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NM_144573.4(NEXN):c.835C>T (p.Arg279Cys)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(2);Likely benign(2);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
7 (Most recent: Jan 7, 2021)
Last evaluated:
Nov 14, 2020
Accession:
VCV000030994.7
Variation ID:
30994
Description:
single nucleotide variant
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NM_144573.4(NEXN):c.835C>T (p.Arg279Cys)

Allele ID
39951
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
1p31.1
Genomic location
1: 77926863 (GRCh38) GRCh38 UCSC
1: 78392548 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000001.10:g.78392548C>T
NC_000001.11:g.77926863C>T
NM_144573.4:c.835C>T MANE Select NP_653174.3:p.Arg279Cys missense
... more HGVS
Protein change
R279C, R215C
Other names
-
Canonical SPDI
NC_000001.11:77926862:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00120 (T)

Allele frequency
1000 Genomes Project 0.00120
Trans-Omics for Precision Medicine (TOPMed) 0.00053
The Genome Aggregation Database (gnomAD) 0.00025
Links
ClinGen: CA129605
UniProtKB: Q0ZGT2#VAR_065478
OMIM: 613121.0005
dbSNP: rs146245480
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely benign 2 criteria provided, multiple submitters, no conflicts Aug 15, 2017 RCV000041184.4
Uncertain significance 2 criteria provided, single submitter Mar 18, 2016 RCV000023985.4
Benign 1 criteria provided, single submitter Nov 14, 2020 RCV000460527.5
Benign 1 criteria provided, single submitter Jan 21, 2019 RCV000769818.2
Uncertain significance 1 no assertion criteria provided Jan 30, 2014 RCV000143936.1
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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
352 374

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Mar 18, 2016)
criteria provided, single submitter
Method: reference population
Familial hypertrophic cardiomyopathy 20
Allele origin: germline
Soonchunhyang University Bucheon Hospital,Soonchunhyang University Medical Center
Accession: SCV000267418.1
Submitted: (Apr 14, 2016)
Evidence details
Publications
PubMed (1)
Likely benign
(Aug 15, 2017)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000515693.4
Submitted: (Mar 26, 2018)
Evidence details
Comment:
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at … (more)
Likely benign
(Aug 13, 2012)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine
Accession: SCV000064875.6
Submitted: (Mar 21, 2019)
Evidence details
Publications
PubMed (1)
Comment:
Arg279Cys in exon 8 of NEXN: This variant has been reported in 1 Asian individua l with HCM, segregated in 2 affected relatives, was absent … (more)
Benign
(Jan 21, 2019)
criteria provided, single submitter
Method: clinical testing
Cardiomyopathy
Allele origin: germline
CHEO Genetics Diagnostic Laboratory,Children's Hospital of Eastern Ontario
Accession: SCV000901244.2
Submitted: (Mar 03, 2020)
Evidence details
Benign
(Nov 14, 2020)
criteria provided, single submitter
Method: clinical testing
Dilated cardiomyopathy 1CC
Familial hypertrophic cardiomyopathy 20
Allele origin: germline
Invitae
Accession: SCV000560172.6
Submitted: (Jan 07, 2021)
Evidence details
Uncertain significance
(Jan 30, 2014)
no assertion criteria provided
Method: clinical testing
Primary familial hypertrophic cardiomyopathy
Allele origin: germline
Blueprint Genetics
Accession: SCV000188814.1
Submitted: (Aug 28, 2014)
Evidence details
Publications
PubMed (1)
Pathogenic
(Nov 12, 2010)
no assertion criteria provided
Method: literature only
CARDIOMYOPATHY, FAMILIAL HYPERTROPHIC, 20
Allele origin: germline
OMIM
Accession: SCV000045276.2
Submitted: (Feb 03, 2012)
Evidence details
Publications
PubMed (1)

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
Mutations in NEXN, a Z-disc gene, are associated with hypertrophic cardiomyopathy. Wang H American journal of human genetics 2010 PMID: 20970104

Text-mined citations for rs146245480...

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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 Jul 07, 2021