NM_007078.3(LDB3):c.785_818dup (p.Ser274fs) AND Myofibrillar myopathy 4

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Oct 7, 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:: RCV002867919.2

Allele description [Variation Report for NM_007078.3(LDB3):c.785_818dup (p.Ser274fs)]

NM_007078.3(LDB3):c.785_818dup (p.Ser274fs)

Gene:

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

Variant type:

Duplication

Cytogenetic location:

10q23.2

Genomic location:

Preferred name:

NM_007078.3(LDB3):c.785_818dup (p.Ser274fs)

HGVS:

NC_000010.11:g.86691991_86692024dup
NG_008876.1:g.28428_28461dup
NM_001080114.2:c.644_677dup
NM_001080115.2:c.785_818dup
NM_001080116.1:c.644_677dup
NM_001171610.2:c.989_1022dup
NM_001171611.2:c.989_1022dup
NM_001368063.1:c.785_818dup
NM_001368064.1:c.785_818dup
NM_001368065.1:c.785_818dup
NM_001368066.1:c.644_677dup
NM_001368067.1:c.644_677dup
NM_001368068.1:c.644_677dup
NM_007078.3:c.785_818dupMANE SELECT
NP_001073583.1:p.Ser227fs
NP_001073584.1:p.Ser274fs
NP_001073585.1:p.Ser227fs
NP_001165081.1:p.Ser342fs
NP_001165082.1:p.Ser342fs
NP_001354992.1:p.Ser274fs
NP_001354993.1:p.Ser274fs
NP_001354994.1:p.Ser274fs
NP_001354995.1:p.Ser227fs
NP_001354996.1:p.Ser227fs
NP_001354997.1:p.Ser227fs
NP_009009.1:p.Ser274Valfs
NP_009009.1:p.Ser274fs
LRG_385t1:c.785_818dup
LRG_385t2:c.644_677dup
LRG_385:g.28428_28461dup
LRG_385p1:p.Ser274Valfs
LRG_385p2:p.Ser227fs
NC_000010.10:g.88451745_88451746insCGAGTGGGCACGCCGTTCCTCCAACCTGCAGTCT
NC_000010.10:g.88451748_88451781dup
NM_007078.2:c.785_818dup

Protein change:

S227fs

Molecular consequence:

NM_001080114.2:c.644_677dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001080115.2:c.785_818dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001080116.1:c.644_677dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001171610.2:c.989_1022dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001171611.2:c.989_1022dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001368063.1:c.785_818dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001368064.1:c.785_818dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001368065.1:c.785_818dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001368066.1:c.644_677dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001368067.1:c.644_677dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001368068.1:c.644_677dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_007078.3:c.785_818dup - frameshift variant - [Sequence Ontology: SO:0001589]

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
SCV003240430	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Oct 7, 2022)	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

SCV003240430

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Oct 7, 2022)

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):240-242.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV003240430.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

This sequence change creates a premature translational stop signal (p.Ser227Valfs*29) in the LDB3 gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 57 amino acid(s) of the LDB3 protein. This variant is not present in population databases (gnomAD no frequency). 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. This variant has not been reported in the literature in individuals affected with LDB3-related conditions.

#	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: Feb 20, 2024

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