NM_000335.5(SCN5A):c.818T>A (p.Met273Lys) AND Cardiovascular phenotype

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: May 24, 2016
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:: RCV000619004.3

Allele description [Variation Report for NM_000335.5(SCN5A):c.818T>A (p.Met273Lys)]

NM_000335.5(SCN5A):c.818T>A (p.Met273Lys)

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.818T>A (p.Met273Lys)

HGVS:

NC_000003.12:g.38609850A>T
NG_008934.1:g.44823T>A
NM_000335.5:c.818T>AMANE SELECT
NM_001099404.2:c.818T>A
NM_001099405.2:c.818T>A
NM_001160160.2:c.818T>A
NM_001160161.2:c.818T>A
NM_001354701.2:c.818T>A
NM_198056.3:c.818T>A
NP_000326.2:p.Met273Lys
NP_001092874.1:p.Met273Lys
NP_001092875.1:p.Met273Lys
NP_001153632.1:p.Met273Lys
NP_001153633.1:p.Met273Lys
NP_001341630.1:p.Met273Lys
NP_932173.1:p.Met273Lys
NP_932173.1:p.Met273Lys
LRG_289t1:c.818T>A
LRG_289:g.44823T>A
LRG_289p1:p.Met273Lys
NC_000003.11:g.38651341A>T
NM_198056.2:c.818T>A

Protein change:

M273K

Links:

dbSNP: rs200076065

NCBI 1000 Genomes Browser:

rs200076065

Molecular consequence:

NM_000335.5:c.818T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001099404.2:c.818T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001099405.2:c.818T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001160160.2:c.818T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001160161.2:c.818T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354701.2:c.818T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_198056.3:c.818T>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Cardiovascular phenotype
Identifiers:: MedGen: CN230736

Recent activity

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O-Acetylcyclocalopin A AND 1[s_discriminator] (140)
dbGaP
Borreliella lanei strain DSM 17992 Ga0416728_10, whole genome shotgun sequence
Borreliella lanei strain DSM 17992 Ga0416728_10, whole genome shotgun sequence
gi|1891890019|ref|NZ_JACHFC01000001 gnl|WGS:NZ_JACHFC01|Ga0416728_10

Nucleotide
PREDICTED: Danio rerio lactamase, beta-like 1a (lactbl1a), transcript variant X2...
PREDICTED: Danio rerio lactamase, beta-like 1a (lactbl1a), transcript variant X2, mRNA
gi|2800573441|ref|XM_021469952.2|

Nucleotide
Homologene neighbors for GEO Profiles (Select 113718166) (0)
GEO Profiles
Profile neighbors for GEO Profiles (Select 119710304) (199)
GEO Profiles

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000737507	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (May 24, 2016)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000737507

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(May 24, 2016)

germline

clinical testing

Citation Link

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

Details of each submission

From Ambry Genetics, SCV000737507.5

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

Description

The p.M273K variant (also known as c.818T>A), located in coding exon 6 of the SCN5A gene, results from a T to A substitution at nucleotide position 818. The methionine at codon 273 is replaced by lysine, an amino acid with some similar properties. This variant was not reported in population based cohorts in the following databases: Database of Single Nucleotide Polymorphisms (dbSNP), NHLBI Exome Sequencing Project (ESP), and 1000 Genomes Project. In the ESP, this variant was not observed in 6472 samples (12944 alleles) with coverage at this position. This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

#	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: May 1, 2024

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