NM_000335.5(SCN5A):c.5573A>G (p.Lys1858Arg) AND Cardiac arrhythmia

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Sep 12, 2019
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:: RCV001843176.11

Allele description [Variation Report for NM_000335.5(SCN5A):c.5573A>G (p.Lys1858Arg)]

NM_000335.5(SCN5A):c.5573A>G (p.Lys1858Arg)

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.5573A>G (p.Lys1858Arg)

HGVS:

NC_000003.12:g.38550796T>C
NG_008934.1:g.103877A>G
NM_000335.5:c.5573A>GMANE SELECT
NM_001099404.2:c.5576A>G
NM_001099405.2:c.5522A>G
NM_001160160.2:c.5477A>G
NM_001160161.2:c.5414A>G
NM_001354701.2:c.5519A>G
NM_198056.3:c.5576A>G
NP_000326.2:p.Lys1858Arg
NP_001092874.1:p.Lys1859Arg
NP_001092875.1:p.Lys1841Arg
NP_001153632.1:p.Lys1826Arg
NP_001153633.1:p.Lys1805Arg
NP_001341630.1:p.Lys1840Arg
NP_932173.1:p.Lys1859Arg
LRG_289t1:c.5576A>G
LRG_289:g.103877A>G
NC_000003.11:g.38592287T>C
NM_198056.2:c.5576A>G

Protein change:

K1805R

Links:

dbSNP: rs2061018536

NCBI 1000 Genomes Browser:

rs2061018536

Molecular consequence:

NM_000335.5:c.5573A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001099404.2:c.5576A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001099405.2:c.5522A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001160160.2:c.5477A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001160161.2:c.5414A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354701.2:c.5519A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_198056.3:c.5576A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Cardiac arrhythmia
Synonyms:: Cardiac rhythm disease
Identifiers:: EFO: EFO_0004269; MONDO: MONDO:0007263; MedGen: C0003811; Human Phenotype Ontology: HP:0011675

Recent activity

Clear Turn Off Turn On

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4 isoform 1 [Homo sapi...
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4 isoform 1 [Homo sapiens]
gi|6041669|ref|NP_004538.2|

Protein

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001349438	Color Diagnostics, LLC DBA Color Health	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Sep 12, 2019)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001349438

Color Diagnostics, LLC DBA Color Health

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Sep 12, 2019)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical 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 Diagnostics, LLC DBA Color Health, SCV001349438.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

This missense variant replaces lysine with arginine at codon 1859 of the SCN5A protein. Computational prediction tool suggests that this variant may have deleterious impact on protein structure and function (internally defined REVEL score threshold ≥0.7, PMID: 27666373). Splice site prediction tools suggest that this variant may not impact RNA splicing. To our knowledge, functional studies have not been performed for this variant. 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.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Nov 3, 2024

ClinVar

Relating variation to medicine