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NM_000117.2(EMD):c.454C>T (p.Arg152Cys)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(1);Uncertain significance(2)

Review status:
criteria provided, conflicting interpretations
Submissions:
4 (Most recent: Jan 7, 2021)
Last evaluated:
Aug 7, 2020
Accession:
VCV000198043.4
Variation ID:
198043
Description:
single nucleotide variant
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NM_000117.2(EMD):c.454C>T (p.Arg152Cys)

Allele ID
195204
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
Xq28
Genomic location
X: 154380886 (GRCh38) GRCh38 UCSC
X: 153609246 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000023.10:g.153609246C>T
NC_000023.11:g.154380886C>T
NM_000117.2:c.454C>T NP_000108.1:p.Arg152Cys missense
... more HGVS
Protein change
R152C
Other names
-
Canonical SPDI
NC_000023.11:154380885:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Exome Aggregation Consortium (ExAC) 0.00003
Trans-Omics for Precision Medicine (TOPMed) 0.00009
The Genome Aggregation Database (gnomAD), exomes 0.00006
Links
ClinGen: CA246531
dbSNP: rs376456050
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, single submitter Aug 7, 2020 RCV000616618.4
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Mar 26, 2019 RCV000179255.4
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
EMD - - GRCh38
GRCh37
278 517

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(Mar 26, 2019)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Athena Diagnostics Inc
Accession: SCV001143862.1
Submitted: (Sep 25, 2019)
Evidence details
Publications
PubMed (3)
Uncertain significance
(Aug 07, 2020)
criteria provided, single submitter
Method: clinical testing
Emery-Dreifuss muscular dystrophy 1, X-linked
Allele origin: germline
Invitae
Accession: SCV000820492.3
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (3)
Comment:
This sequence change replaces arginine with cysteine at codon 152 of the EMD protein (p.Arg152Cys). The arginine residue is highly conserved and there is a … (more)
Uncertain significance
(Oct 10, 2017)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000231475.5
Submitted: (Sep 19, 2018)
Evidence details
Publications
PubMed (1)
Other databases
http://www.egl-eurofins.com/emvc…
Uncertain significance
(-)
no assertion criteria provided
Method: clinical testing
Emery-Dreifuss muscular dystrophy 1, X-linked
Allele origin: germline
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV000734765.1
Submitted: (Apr 04, 2018)
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
Utility and limitations of exome sequencing as a genetic diagnostic tool for conditions associated with pediatric sudden cardiac arrest/sudden cardiac death. Li MH Human genomics 2015 PMID: 26187847
Targeted sequence capture and GS-FLX Titanium sequencing of 23 hypertrophic and dilated cardiomyopathy genes: implementation into diagnostics. Mook OR Journal of medical genetics 2013 PMID: 23785128
Genetic analysis in 418 index patients with idiopathic dilated cardiomyopathy: overview of 10 years' experience. van Spaendonck-Zwarts KY European journal of heart failure 2013 PMID: 23349452
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=EMD - - - -

Text-mined citations for rs376456050...

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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 Jun 14, 2021