Traits

Traits linked to SCN3A

sodium voltage-gated channel alpha subunit 3

The Human Phenotype Ontology links 85 traits to SCN3A, by body system: features seen in people with one of the gene's rare conditions.

Abnormality of the nervous system

Trait	How often it is seen
Abnormal autonomic nervous system physiology	Always
Epilepsy	Always
Global developmental delay	Always
Seizure affecting one half of brain	Always
EEG with focal epileptiform discharges	Very often (80–99%)
Encephalopathy	Very often (80–99%)
Abnormal cerebral white matter morphology	Often (30–79%)
Abnormality of coordination	Often (30–79%)
Decreased reflex response	Often (30–79%)
Delayed speech and language development	Often (30–79%)
EEG with multifocal slow activity	Often (30–79%)
Focal impaired awareness seizure	Often (30–79%)
Grand mal seizures	Often (30–79%)
Inability to walk	Often (30–79%)
Intellectual disability	Often (30–79%)
Interictal EEG abnormality	Often (30–79%)
Loss of developmental milestones	Often (30–79%)
More grooves in brain	Often (30–79%)
Nocturnal seizures	Often (30–79%)
Underdevelopment of part of brain called corpus callosum	Often (30–79%)
Abnormal corpus callosum morphology	Sometimes (5–29%)
Abnormal gait	Sometimes (5–29%)
Abnormal myelination	Sometimes (5–29%)
Ataxia	Sometimes (5–29%)
Attention deficit	Sometimes (5–29%)
Autism	Sometimes (5–29%)
Autism spectrum disorder	Sometimes (5–29%)
Behavioral abnormality	Sometimes (5–29%)
Brain degeneration	Sometimes (5–29%)
Clonic seizure	Sometimes (5–29%)
Cognitive impairment	Sometimes (5–29%)
Degeneration of cerebrum	Sometimes (5–29%)
Deja vu	Sometimes (5–29%)
Diminished deep tendon reflex	Sometimes (5–29%)
Disorder of involuntary muscle movements	Sometimes (5–29%)
Focal aware seizure	Sometimes (5–29%)
Focal cortical dysplasia	Sometimes (5–29%)
Hallucinations of sound	Sometimes (5–29%)
Hypsarrhythmia	Sometimes (5–29%)
Impulsivity	Sometimes (5–29%)
Infantile spasms	Sometimes (5–29%)
Intellectual disability, borderline	Sometimes (5–29%)
Involuntary movements	Sometimes (5–29%)
Jerking	Sometimes (5–29%)
Loss of expressive speech	Sometimes (5–29%)
Mental deterioration	Sometimes (5–29%)
Multifocal epileptiform discharges	Sometimes (5–29%)
Pins and needles feeling	Sometimes (5–29%)
Simple febrile seizure	Sometimes (5–29%)
Tremor	Sometimes (5–29%)
Unsteady walk	Sometimes (5–29%)
Visual hallucinations	Sometimes (5–29%)
Hemimegalencephaly	Rarely (1–4%)
Repeated seizures without recovery between them	Rarely (1–4%)
Absent speech development	Not recorded
Epileptic encephalopathy	Not recorded

Abnormality of the eye

Trait	How often it is seen
Cerebral visual impairment	Sometimes (5–29%)
Drooping upper eyelid	Sometimes (5–29%)
Involuntary, rapid, rhythmic eye movements	Sometimes (5–29%)
Abnormal involuntary eye movements	Rarely (1–4%)
Abnormality of vision	Rarely (1–4%)
Optic atrophy	Rarely (1–4%)
Retina degeneration	Rarely (1–4%)

Abnormality of the musculoskeletal system

Trait	How often it is seen
Low muscle tone	Always
Generalized decreased muscle tone	Often (30–79%)
Involuntary muscle stiffness, contraction, or spasm	Sometimes (5–29%)
Poor head control	Sometimes (5–29%)
Rigidity	Sometimes (5–29%)
Spastic tetraplegia	Sometimes (5–29%)

Abnormality of head or neck

Trait	How often it is seen
Small face	Always
Abnormally small head	Sometimes (5–29%)
Downward slanting of the opening between the eyelids	Sometimes (5–29%)
Failure of development of between one and six teeth	Sometimes (5–29%)
High forehead	Sometimes (5–29%)

Abnormality of the digestive system

Trait	How often it is seen
Acid reflux	Sometimes (5–29%)
Feeding difficulties	Sometimes (5–29%)
Gastrostomy tube feeding in infancy	Sometimes (5–29%)
Poor swallowing	Sometimes (5–29%)

Abnormality of the integument

Trait	How often it is seen
Flushing	Sometimes (5–29%)
Paleness	Sometimes (5–29%)

Growth abnormality

Trait	How often it is seen
Faltering weight	Often (30–79%)
Short stature	Sometimes (5–29%)

Abnormality of limbs

Trait	How often it is seen
Increased muscle tone of arm or leg	Rarely (1–4%)

Abnormality of prenatal development or birth

Trait	How often it is seen
Less than 10 fetal movements in 12 hours	Sometimes (5–29%)

Constitutional symptom

Trait	How often it is seen
Pain	Sometimes (5–29%)

How often is among people with one of the gene's conditions, the most often across them, as the Human Phenotype Ontology records it. These pages describe traits and the research behind them; they are not a diagnosis, and a doctor or genetic counsellor is the person to ask about symptoms.

Where this comes from

The Human Phenotype Ontology, release 2026-09-01: the traits linked to SCN3A and how often each is seen. Find out more at hpo.jax.org.

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