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NM_007078.3(LDB3):c.2123C>T (p.Pro708Leu) AND Myofibrillar myopathy 4

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Dec 2, 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:
RCV000693041.8

Allele description [Variation Report for NM_007078.3(LDB3):c.2123C>T (p.Pro708Leu)]

NM_007078.3(LDB3):c.2123C>T (p.Pro708Leu)

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.2123C>T (p.Pro708Leu)
HGVS:
  • NC_000010.11:g.86732915C>T
  • NG_008876.1:g.69352C>T
  • NM_001080114.2:c.1793C>T
  • NM_001171610.2:c.2138C>T
  • NM_001368064.1:c.1934C>T
  • NM_001368065.1:c.1934C>T
  • NM_001368066.1:c.1982C>T
  • NM_007078.3:c.2123C>TMANE SELECT
  • NP_001073583.1:p.Pro598Leu
  • NP_001165081.1:p.Pro713Leu
  • NP_001354993.1:p.Pro645Leu
  • NP_001354994.1:p.Pro645Leu
  • NP_001354995.1:p.Pro661Leu
  • NP_009009.1:p.Pro708Leu
  • LRG_385t1:c.2123C>T
  • LRG_385:g.69352C>T
  • NC_000010.10:g.88492672C>T
  • NM_007078.2:c.2123C>T
Protein change:
P598L
Links:
dbSNP: rs774815578
NCBI 1000 Genomes Browser:
rs774815578
Molecular consequence:
  • NM_001080114.2:c.1793C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001171610.2:c.2138C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001368064.1:c.1934C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001368065.1:c.1934C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001368066.1:c.1982C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_007078.3:c.2123C>T - 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

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000820895Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Dec 2, 2023) 		germlineclinical testing

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

Help

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):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV000820895.6

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

Description

The LDB3 gene has multiple clinically relevant transcripts. This variant occurs in alternate transcript NM_007078.3, and corresponds to NM_001080116.1:c.*33541C>T in the primary transcript. This sequence change replaces proline, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 708 of the LDB3 protein (p.Pro708Leu). This variant is present in population databases (rs774815578, gnomAD 0.004%). This variant has not been reported in the literature in individuals affected with LDB3-related conditions. 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.

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

Last Updated: Feb 20, 2024