NM_007078.3(LDB3):c.55G>T (p.Gly19Trp) AND Myofibrillar myopathy 4

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Sep 10, 2018
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:: RCV000795954.7

Allele description [Variation Report for NM_007078.3(LDB3):c.55G>T (p.Gly19Trp)]

NM_007078.3(LDB3):c.55G>T (p.Gly19Trp)

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.55G>T (p.Gly19Trp)

HGVS:

NC_000010.11:g.86668746G>T
NG_008876.1:g.5183G>T
NM_001080114.2:c.55G>T
NM_001080115.2:c.55G>T
NM_001080116.1:c.55G>T
NM_001171610.2:c.55G>T
NM_001171611.2:c.55G>T
NM_001368063.1:c.55G>T
NM_001368064.1:c.55G>T
NM_001368065.1:c.55G>T
NM_001368066.1:c.55G>T
NM_001368067.1:c.55G>T
NM_001368068.1:c.55G>T
NM_007078.3:c.55G>TMANE SELECT
NP_001073583.1:p.Gly19Trp
NP_001073584.1:p.Gly19Trp
NP_001073585.1:p.Gly19Trp
NP_001165081.1:p.Gly19Trp
NP_001165082.1:p.Gly19Trp
NP_001354992.1:p.Gly19Trp
NP_001354993.1:p.Gly19Trp
NP_001354994.1:p.Gly19Trp
NP_001354995.1:p.Gly19Trp
NP_001354996.1:p.Gly19Trp
NP_001354997.1:p.Gly19Trp
NP_009009.1:p.Gly19Trp
LRG_385t2:c.55G>T
LRG_385:g.5183G>T
LRG_385p2:p.Gly19Trp
NC_000010.10:g.88428503G>T
NM_007078.2:c.55G>T

Protein change:

G19W

Links:

dbSNP: rs777413488

NCBI 1000 Genomes Browser:

rs777413488

Molecular consequence:

NM_001080114.2:c.55G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001080115.2:c.55G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001080116.1:c.55G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001171610.2:c.55G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001171611.2:c.55G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001368063.1:c.55G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001368064.1:c.55G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001368065.1:c.55G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001368066.1:c.55G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001368067.1:c.55G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001368068.1:c.55G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_007078.3:c.55G>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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hypothetical protein YPN_0613 [Yersinia pestis Nepal516]
hypothetical protein YPN_0613 [Yersinia pestis Nepal516]
gi|108774426|gnl|jgi|YPN_0613|gb|AB 5.1|

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000935436	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Sep 10, 2018)	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

SCV000935436

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Sep 10, 2018)

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, SCV000935436.4

#	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. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). This variant has not been reported in the literature in individuals with LDB3-related disease. This variant is not present in population databases (ExAC no frequency). This sequence change replaces glycine with tryptophan at codon 19 of the LDB3 protein (p.Gly19Trp). The glycine residue is moderately conserved and there is a large physicochemical difference between glycine and tryptophan.

#	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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