
PMC3995020

Details of each submission

From Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, SCV000271911.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)

Description

Variant classified as Uncertain Significance - Favor Benign. The p.Met556Arg var iant in LDB3 has not been previously reported in individuals with cardiomyopathy , but has been identified in 0.2% (14/8652) of East Asian chromosomes by the Exo me Aggregation Consortium (ExAC, http://exac.broadinstitute.org; dbSNP rs5664631 38). Computational prediction tools and conservation analysis suggest that the p .Met556Arg variant may impact the protein, though this information is not predic tive enough to determine pathogenicity. In summary, while the clinical significa nce of the p.Met556Arg variant is uncertain, its frequency in the general popula tion suggests that it is more likely to be benign.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot provided1not provided1not provided

Last Updated: Jul 7, 2021

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