NM_007078.3(LDB3):c.1422G>A (p.Ser474=) AND not specified

Clinical significance:Benign/Likely benign (Last evaluated: Jun 19, 2017)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
2 submissions [Details]
Record status:

Allele description [Variation Report for NM_007078.3(LDB3):c.1422G>A (p.Ser474=)]

NM_007078.3(LDB3):c.1422G>A (p.Ser474=)

LDB3:LIM domain binding 3 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Genomic location:
Preferred name:
NM_007078.3(LDB3):c.1422G>A (p.Ser474=)
  • NC_000010.11:g.86716517G>A
  • NG_008876.1:g.52954G>A
  • NM_001080114.2:c.1092G>A
  • NM_001080116.1:c.*17143G>A
  • NM_001171610.2:c.1437G>A
  • NM_001368064.1:c.1233G>A
  • NM_001368065.1:c.1233G>A
  • NM_001368066.1:c.1281G>A
  • NM_007078.3:c.1422G>AMANE SELECT
  • NP_001073583.1:p.Ser364=
  • NP_001165081.1:p.Ser479=
  • NP_001354993.1:p.Ser411=
  • NP_001354994.1:p.Ser411=
  • NP_001354995.1:p.Ser427=
  • NP_009009.1:p.Ser474=
  • LRG_385t1:c.1422G>A
  • LRG_385t2:c.*17143G>A
  • LRG_385:g.52954G>A
  • NC_000010.10:g.88476274G>A
  • NM_007078.2:c.1422G>A
  • c.1422G>A
dbSNP: rs142625982
NCBI 1000 Genomes Browser:
Molecular consequence:
  • NM_001080116.1:c.*17143G>A - genic downstream transcript variant - [Sequence Ontology: SO:0002152]
  • NM_001080114.2:c.1092G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001171610.2:c.1437G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001368064.1:c.1233G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001368065.1:c.1233G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001368066.1:c.1281G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_007078.3:c.1422G>A - synonymous variant - [Sequence Ontology: SO:0001819]


MedGen: CN169374

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
SCV000062404Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicinecriteria provided, single submitter
Likely benign
(Feb 18, 2015)
germlineclinical testing

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

SCV000698753Women's Health and Genetics/Laboratory Corporation of America, LabCorpcriteria provided, single submitter
(Jun 19, 2017)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot provided1010not providednot providednot providedclinical testing
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing



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]

Details of each submission

From Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, SCV000062404.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided10not providednot providedclinical testing PubMed (1)


p.Ser474Ser in exon 12 of LDB3: This variant is not expected to have clinical s ignificance because it does not alter an amino acid residue, is not located with in the splice consensus sequence, and has been identified in 0.1% (91/66282) of European chromosomes by the Exome Aggregation Consortium (ExAC, http://exac.broa dinstitute.org; dbSNP rs142625982).

OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot provided10not provided10not provided

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000698753.2

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


Variant summary: The LDB3 c.1422G>A (p.Ser474Ser) variant involves the alteration of a non-conserved nucleotide causing a synonymous change that 4/5 splice prediction tools predict change of a cryptic splicing acceptor site. ESE finder predicts that this variant may alter ESE binding. However, these predictions have yet to be confirmed by functional studies. This variant was found in 301/264076 control chromosomes (gnomAD) at a frequency of 0.0011398, which is approximately 46 times the estimated maximal expected allele frequency of a pathogenic LDB3 variant (0.000025), suggesting this variant is likely a benign polymorphism. In addition, multiple clinical diagnostic laboratories classified this variant as likely benign/benign. Therefore, due to the nature and location of this variant, control population frequency, and additional clinical diagnostic laboratories classifying the variant as "likely benign/benign," the variant of interest has been classified as Benign.

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

Last Updated: Sep 6, 2021

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