NM_007078.3(LDB3):c.1602_1603insTGCCAC (p.Gly534_Thr535insCysHis) AND Myofibrillar myopathy 4

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jan 4, 2024
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:: RCV002726606.3

Allele description [Variation Report for NM_007078.3(LDB3):c.1602_1603insTGCCAC (p.Gly534_Thr535insCysHis)]

NM_007078.3(LDB3):c.1602_1603insTGCCAC (p.Gly534_Thr535insCysHis)

Gene:

LDB3:LIM domain binding 3 [Gene - OMIM - HGNC]

Variant type:

Insertion

Cytogenetic location:

10q23.2

Genomic location:

Preferred name:

NM_007078.3(LDB3):c.1602_1603insTGCCAC (p.Gly534_Thr535insCysHis)

HGVS:

NC_000010.11:g.86716697_86716698insTGCCAC
NG_008876.1:g.53134_53135insTGCCAC
NM_001080114.2:c.1272_1273insTGCCAC
NM_001171610.2:c.1617_1618insTGCCAC
NM_001368064.1:c.1413_1414insTGCCAC
NM_001368065.1:c.1413_1414insTGCCAC
NM_001368066.1:c.1461_1462insTGCCAC
NM_007078.3:c.1602_1603insTGCCACMANE SELECT
NP_001073583.1:p.Gly424_Thr425insCysHis
NP_001165081.1:p.Gly539_Thr540insCysHis
NP_001354993.1:p.Gly471_Thr472insCysHis
NP_001354994.1:p.Gly471_Thr472insCysHis
NP_001354995.1:p.Gly487_Thr488insCysHis
NP_009009.1:p.Gly534_Thr535insCysHis
NP_009009.1:p.Gly534_Thr535insCysHis
LRG_385t1:c.1602_1603insTGCCAC
LRG_385:g.53134_53135insTGCCAC
LRG_385p1:p.Gly534_Thr535insCysHis
NC_000010.10:g.88476454_88476455insTGCCAC
NM_007078.2:c.1602_1603insTGCCAC

Molecular consequence:

NM_001080114.2:c.1272_1273insTGCCAC - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_001171610.2:c.1617_1618insTGCCAC - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_001368064.1:c.1413_1414insTGCCAC - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_001368065.1:c.1413_1414insTGCCAC - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_001368066.1:c.1461_1462insTGCCAC - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_007078.3:c.1602_1603insTGCCAC - inframe_insertion - [Sequence Ontology: SO:0001821]

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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003003877	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jan 4, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003003877

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jan 4, 2024)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical 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, SCV003003877.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical 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.*17324delinsTGCCACT in the primary transcript. This variant, c.1603delinsTGCCACT, is a complex sequence change that results in the deletion of 1 and insertion of 3 amino acid(s) in the LDB3 protein (p.Thr535delinsCysHisSer). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with LDB3-related conditions. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. 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.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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