NM_000335.5(SCN5A):c.5660_5662del (p.Ser1887del) AND Cardiovascular phenotype

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Sep 26, 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:: RCV002347332.2

Allele description [Variation Report for NM_000335.5(SCN5A):c.5660_5662del (p.Ser1887del)]

NM_000335.5(SCN5A):c.5660_5662del (p.Ser1887del)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

3p22.2

Genomic location:

Preferred name:

NM_000335.5(SCN5A):c.5660_5662del (p.Ser1887del)

HGVS:

NC_000003.12:g.38550709_38550711del
NG_008934.1:g.103964_103966del
NM_000335.5:c.5660_5662delMANE SELECT
NM_001099404.2:c.5663_5665del
NM_001099405.2:c.5609_5611del
NM_001160160.2:c.5564_5566del
NM_001160161.2:c.5501_5503del
NM_001354701.2:c.5606_5608del
NM_198056.3:c.5663_5665del
NP_000326.2:p.Ser1887del
NP_000326.2:p.Ser1887del
NP_001092874.1:p.Ser1888del
NP_001092874.1:p.Ser1888del
NP_001092875.1:p.Ser1870del
NP_001153632.1:p.Ser1855del
NP_001153633.1:p.Ser1834del
NP_001341630.1:p.Ser1869del
NP_932173.1:p.Ser1888del
NP_932173.1:p.Ser1888del
LRG_289t1:c.5661_5663del
LRG_289t2:c.5658_5660del
LRG_289t3:c.5661_5663del
LRG_289:g.103964_103966del
LRG_289p1:p.Ser1888del
LRG_289p2:p.Ser1887del
LRG_289p3:p.Ser1888del
NC_000003.11:g.38592200_38592202del
NM_000335.4:c.5658_5660delCTC
NM_001099404.1:c.5661_5663delCTC
NM_198056.2:c.5661_5663delCTC
NM_198056.2:c.5663_5665delCCT
NR_176299.1:n.6407_6409delCTC

Protein change:

S1834del

Molecular consequence:

NM_000335.5:c.5660_5662del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001099404.2:c.5663_5665del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001099405.2:c.5609_5611del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001160160.2:c.5564_5566del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001160161.2:c.5501_5503del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001354701.2:c.5606_5608del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_198056.3:c.5663_5665del - inframe_deletion - [Sequence Ontology: SO:0001822]

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
SCV002652387	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (Sep 26, 2019)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002652387

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(Sep 26, 2019)

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, SCV002652387.2

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

Description

The c.5663_5665delCCT variant (also known as p.S1888del), located in coding exon 27 of the SCN5A gene, results from an in-frame CCT deletion at nucleotide positions 5663 to 5665. This results in the in-frame deletion of a serine residue at codon 1888, located in the C-terminal, cytoplasmic region. This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis (Choi Y et al. PLoS ONE. 2012; 7(10):e46688). 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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