Gene
SCN9A
sodium voltage-gated channel alpha subunit 9
- HGNC 10597(opens in a new tab)
- Ensembl gene ENSG00000169432(opens in a new tab)
- NCBI Gene 6335(opens in a new tab)
Summary
- Cytogenetic location
- 2q24.3
- Coordinates
- Chromosome 2: 166,195,185–166,375,944 (GRCh38)
- Exons
- 27 exons across 180.8 kb
- Protein
- 1,988 amino acids
- Also known as
- Nav1.7, PN1, NE-NA, NENA, ETHA
- MANE Select transcript
- ENST00000642356.2NM_001365536.1
- 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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Get my Genome TestCurated reports relevant to this gene
Hereditary Sensory and Autonomic Neuropathies (incl. Familial Dysautonomia)
- Hereditary Sensory and Autonomic Neuropathy
A group of neuropathies, including familial dysautonomia (ELP1), HSAN1 (SPTLC1/SPTLC2), HSAN2 (WNK1, RETREG1) and congenital insensitivity to pain (NTRK1, SCN9A, PRDM12), most of which are recessive while HSAN1 is dominant.
- 2 GenCC submitters rate it definitive or strong
What knowing changes
Protection against unnoticed injuries, burns and infections, management of autonomic symptoms, and carrier testing for relatives (familial dysautonomia is included in Ashkenazi Jewish carrier screening).
Broader groupings
Epilepsy (Full Panel)
- Epilepsy
One of 171 genes linked to it
A brain disorder characterized by episodes of abnormally increased neuronal discharge resulting in transient episodes of sensory or motor neurological dysfunction, or psychic dysfunction. These episodes may or may not be associated with loss of consciousness or convulsions.
- 1 GenCC submitter rates it definitive or strong
How SCN9A is laid out
- Coding sequence
- Untranslated region
- Intron
- Direction of transcription
- Known disease-causing sites
- Stretches short reads find hard
Exons of the gene's MANE Select transcript (release v1.5), from NCBI and EMBL-EBI, on the GRCh38 reference genome.
Chromosome bands from UCSC's GRCh38 ideogram (2022-10-29).
Nearby genes from Ensembl release 116, on GRCh38.
Exons make up 9.8 kb of the gene's 180.8 kb; 5,967 of those bases code for the protein.
How a genome test reads SCN9A
155
positions in SCN9A where ClinVar classes a change as pathogenic or likely pathogenic
6 of them (3.9%) fall in regions short reads find hard.
- Low mappability (6 sites)Regions where 100 bp or 250 bp reads cannot be placed uniquely.
A whole genome covers all 180.8 kb of SCN9A, introns included, not only the 9.8 kb of exons.
Traits linked to SCN9A
The Human Phenotype Ontology lists these as features of the rare conditions SCN9A can cause. Each trait's page lists the other genes linked to it.
Abnormality of the nervous system
- Pain insensitivity
- Epilepsy
- Generalized-onset seizure
- Loss of developmental milestones
- Peripheral neuropathy
- Progressive gait ataxia
- Seizure affecting one half of brain
- Anxiety
Show 49 more traits
- Atypical absence seizure
- Autism spectrum disorder
- Brief seizures with staring spells
- Cognitive impairment
- Complex febrile seizure
- Epilepsia partialis continua
- Febrile seizure (within the age range of 3 months to 6 years)
- Focal aware seizure
- Focal hemiclonic seizure
- Focal impaired awareness seizure
- Generalized clonic seizure
- Generalized myoclonic seizure
- Interictal epileptiform activity
- Jerking
- Multifocal epileptiform discharges
- Obsessive-compulsive trait
- Parkinsonism
- Photosensitive myoclonic seizure
- Photosensitive tonic-clonic seizure
- Slow movements
- Abnormal autonomic nervous system physiology
- Action tremor
- Ataxia
- Atypical absence status epilepticus
- Cortical dysplasia
- Decreased sensation in extremities
- Dysesthesia
- Dysgenesis of the hippocampus
- EEG with focal epileptiform discharges
- EEG with generalized epileptiform discharges
- EEG with spike-wave complexes
- Generalized brain degeneration
- Generalized cerebral degeneration/underdevelopment
- Grand mal seizures
- Impulsivity
- Incoordination
- Poor fine motor coordination
- Short attention span
- Status epilepticus without prominent motor symptoms
- Sudden loss of muscle tone
- Generalized tonic seizure
- Repeated seizures without recovery between them
- Tremor
- Absent reflexes
- Decreased nerve conduction velocity
- Decreased number of peripheral myelinated nerve fibers
- Decreased reflex response
- Decreased sensory nerve conduction velocity
- Impaired pain sensation
Abnormality of the integument
- Excessive sweating
- Poor fingernail formation
- Poor toenail formation
- Itching
- Cyanotic episode
- Paleness
- Acral ulceration
- Decreased ability to sweat
Show 4 more traits
Abnormality of head or neck
- Extra bones within cranial sutures
- Facial tics
- Limited neck range of motion
- Drooling
- Decreased salivary flow
- Decreased taste
- Dry eye syndrome
- Hyposmia
Show 2 more traits
External links
Gene records
Transcript
Protein
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
Dante Labs. (n.d.). SCN9A gene: sodium voltage-gated channel alpha subunit 9. Retrieved 16 October 2026, from https://dantelabs.com/genes/scn9a
Dante Labs. SCN9A gene: sodium voltage-gated channel alpha subunit 9 [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/scn9a
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