NM_000335.5(SCN5A):c.893G>A (p.Gly298Asp) AND not provided

This record was updated by the submitter. Please see the current version.

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Oct 13, 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:: RCV003655202.1

Allele description

NM_000335.5(SCN5A):c.893G>A (p.Gly298Asp)

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.893G>A (p.Gly298Asp)

HGVS:

NC_000003.12:g.38609775C>T
NG_008934.1:g.44898G>A
NM_000335.5:c.893G>AMANE SELECT
NM_001099404.2:c.893G>A
NM_001099405.2:c.893G>A
NM_001160160.2:c.893G>A
NM_001160161.2:c.893G>A
NM_001354701.2:c.893G>A
NM_198056.3:c.893G>A
NP_000326.2:p.Gly298Asp
NP_001092874.1:p.Gly298Asp
NP_001092875.1:p.Gly298Asp
NP_001153632.1:p.Gly298Asp
NP_001153633.1:p.Gly298Asp
NP_001341630.1:p.Gly298Asp
NP_932173.1:p.Gly298Asp
NP_932173.1:p.Gly298Asp
LRG_289t1:c.893G>A
LRG_289:g.44898G>A
LRG_289p1:p.Gly298Asp
NC_000003.11:g.38651266C>T
NM_198056.2:c.893G>A

Protein change:

G298D

Links:

dbSNP: rs759383134

NCBI 1000 Genomes Browser:

rs759383134

Molecular consequence:

NM_000335.5:c.893G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001099404.2:c.893G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001099405.2:c.893G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001160160.2:c.893G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001160161.2:c.893G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354701.2:c.893G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_198056.3:c.893G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Microbe sample from Sphingobium fluviale
Microbe sample from Sphingobium fluviale

biosample
BioSample links for Nucleotide (Select 1568858481) (1)
BioSample
Sphingobium fluviale strain CHR27 NODE_44_length_592_cov_1149, whole genome shot...
Sphingobium fluviale strain CHR27 NODE_44_length_592_cov_1149, whole genome shotgun sequence
gi|1568858490|ref|NZ_SBKP01000044.1 |WGS:NZ_SBKP01|NODE_44_length_592_cov_1149

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000830554	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Oct 13, 2023)	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

SCV000830554

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Oct 13, 2023)

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

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 Invitae, SCV000830554.3

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

Description

This sequence change replaces glycine, which is neutral and non-polar, with aspartic acid, which is acidic and polar, at codon 298 of the SCN5A protein (p.Gly298Asp). This variant is present in population databases (rs759383134, gnomAD 0.009%). This variant has not been reported in the literature in individuals affected with SCN5A-related conditions. ClinVar contains an entry for this variant (Variation ID: 578662). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Not Available"; PolyPhen-2: "Benign"; Align-GVGD: "Not Available". The aspartic acid amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect 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.

#	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: Sep 16, 2024

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