NM_198056.2(SCN5A):c.86_87invCA (p.Ala29Val) AND SCN5A-related disorder

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: May 8, 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:: RCV004532970.1

Allele description [Variation Report for NM_198056.2(SCN5A):c.86_87invCA (p.Ala29Val)]

NM_198056.2(SCN5A):c.86_87invCA (p.Ala29Val)

Gene:

SCN5A:sodium voltage-gated channel alpha subunit 5 [Gene - OMIM - HGNC]

Variant type:

Inversion

Cytogenetic location:

3p22.2

Genomic location:

Preferred name:

NM_198056.2(SCN5A):c.86_87invCA (p.Ala29Val)

HGVS:

NC_000003.12:g.38633221_38633222inv
NG_008934.1:g.21451_21452inv
NM_000335.5:c.86_87invMANE SELECT
NM_001099404.2:c.86_87inv
NM_001099405.2:c.86_87inv
NM_001160160.2:c.86_87inv
NM_001160161.2:c.86_87inv
NM_001354701.2:c.86_87inv
NM_198056.2:c.86_87inv
NM_198056.3:c.86_87inv
NP_000326.2:p.Ala29Val
NP_001092874.1:p.Ala29Val
NP_001092875.1:p.Ala29Val
NP_001153632.1:p.Ala29Val
NP_001153633.1:p.Ala29Val
NP_001341630.1:p.Ala29Val
NP_932173.1:p.Ala29Val
LRG_289t1:c.86_87inv
LRG_289:g.21451_21452inv
LRG_289p1:p.Ala29Val
NC_000003.11:g.38674712_38674713delinsCA
NC_000003.11:g.38674712_38674713inv
NM_001099404.1:c.86_87delinsTG
NM_198056.2:c.86_87delinsTG
NM_198056.2:c.86_87delinsTG
NM_198056.2:c.86_87inv
NM_198056.2:c.86_87invCA
NM_198056.3:c.86_87delinsTG

Protein change:

A29V

Molecular consequence:

NM_000335.5:c.86_87inv - missense variant - [Sequence Ontology: SO:0001583]
NM_001099404.2:c.86_87inv - missense variant - [Sequence Ontology: SO:0001583]
NM_001099405.2:c.86_87inv - missense variant - [Sequence Ontology: SO:0001583]
NM_001160160.2:c.86_87inv - missense variant - [Sequence Ontology: SO:0001583]
NM_001160161.2:c.86_87inv - missense variant - [Sequence Ontology: SO:0001583]
NM_001354701.2:c.86_87inv - missense variant - [Sequence Ontology: SO:0001583]
NM_198056.3:c.86_87inv - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: SCN5A-related disorder
Identifiers:

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004112173	PreventionGenetics, part of Exact Sciences	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (May 8, 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

SCV004112173

PreventionGenetics, part of Exact Sciences

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(May 8, 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

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 PreventionGenetics, part of Exact Sciences, SCV004112173.1

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

Description

The SCN5A c.86_87delinsTG variant is predicted to result in an in-frame deletion and insertion. This variant was reported in an individual with Brugada syndrome (Table S5, Ciconte et al. 2020. PubMed ID: 33221895). Of note, this variant may be reported in a large population database as two separate entries as c.87A>G (https://gnomad.broadinstitute.org/variant/3-38674712-T-C) and c.86C>T (https://gnomad.broadinstitute.org/variant/3-38674713-G-A). A similar variant resulting in the same amino acid substitution, c.86C>T (p.Ala29Val), has been reported in individuals with long QT syndrome, dilated cardiomyopathy, or sudden death (Stattin et al. 2012. PubMed ID: 23098067; Table S2, Methner et al. 2016. PubMed ID: 27435932; Table S2, Haskell et al. 2017. PubMed ID: 28611029). At this time, the clinical significance of the c.86_87delinsTG (p.Ala29Val) variant is uncertain due to the absence of conclusive functional and genetic evidence.

#	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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