NM_000335.5(SCN5A):c.1705C>G (p.Arg569Gly) AND Arrhythmia

Clinical significance:Uncertain significance (Last evaluated: Dec 31, 2019)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV001182790.1

Allele description [Variation Report for NM_000335.5(SCN5A):c.1705C>G (p.Arg569Gly)]

NM_000335.5(SCN5A):c.1705C>G (p.Arg569Gly)

Gene:
SCN5A:sodium voltage-gated channel alpha subunit 5 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
3p22.2
Genomic location:
Preferred name:
NM_000335.5(SCN5A):c.1705C>G (p.Arg569Gly)
Other names:
p.R569G:CGG>GGG
HGVS:
  • NC_000003.12:g.38603897G>C
  • NG_008934.1:g.50776C>G
  • NM_000335.5:c.1705C>GMANE SELECT
  • NM_001099404.2:c.1705C>G
  • NM_001099405.1:c.1705C>G
  • NM_001099405.2:c.1705C>G
  • NM_001160160.2:c.1705C>G
  • NM_001160161.2:c.1705C>G
  • NM_001354701.2:c.1705C>G
  • NM_198056.2:c.1705C>G
  • NM_198056.3:c.1705C>G
  • NP_000326.2:p.Arg569Gly
  • NP_001092874.1:p.Arg569Gly
  • NP_001092875.1:p.Arg569Gly
  • NP_001092875.1:p.Arg569Gly
  • NP_001153632.1:p.Arg569Gly
  • NP_001153633.1:p.Arg569Gly
  • NP_001341630.1:p.Arg569Gly
  • NP_932173.1:p.Arg569Gly
  • NP_932173.1:p.Arg569Gly
  • LRG_289t1:c.1705C>G
  • LRG_289:g.50776C>G
  • LRG_289p1:p.Arg569Gly
  • NC_000003.11:g.38645388G>C
Protein change:
R569G
Links:
dbSNP: rs199473576
NCBI 1000 Genomes Browser:
rs199473576
Molecular consequence:
  • NM_000335.5:c.1705C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001099404.2:c.1705C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001099405.1:c.1705C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001099405.2:c.1705C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001160160.2:c.1705C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001160161.2:c.1705C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354701.2:c.1705C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_198056.2:c.1705C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_198056.3:c.1705C>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Arrhythmia
Synonyms:
Abnormal electrocardiogram; Arrhythmias; Cardiac arrhythmias; See all synonyms [MedGen]
Identifiers:
EFO: EFO_0004269; MedGen: C0855329; Human Phenotype Ontology: HP:0011675

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001348371Color Health, Inccriteria provided, single submitter
Uncertain significance
(Dec 31, 2019)
germlineclinical testing

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

Description

This missense variant replaces arginine with glycine at codon 569 of the SCN5A protein. Computational prediction is inconclusive regarding the impact of this variant on protein structure and function (internally defined REVEL score threshold 0.5 < inconclusive < 0.7, PMID: 27666373). Splice site prediction tools suggest that this variant may not impact RNA splicing. A functional study has shown that this variant affects sodium channel function (PMID: 25904541). This variant has not been reported in individuals affected with cardiovascular disorders in the literature. This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.

SCV001348371

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From Color Health, Inc, SCV001348371.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 25, 2021

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