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NM_007078.3(LDB3):c.1497G>A (p.Lys499=) AND Cardiovascular phenotype

Germline classification:
Likely benign (1 submission)
Last evaluated:
Nov 21, 2023
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
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:
RCV004517250.1

Allele description [Variation Report for NM_007078.3(LDB3):c.1497G>A (p.Lys499=)]

NM_007078.3(LDB3):c.1497G>A (p.Lys499=)

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.1497G>A (p.Lys499=)
HGVS:
  • NC_000010.11:g.86716592G>A
  • NG_008876.1:g.53029G>A
  • NM_001080114.2:c.1167G>A
  • NM_001171610.2:c.1512G>A
  • NM_001368064.1:c.1308G>A
  • NM_001368065.1:c.1308G>A
  • NM_001368066.1:c.1356G>A
  • NM_007078.3:c.1497G>AMANE SELECT
  • NP_001073583.1:p.Lys389=
  • NP_001165081.1:p.Lys504=
  • NP_001354993.1:p.Lys436=
  • NP_001354994.1:p.Lys436=
  • NP_001354995.1:p.Lys452=
  • NP_009009.1:p.Lys499=
  • NP_009009.1:p.Lys499=
  • LRG_385t1:c.1497G>A
  • LRG_385:g.53029G>A
  • LRG_385p1:p.Lys499=
  • NC_000010.10:g.88476349G>A
  • NM_007078.2:c.1497G>A
Molecular consequence:
  • NM_001080114.2:c.1167G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001171610.2:c.1512G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001368064.1:c.1308G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001368065.1:c.1308G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001368066.1:c.1356G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_007078.3:c.1497G>A - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:
Cardiovascular phenotype
Identifiers:
MedGen: CN230736

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV005024843Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Likely benign
(Nov 21, 2023) 		germlineclinical testing

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From Ambry Genetics, SCV005024843.1

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

Description

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

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

Last Updated: May 7, 2024