NM_007078.3(LDB3):c.1603_1605delinsTGCCACTCA (p.Thr535delinsCysHisSer) AND Myofibrillar myopathy 4

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Oct 12, 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:: RCV000816073.7

Allele description [Variation Report for NM_007078.3(LDB3):c.1603_1605delinsTGCCACTCA (p.Thr535delinsCysHisSer)]

NM_007078.3(LDB3):c.1603_1605delinsTGCCACTCA (p.Thr535delinsCysHisSer)

Gene:

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

Variant type:

Indel

Cytogenetic location:

10q23.2

Genomic location:

Preferred name:

NM_007078.3(LDB3):c.1603_1605delinsTGCCACTCA (p.Thr535delinsCysHisSer)

HGVS:

NC_000010.11:g.86716698_86716700delinsTGCCACTCA
NG_008876.1:g.53135_53137delinsTGCCACTCA
NM_001080114.2:c.1273_1275delinsTGCCACTCA
NM_001171610.2:c.1618_1620delinsTGCCACTCA
NM_001368064.1:c.1414_1416delinsTGCCACTCA
NM_001368065.1:c.1414_1416delinsTGCCACTCA
NM_001368066.1:c.1462_1464delinsTGCCACTCA
NM_007078.3:c.1603_1605delinsTGCCACTCAMANE SELECT
NP_001073583.1:p.Thr425delinsCysHisSer
NP_001165081.1:p.Thr540delinsCysHisSer
NP_001354993.1:p.Thr472delinsCysHisSer
NP_001354994.1:p.Thr472delinsCysHisSer
NP_001354995.1:p.Thr488delinsCysHisSer
NP_009009.1:p.Thr535delinsCysHisSer
LRG_385t1:c.1603_1605delinsTGCCACTCA
LRG_385:g.53135_53137delinsTGCCACTCA
NC_000010.10:g.88476455_88476457delinsTGCCACTCA
NM_007078.2:c.1603_1605delACCinsTGCCACTCA
NM_007078.2:c.1603_1605delinsTGCCACTCA

Links:

dbSNP: rs1589675306

NCBI 1000 Genomes Browser:

rs1589675306

Molecular consequence:

NM_001080114.2:c.1273_1275delinsTGCCACTCA - inframe_indel - [Sequence Ontology: SO:0001820]
NM_001171610.2:c.1618_1620delinsTGCCACTCA - inframe_indel - [Sequence Ontology: SO:0001820]
NM_001368064.1:c.1414_1416delinsTGCCACTCA - inframe_indel - [Sequence Ontology: SO:0001820]
NM_001368065.1:c.1414_1416delinsTGCCACTCA - inframe_indel - [Sequence Ontology: SO:0001820]
NM_001368066.1:c.1462_1464delinsTGCCACTCA - inframe_indel - [Sequence Ontology: SO:0001820]
NM_007078.3:c.1603_1605delinsTGCCACTCA - inframe_indel - [Sequence Ontology: SO:0001820]

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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RecName: Full=Pleckstrin homology domain-containing family M member 1; Short=PH ...
RecName: Full=Pleckstrin homology domain-containing family M member 1; Short=PH domain-containing family M member 1; AltName: Full=162 kDa adapter protein; Short=AP162
gi|160419247|sp|Q9Y4G2.3|PKHM1_HUMA

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000956563	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Oct 12, 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

SCV000956563

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Oct 12, 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, SCV000956563.3

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

Description

Experimental studies and prediction algorithms are not available for this variant, and the functional significance of the affected amino acids is currently unknown. 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 variant,¬†c.1603_1605delinsTGCCACTCA, results in the deletion of 1 amino acid and insertion of 3 amino acids of the¬†LDB3¬†protein (p.Thr535delinsCysHisSer), but otherwise preserves the integrity of the reading frame. The LDB3 gene has multiple clinically relevant transcripts. The¬†c.1603_1605delinsTGCCACTCA¬†variant occurs in alternate transcript NM_007078.2 which corresponds to position c.*17324_*17326 in NM_001080116.1, the primary transcript listed in the Methods. 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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