NM_007078.3(LDB3):c.273G>A (p.Thr91=) AND not specified

Clinical significance:Benign/Likely benign (Last evaluated: Sep 2, 2016)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
3 submissions [Details]
Record status:
current
Accession:
RCV000038753.6

Allele description [Variation Report for NM_007078.3(LDB3):c.273G>A (p.Thr91=)]

NM_007078.3(LDB3):c.273G>A (p.Thr91=)

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.273G>A (p.Thr91=)
HGVS:
  • NC_000010.11:g.86680109G>A
  • NG_008876.1:g.16546G>A
  • NM_001080114.2:c.273G>A
  • NM_001080115.2:c.273G>A
  • NM_001080116.1:c.273G>A
  • NM_001171610.2:c.273G>A
  • NM_001171611.2:c.273G>A
  • NM_001368063.1:c.273G>A
  • NM_001368064.1:c.273G>A
  • NM_001368065.1:c.273G>A
  • NM_001368066.1:c.273G>A
  • NM_001368067.1:c.273G>A
  • NM_001368068.1:c.273G>A
  • NM_007078.3:c.273G>AMANE SELECT
  • NP_001073583.1:p.Thr91=
  • NP_001073584.1:p.Thr91=
  • NP_001073585.1:p.Thr91=
  • NP_001165081.1:p.Thr91=
  • NP_001165082.1:p.Thr91=
  • NP_001354992.1:p.Thr91=
  • NP_001354993.1:p.Thr91=
  • NP_001354994.1:p.Thr91=
  • NP_001354995.1:p.Thr91=
  • NP_001354996.1:p.Thr91=
  • NP_001354997.1:p.Thr91=
  • NP_009009.1:p.Thr91=
  • LRG_385t1:c.273G>A
  • LRG_385t2:c.273G>A
  • LRG_385:g.16546G>A
  • LRG_385p2:p.Thr91=
  • NC_000010.10:g.88439866G>A
  • NM_007078.2:c.273G>A
  • c.273G>A
  • p.Thr91Thr
Links:
dbSNP: rs45613039
NCBI 1000 Genomes Browser:
rs45613039
Molecular consequence:
  • NM_001080114.2:c.273G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001080115.2:c.273G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001080116.1:c.273G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001171610.2:c.273G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001171611.2:c.273G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001368063.1:c.273G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001368064.1:c.273G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001368065.1:c.273G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001368066.1:c.273G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001368067.1:c.273G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001368068.1:c.273G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_007078.3:c.273G>A - synonymous variant - [Sequence Ontology: SO:0001819]
Observations:
5

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
SCV000062431Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicinecriteria provided, single submitter
Benign
(Apr 28, 2015)
germlineclinical testing

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

SCV000523511GeneDxcriteria provided, single submitter
Likely benign
(Sep 2, 2016)
germlineclinical testing

Citation Link,

SCV001924289Clinical Genetics,Academic Medical Center - VKGL Data-share Consensus

See additional submitters

no assertion criteria providedBenigngermlineclinical testing

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlinenot provided55not 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, SCV000062431.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided5not providednot providedclinical testing PubMed (1)

Description

p.Thr91Thr in exon 3 of LDB3: This variant is not expected to have clinical sign ificance because it does not alter an amino acid residue, is not located within the splice consensus sequence, and has been identified in 2.0% (330/16496) of So uth Asian chromosomes by the Exome Aggregation Consortium (ExAC, http://exac.bro adinstitute.org; dbSNP rs45613039).

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot provided5not provided5not provided

From GeneDx, SCV000523511.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Clinical Genetics,Academic Medical Center - VKGL Data-share Consensus, SCV001924289.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 24, 2021

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