NM_000335.5(SCN5A):c.5847C>A (p.Tyr1949Ter) AND Cardiovascular phenotype

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jan 31, 2024
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:: RCV004525070.1

Allele description [Variation Report for NM_000335.5(SCN5A):c.5847C>A (p.Tyr1949Ter)]

NM_000335.5(SCN5A):c.5847C>A (p.Tyr1949Ter)

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.5847C>A (p.Tyr1949Ter)

HGVS:

NC_000003.12:g.38550522G>T
NG_008934.1:g.104151C>A
NM_000335.5:c.5847C>AMANE SELECT
NM_001099404.2:c.5850C>A
NM_001099405.2:c.5796C>A
NM_001160160.2:c.5751C>A
NM_001160161.2:c.5688C>A
NM_001354701.2:c.5793C>A
NM_198056.3:c.5850C>A
NP_000326.2:p.Tyr1949Ter
NP_000326.2:p.Tyr1949Ter
NP_001092874.1:p.Tyr1950Ter
NP_001092874.1:p.Tyr1950Ter
NP_001092875.1:p.Tyr1932Ter
NP_001153632.1:p.Tyr1917Ter
NP_001153633.1:p.Tyr1896Ter
NP_001341630.1:p.Tyr1931Ter
NP_932173.1:p.Tyr1950Ter
NP_932173.1:p.Tyr1950Ter
LRG_289t1:c.5850C>A
LRG_289t2:c.5847C>A
LRG_289t3:c.5850C>A
LRG_289:g.104151C>A
LRG_289p1:p.Tyr1950Ter
LRG_289p2:p.Tyr1949Ter
LRG_289p3:p.Tyr1950Ter
NC_000003.11:g.38592013G>T
NM_000335.4:c.5847C>A
NM_001099404.1:c.5850C>A
NM_198056.2:c.5850C>A
NR_176299.1:n.6596C>A

Protein change:

Y1896*

Molecular consequence:

NR_176299.1:n.6596C>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_000335.5:c.5847C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001099404.2:c.5850C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001099405.2:c.5796C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001160160.2:c.5751C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001160161.2:c.5688C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001354701.2:c.5793C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_198056.3:c.5850C>A - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:: Cardiovascular phenotype
Identifiers:: MedGen: CN230736

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV005031281	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (Jan 31, 2024)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV005031281

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(Jan 31, 2024)

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, SCV005031281.1

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

Description

The p.Y1950* variant (also known as c.5850C>A), located in coding exon 27 of the SCN5A gene, results from a C to A substitution at nucleotide position 5850. This changes the amino acid from a tyrosine to a stop codon within coding exon 27. This alteration occurs at the 3' terminus of theSCN5A gene, is not expected to trigger nonsense-mediated mRNAdecay, and only impacts the last 3% of the protein. The exact functional effect of this alteration is unknown. Based on the available evidence, 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 7, 2024

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