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NM_000117.3(EMD):c.610C>T (p.Arg204Cys) AND X-linked Emery-Dreifuss muscular dystrophy

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jun 30, 2023
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:
RCV000638225.12

Allele description [Variation Report for NM_000117.3(EMD):c.610C>T (p.Arg204Cys)]

NM_000117.3(EMD):c.610C>T (p.Arg204Cys)

Gene:
EMD:emerin [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Xq28
Genomic location:
Preferred name:
NM_000117.3(EMD):c.610C>T (p.Arg204Cys)
Other names:
p.R204C:CGT>TGT
HGVS:
  • NC_000023.11:g.154381042C>T
  • NG_008677.1:g.11607C>T
  • NM_000117.3:c.610C>TMANE SELECT
  • NP_000108.1:p.Arg204Cys
  • NP_000108.1:p.Arg204Cys
  • LRG_745t1:c.610C>T
  • LRG_745:g.11607C>T
  • LRG_745p1:p.Arg204Cys
  • NC_000023.10:g.153609402C>T
  • NM_000117.2:c.610C>T
Protein change:
R204C
Links:
dbSNP: rs782299893
NCBI 1000 Genomes Browser:
rs782299893
Molecular consequence:
  • NM_000117.3:c.610C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
X-linked Emery-Dreifuss muscular dystrophy
Synonyms:
Muscular dystrophy, tardive Emery-Dreifuss type, with contractures
Identifiers:
MONDO: MONDO:0010680; MedGen: C0751337; Orphanet: 261; Orphanet: 98863

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000759711Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Uncertain significance
(Jun 30, 2023)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical 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, SCV000759711.6

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 204 of the EMD protein (p.Arg204Cys). This variant is present in population databases (rs782299893, gnomAD 0.005%), including at least one homozygous and/or hemizygous individual. This variant has not been reported in the literature in individuals affected with EMD-related conditions. ClinVar contains an entry for this variant (Variation ID: 201776). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt EMD protein function. 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.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024