NM_007078.3(LDB3):c.1471G>T (p.Val491Leu) AND Myofibrillar myopathy 4

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Dec 2, 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:: RCV001369095.6

Allele description [Variation Report for NM_007078.3(LDB3):c.1471G>T (p.Val491Leu)]

NM_007078.3(LDB3):c.1471G>T (p.Val491Leu)

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.1471G>T (p.Val491Leu)

HGVS:

NC_000010.11:g.86716566G>T
NG_008876.1:g.53003G>T
NM_001080114.2:c.1141G>T
NM_001171610.2:c.1486G>T
NM_001368064.1:c.1282G>T
NM_001368065.1:c.1282G>T
NM_001368066.1:c.1330G>T
NM_007078.3:c.1471G>TMANE SELECT
NP_001073583.1:p.Val381Leu
NP_001165081.1:p.Val496Leu
NP_001354993.1:p.Val428Leu
NP_001354994.1:p.Val428Leu
NP_001354995.1:p.Val444Leu
NP_009009.1:p.Val491Leu
LRG_385t1:c.1471G>T
LRG_385:g.53003G>T
NC_000010.10:g.88476323G>T
NM_007078.2:c.1471G>T
c.1471G>T

Protein change:

V381L

Links:

dbSNP: rs397517215

NCBI 1000 Genomes Browser:

rs397517215

Molecular consequence:

NM_001080114.2:c.1141G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001171610.2:c.1486G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001368064.1:c.1282G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001368065.1:c.1282G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001368066.1:c.1330G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_007078.3:c.1471G>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

Recent activity

Clear Turn Off Turn On

Eleocharis grandis (494)
Taxonomy
Spermine synthase [Gossypium arboreum]
Spermine synthase [Gossypium arboreum]
gi|728811605|gb|KHG00313.1||gnl|WGS |F383_17674-1

Protein

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001565524	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Dec 2, 2022)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 33500567, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001565524

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Dec 2, 2022)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

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

Systematic large-scale assessment of the genetic architecture of left ventricular noncompaction reveals diverse etiologies.

Mazzarotto F, Hawley MH, Beltrami M, Beekman L, de Marvao A, McGurk KA, Statton B, Boschi B, Girolami F, Roberts AM, Lodder EM, Allouba M, Romeih S, Aguib Y, Baksi AJ, Pantazis A, Prasad SK, Cerbai E, Yacoub MH, O'Regan DP, Cook SA, Ware JS, et al.

Genet Med. 2021 May;23(5):856-864. doi: 10.1038/s41436-020-01049-x. Epub 2021 Jan 26.

PubMed [citation]

PMID:: 33500567
PMCID:: PMC8105165

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, SCV001565524.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

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 missense change has been observed in individual(s) with clinical features of LDB3-related conditions (PMID: 33500567). This variant is not present in population databases (gnomAD no frequency). This sequence change replaces valine, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 491 of the LDB3 protein (p.Val491Leu). The LDB3 gene has multiple clinically relevant transcripts. This variant occurs in alternate transcript NM_007078.3, and corresponds to NM_001080116.1:c.*17192G>T 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

ClinVar

Relating variation to medicine