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NM_007078.3(LDB3):c.2109T>A (p.Asn703Lys) AND Myofibrillar myopathy 4

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Dec 20, 2022
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:
RCV003612689.2

Allele description [Variation Report for NM_007078.3(LDB3):c.2109T>A (p.Asn703Lys)]

NM_007078.3(LDB3):c.2109T>A (p.Asn703Lys)

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.2109T>A (p.Asn703Lys)
HGVS:
  • NC_000010.11:g.86732901T>A
  • NG_008876.1:g.69338T>A
  • NM_001080114.2:c.1779T>A
  • NM_001171610.2:c.2124T>A
  • NM_001368064.1:c.1920T>A
  • NM_001368065.1:c.1920T>A
  • NM_001368066.1:c.1968T>A
  • NM_007078.3:c.2109T>AMANE SELECT
  • NP_001073583.1:p.Asn593Lys
  • NP_001165081.1:p.Asn708Lys
  • NP_001354993.1:p.Asn640Lys
  • NP_001354994.1:p.Asn640Lys
  • NP_001354995.1:p.Asn656Lys
  • NP_009009.1:p.Asn703Lys
  • NP_009009.1:p.Asn703Lys
  • LRG_385t1:c.2109T>A
  • LRG_385:g.69338T>A
  • LRG_385p1:p.Asn703Lys
  • NC_000010.10:g.88492658T>A
  • NM_007078.2:c.2109T>A
Protein change:
N593K
Molecular consequence:
  • NM_001080114.2:c.1779T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001171610.2:c.2124T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001368064.1:c.1920T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001368065.1:c.1920T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001368066.1:c.1968T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_007078.3:c.2109T>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Myofibrillar myopathy 4
Synonyms:
Myofibrillar myopathy, ZASP-related; Zaspopathy (type)
Identifiers:
MONDO: MONDO:0012277; MedGen: C4721886; OMIM: 609452

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV004409881Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Uncertain significance
(Dec 20, 2022)
germlineclinical testing

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

Summary from all submissions

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

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group, Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004409881.1

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

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. This variant has not been reported in the literature in individuals affected with LDB3-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces asparagine, which is neutral and polar, with lysine, which is basic and polar, at codon 703 of the LDB3 protein (p.Asn703Lys). The LDB3 gene has multiple clinically relevant transcripts. This variant occurs in alternate transcript NM_007078.3, and corresponds to NM_001080116.1:c.*33527T>A in the primary transcript.

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

Last Updated: Sep 29, 2024