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NM_144573.4(NEXN):c.1401AGA[2] (p.Glu470del)

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Interpretation:
Uncertain significance​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
7 (Most recent: Aug 17, 2021)
Last evaluated:
Nov 19, 2020
Accession:
VCV000047890.10
Variation ID:
47890
Description:
3bp microsatellite
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NM_144573.4(NEXN):c.1401AGA[2] (p.Glu470del)

Allele ID
57054
Variant type
Microsatellite
Variant length
3 bp
Cytogenetic location
1p31.1
Genomic location
1: 77935972-77935974 (GRCh38) GRCh38 UCSC
1: 78401657-78401659 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NM_144573.3:c.1405_1407delGAA
LRG_442:g.52458AGA[2]
LRG_442t1:c.1407_1409del
... more HGVS
Protein change
E470del, E406del
Other names
-
Canonical SPDI
NC_000001.11:77935971:AGAAGAAGA:AGAAGA
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
ClinGen: CA142113
dbSNP: rs397517846
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 2 criteria provided, multiple submitters, no conflicts Nov 19, 2020 RCV001256889.3
Uncertain significance 1 criteria provided, single submitter Feb 10, 2015 RCV000041160.4
Uncertain significance 1 criteria provided, single submitter Feb 9, 2016 RCV000240639.2
Uncertain significance 1 criteria provided, single submitter Jun 8, 2018 RCV000621584.1
Uncertain significance 1 criteria provided, single submitter Oct 1, 2020 RCV000701648.3
Uncertain significance 1 no assertion criteria provided May 1, 2016 RCV000491718.2
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
NEXN - - GRCh38
GRCh37
359 381

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(May 21, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Molecular Diagnostic Laboratory for Inherited Cardiovascular Disease,Montreal Heart Institute
Accession: SCV001433386.1
Submitted: (Jul 24, 2020)
Evidence details
Uncertain significance
(Jun 08, 2018)
criteria provided, single submitter
Method: clinical testing
Cardiovascular phenotype
Allele origin: germline
Ambry Genetics
Accession: SCV000739980.3
Submitted: (Nov 30, 2020)
Evidence details
Publications
PubMed (2)
Comment:
The c.1407_1409delAGA variant (also known as p.E470del) is located in coding exon 10 of the NEXN gene. This variant results from an in-frame AGA deletion … (more)
Uncertain significance
(Feb 09, 2016)
criteria provided, single submitter
Method: clinical testing
Dilated cardiomyopathy 1CC
Allele origin: germline
Center for Medical Genetics Ghent,University of Ghent
Accession: SCV000299267.2
Submitted: (Jun 11, 2018)
Evidence details
Comment:
This variant has not been identified in large population databases (Gnomad, 1000 Genomes, Go NL, Exome Variant Server). The variant results in an inframe deletion … (more)
Uncertain significance
(Feb 10, 2015)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine
Accession: SCV000064851.6
Submitted: (Mar 21, 2019)
Evidence details
Publications
PubMed (1)
Comment:
The p.Glu470del variant in NEXN has been identified by our laboratory in 1 infan t with DCM, 1 adult with LVNC (Pugh 2014), and 1 … (more)
Uncertain significance
(Oct 01, 2020)
criteria provided, single submitter
Method: clinical testing
Dilated cardiomyopathy 1CC
Familial hypertrophic cardiomyopathy 20
Allele origin: germline
Invitae
Accession: SCV000830459.3
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (4)
Comment:
This variant, c.1407_1409delAGA, results in the deletion of 1 amino acid of the NEXN protein (p.Glu470del), but otherwise preserves the integrity of the reading frame. … (more)
Uncertain significance
(Nov 19, 2020)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001790626.1
Submitted: (Aug 17, 2021)
Evidence details
Comment:
Reported in association with DCM (Pugh et al., 2014; Walsh et al., 2017); Reported in ClinVar as a variant of uncertain significance by several clinical … (more)
Uncertain significance
(May 01, 2016)
no assertion criteria provided
Method: clinical testing
Arrhythmogenic right ventricular dysplasia 9
Allele origin: germline
Institut für Laboratoriums- und Transfusionsmedizin, Herz- und Diabeteszentrum Nordrhein-Westfalen
Accession: SCV000298157.1
Submitted: (Jun 24, 2016)
Evidence details

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. Nykamp K Genetics in medicine : official journal of the American College of Medical Genetics 2017 PMID: 28492532
Pathogenic variant burden in the ExAC database: an empirical approach to evaluating population data for clinical variant interpretation. Kobayashi Y Genome medicine 2017 PMID: 28166811
Reassessment of Mendelian gene pathogenicity using 7,855 cardiomyopathy cases and 60,706 reference samples. Walsh R Genetics in medicine : official journal of the American College of Medical Genetics 2017 PMID: 27532257
The landscape of genetic variation in dilated cardiomyopathy as surveyed by clinical DNA sequencing. Pugh TJ Genetics in medicine : official journal of the American College of Medical Genetics 2014 PMID: 24503780

Text-mined citations for rs397517846...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Oct 07, 2021