NM_007078.3(LDB3):c.1606G>A (p.Val536Ile) AND Myofibrillar myopathy 4

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jun 18, 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:: RCV000689385.8

Allele description [Variation Report for NM_007078.3(LDB3):c.1606G>A (p.Val536Ile)]

NM_007078.3(LDB3):c.1606G>A (p.Val536Ile)

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.1606G>A (p.Val536Ile)

HGVS:

NC_000010.11:g.86716701G>A
NG_008876.1:g.53138G>A
NM_001080114.2:c.1276G>A
NM_001171610.2:c.1621G>A
NM_001368064.1:c.1417G>A
NM_001368065.1:c.1417G>A
NM_001368066.1:c.1465G>A
NM_007078.3:c.1606G>AMANE SELECT
NP_001073583.1:p.Val426Ile
NP_001165081.1:p.Val541Ile
NP_001354993.1:p.Val473Ile
NP_001354994.1:p.Val473Ile
NP_001354995.1:p.Val489Ile
NP_009009.1:p.Val536Ile
LRG_385t1:c.1606G>A
LRG_385:g.53138G>A
NC_000010.10:g.88476458G>A
NM_007078.2:c.1606G>A

Protein change:

V426I

Links:

dbSNP: rs113817827

NCBI 1000 Genomes Browser:

rs113817827

Molecular consequence:

NM_001080114.2:c.1276G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001171610.2:c.1621G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001368064.1:c.1417G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001368065.1:c.1417G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001368066.1:c.1465G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_007078.3:c.1606G>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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000817033	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jun 18, 2023)	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

SCV000817033

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jun 18, 2023)

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, SCV000817033.7

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical 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 present in population databases (rs113817827, gnomAD 0.07%). This sequence change replaces valine, which is neutral and non-polar, with isoleucine, which is neutral and non-polar, at codon 536 of the LDB3 protein (p.Val536Ile). The LDB3 gene has multiple clinically relevant transcripts. This variant occurs in alternate transcript NM_007078.3, and corresponds to NM_001080116.1:c.*17327G>A in the primary transcript.

#	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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