Gene

SCN5A

sodium voltage-gated channel alpha subunit 5

Cytogenetic location: 3p22.2
Coordinates: Chromosome 3: 38,548,062–38,649,687 (GRCh38)
Exons: 28 exons across 101.6 kb
Protein: 2,015 amino acids
Inheritance: Autosomal dominant
Also known as: Nav1.5, LQT3, HB1, HBBD, PFHB1, IVF, HB2, HH1, SSS1, CDCD2, CMPD2, ICCD
Previous symbols: CMD1E
MANE Select transcript: ENST00000423572.7NM_000335.5
Locus type: gene with protein product

Very high
Confident
Low
Very low

Reference genomeGRCh38hg38

Positions on gene and variant pages follow this choice, in this browser.

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Curated reports relevant to this gene

Brugada Syndrome
- A genetically heterogeneous condition characterized by complete or incomplete right bundle branch block accompanied by ST elevation in leads V1-V3. There is a high incidence of ventricular arrhythmia that may result in sudden death.
  - 5 GenCC submitters rate it definitive or strong
  - On the ACMG secondary findings list
  What knowing changes
  ICD placement, fever management, genetic counseling, avoidance of triggering drugs
Progressive Cardiac Conduction Disease & Sick Sinus Syndrome
- SCN5A-Related Cardiac Rhythm DisorderAutosomal dominant
  A range of heart rhythm conditions caused by changes in SCN5A, including conduction disease, sick sinus syndrome, Brugada syndrome, long QT syndrome type 3 and atrial fibrillation, usually in a structurally normal heart.
  - ClinGen rates the link definitive
  - 6 GenCC submitters rate it definitive or strong
  - On the ACMG secondary findings list
  What knowing changes
  Knowing about it supports ECG monitoring, avoiding certain medicines, and ECG screening of relatives.
- Progressive Familial Heart BlockAutosomal dominant
  An inherited conduction disorder, caused by changes in genes such as SCN5A and TRPM4, that can progress to complete heart block, causing dizziness, fainting or, rarely, sudden death.
  - 1 GenCC submitter rates it definitive or strong
  What knowing changes
  Knowing about it supports regular ECG checks and timely pacemaker implantation.
- Familial Sick Sinus Syndrome
  An inherited dysfunction of the heart's natural pacemaker, caused by changes in genes such as HCN4, SCN5A and MYH6, that causes slow or irregular heart rhythms.
  - 1 GenCC submitter rates it definitive or strong
  What knowing changes
  Knowing about it supports monitoring for slow heart rhythms and a pacemaker if symptoms develop.
Dilated Cardiomyopathy
- Enlargement and weakening of the left ventricle not explained by coronary artery or valve disease; inherited forms involve TTN, LMNA, RBM20, FLNC, BAG3, DSP, MYH7, TNNT2, DES, PLN and many other genes, and include Barth syndrome and the Emery-Dreifuss muscular dystrophies.
  - ClinGen rates the link definitive
  - 4 GenCC submitters rate it definitive or strong
  - On the ACMG secondary findings list
  What knowing changes
  Knowing a genetic cause supports earlier heart monitoring and family screening, and for genes with a high arrhythmia risk such as LMNA, FLNC and RBM20 it informs decisions about rhythm monitoring and implantable defibrillators.
Long QT Syndrome
- A disorder of cardiac repolarisation marked by a prolonged QT interval and a risk of dangerous ventricular arrhythmias such as torsades de pointes.
  - 3 GenCC submitters rate it definitive or strong
  - On the ACMG secondary findings list
  What knowing changes
  Beta-blockers, ICD placement, activity restriction, genetic counseling

Inheritance

Autosomal dominant: One changed copy, from either parent, is enough. A parent who has one passes it on to each child with a one-in-two chance.

How a genome test reads SCN5A

245

positions in SCN5A where ClinVar classes a change as pathogenic or likely pathogenic

1 of them (0.4%) falls in a region short reads find hard.

Low mappability (1 site)Regions where 100 bp or 250 bp reads cannot be placed uniquely.

A whole genome covers all 101.6 kb of SCN5A, introns included, not only the 8.5 kb of exons.

Variants with a page (47)

The SCN5A variants with a page here, most review stars first. Each page describes ClinVar's public record of the variant, never a result.

Variant	HGVS c.	Exon or intron	Position (GRCh38)	ClinVar classification	Review status
A997S	c.2989G>T	Exon 17	38,581,170	Likely pathogenic	2 stars out of 4 criteria provided, multiple submitters, no conflicts
A1427S	c.4279G>T	Exon 24	38,557,248	Likely pathogenic	2 stars out of 4 criteria provided, multiple submitters, no conflicts
c.611+1G>A		Intron 5	38,620,842	Pathogenic	2 stars out of 4 criteria provided, multiple submitters, no conflicts
c.935-3C>G		Intron 7	38,608,217	Likely pathogenic	2 stars out of 4 criteria provided, multiple submitters, no conflicts
c.1140+1G>A		Intron 9	38,606,668	Pathogenic/likely pathogenic	2 stars out of 4 criteria provided, multiple submitters, no conflicts
c.1890G>A		Exon 12	38,603,712	Pathogenic/likely pathogenic	2 stars out of 4 criteria provided, multiple submitters, no conflicts
c.4242+1G>C		Intron 23	38,560,146	Pathogenic	2 stars out of 4 criteria provided, multiple submitters, no conflicts
c.4434+5G>A		Intron 25	38,556,436	Likely pathogenic	2 stars out of 4 criteria provided, multiple submitters, no conflicts
D356N	c.1066G>A	Exon 9	38,606,743	Pathogenic/likely pathogenic	2 stars out of 4 criteria provided, multiple submitters, no conflicts
D1274N	c.3820G>A	Exon 21	38,566,426	Pathogenic	2 stars out of 4 criteria provided, multiple submitters, no conflicts

See all 47 SCN5A variants →

Traits linked to SCN5A

The Human Phenotype Ontology lists these as features of the rare conditions SCN5A can cause. Each trait's page lists the other genes linked to it.

Abnormality of the cardiovascular system

Show 51 more traits

Abnormality of the musculoskeletal system

Constitutional symptom

Abnormality of the nervous system

Abnormality of the respiratory system

Laboratory abnormality

Abnormality of blood and blood-forming tissues

Abnormality of the digestive system

Abnormality of the ear

External links

Gene records

Transcript

Protein

Variants

Clinical

Where this comes from

HGNC: the gene's symbol, name, other symbols and location.
MANE Select v1.5, from NCBI and EMBL-EBI: the transcript, its exons and coding sequence.
GenCC and ClinGen, released 2026-10-16: which conditions the gene is linked to, and how strongly.
The ACMG secondary findings list, SF v3.2.
ClinVar and the GIAB stratifications: known disease-causing sites, and the regions short reads find hard.
The Human Phenotype Ontology, release 2026-09-01: the traits linked to the gene. Find out more at hpo.jax.org.
Data release 2026.10.16-c6eea6bf.

Cite this page

APA

Dante Labs. (n.d.). SCN5A gene: sodium voltage-gated channel alpha subunit 5. Retrieved 17 October 2026, from https://dantelabs.com/genes/scn5a

Vancouver

Dante Labs. SCN5A gene: sodium voltage-gated channel alpha subunit 5 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/scn5a

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