Traits

Traits linked to SCN1A

sodium voltage-gated channel alpha subunit 1

The Human Phenotype Ontology links 222 traits to SCN1A, 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
Global developmental delay	Always
Grand mal seizures	Always
Inability to walk	Always
IQ less than 20	Always
Migraine with aura	Always
Multifocal epileptiform discharges	Always
Myoclonic seizure	Always
Abnormal speech pattern	Very often (80–99%)
Absent speech development	Very often (80–99%)
Ataxia	Very often (80–99%)
Cognitive impairment	Very often (80–99%)
EEG abnormality	Very often (80–99%)
EEG with focal sharp slow waves	Very often (80–99%)
EEG with focal spike waves	Very often (80–99%)
Encephalopathy	Very often (80–99%)
Fear of loud sounds	Very often (80–99%)
Focal motor seizure	Very often (80–99%)
Focal sensory seizure	Very often (80–99%)
Generalized myoclonic-atonic seizure	Very often (80–99%)
Generalized-onset seizure	Very often (80–99%)
Intellectual disability	Very often (80–99%)
Loss of developmental milestones	Very often (80–99%)
Neurodevelopmental delay	Very often (80–99%)
Progressive gait ataxia	Very often (80–99%)
Seizure affecting one half of brain	Very often (80–99%)
Abnormal shape of brainstem	Often (30–79%)
Abnormality of coordination	Often (30–79%)
Aggressive behavior	Often (30–79%)
Anxiety	Often (30–79%)
Attention deficit	Often (30–79%)
Atypical absence seizure	Often (30–79%)
Autism spectrum disorder	Often (30–79%)
Balance impairment	Often (30–79%)
Behavioral abnormality	Often (30–79%)
Bilateral tonic-clonic seizure with focal onset	Often (30–79%)
Bilateral tonic-clonic seizure with generalized onset	Often (30–79%)
Brief seizures with staring spells	Often (30–79%)
Choreoathetosis	Often (30–79%)
Complex febrile seizure	Often (30–79%)
Confusion	Often (30–79%)
CSF lymphocytic pleiocytosis	Often (30–79%)
CSF pleocytosis	Often (30–79%)
Decreased reflex response	Often (30–79%)
Degeneration of cerebrum	Often (30–79%)
Delayed speech and language development	Often (30–79%)
Difficulty articulating speech	Often (30–79%)
Dissociated sensory loss	Often (30–79%)
Dystonia	Often (30–79%)
EEG with multifocal slow activity	Often (30–79%)
EEG with polyspike wave complexes	Often (30–79%)
EEG with spike-wave complexes (>3.5 Hz)	Often (30–79%)
Epilepsia partialis continua	Often (30–79%)
Epilepsy	Often (30–79%)
Epileptic spasm	Often (30–79%)
Falls	Often (30–79%)
Febrile seizure (within the age range of 3 months to 6 years)	Often (30–79%)
Focal aware seizure	Often (30–79%)
Focal emotional seizure with laughing	Often (30–79%)
Focal hemiclonic seizure	Often (30–79%)
Focal impaired awareness seizure	Often (30–79%)
Focal manual automatism seizure	Often (30–79%)
Focal pedal automatism seizure	Often (30–79%)
Generalized clonic seizure	Often (30–79%)
Generalized myoclonic seizure	Often (30–79%)
Generalized tonic seizure	Often (30–79%)
Hyperactive movements	Often (30–79%)
Intellectual disability, severe	Often (30–79%)
Interictal epileptiform activity	Often (30–79%)
Involuntary movements	Often (30–79%)
IQ between 34 and 49	Often (30–79%)
Irritability	Often (30–79%)
Jerking	Often (30–79%)
Lack of peer relationships	Often (30–79%)
Mental deterioration	Often (30–79%)
More active than typical	Often (30–79%)
Obsessive-compulsive trait	Often (30–79%)
Parkinsonism	Often (30–79%)
Personality disorder	Often (30–79%)
Photosensitive myoclonic seizure	Often (30–79%)
Photosensitive tonic-clonic seizure	Often (30–79%)
Pins and needles feeling	Often (30–79%)
Slow movements	Often (30–79%)
Small hippocampus	Often (30–79%)
Status epilepticus without prominent motor symptoms	Often (30–79%)
Sudden loss of muscle tone	Often (30–79%)
Tonic seizure	Often (30–79%)
Weakness of one side of body	Often (30–79%)
Abnormal corpus callosum morphology	Sometimes (5–29%)
Abnormal emotional state	Sometimes (5–29%)
Abnormal gait	Sometimes (5–29%)
Abnormal myelination	Sometimes (5–29%)
Action tremor	Sometimes (5–29%)
Alien limb phenomenon	Sometimes (5–29%)
Atypical absence status epilepticus	Sometimes (5–29%)
Autism	Sometimes (5–29%)
Brain degeneration	Sometimes (5–29%)
Brain imaging abnormality	Sometimes (5–29%)
Brisk reflexes	Sometimes (5–29%)
Chorea	Sometimes (5–29%)
Coma	Sometimes (5–29%)
Cortical dysplasia	Sometimes (5–29%)
Decreased vigilance	Sometimes (5–29%)
Degeneration of cerebellum	Sometimes (5–29%)
Delayed myelination	Sometimes (5–29%)
Difficulty finding words	Sometimes (5–29%)
Diminished deep tendon reflex	Sometimes (5–29%)
Disorder of involuntary muscle movements	Sometimes (5–29%)
Dysgenesis of the hippocampus	Sometimes (5–29%)
EEG with focal epileptiform discharges	Sometimes (5–29%)
EEG with generalized epileptiform discharges	Sometimes (5–29%)
EEG with generalized sharp slow waves	Sometimes (5–29%)
EEG with generalized slow activity	Sometimes (5–29%)
EEG with irregular generalized spike and wave complexes	Sometimes (5–29%)
EEG with spike-wave complexes	Sometimes (5–29%)
Fluid-filled sac located in membrane surrounding brain or spinal cord	Sometimes (5–29%)
Generalized brain degeneration	Sometimes (5–29%)
Generalized cerebral degeneration/underdevelopment	Sometimes (5–29%)
Hypsarrhythmia	Sometimes (5–29%)
Impaired temperature sensation	Sometimes (5–29%)
Impulsivity	Sometimes (5–29%)
Incoordination	Sometimes (5–29%)
Lack of feeling, emotion, interest	Sometimes (5–29%)
Language impairment	Sometimes (5–29%)
Myoclonic absence seizure	Sometimes (5–29%)
Paralysis on one side of body	Sometimes (5–29%)
Poor fine motor coordination	Sometimes (5–29%)
Poor social interactions	Sometimes (5–29%)
Psychosis	Sometimes (5–29%)
Repetitive movements	Sometimes (5–29%)
Short attention span	Sometimes (5–29%)
Simple febrile seizure	Sometimes (5–29%)
Spontaneous pain sensation	Sometimes (5–29%)
Tremor	Sometimes (5–29%)
Unsteady walk	Sometimes (5–29%)
Abnormal pyramidal sign	Rarely (1–4%)
EEG with focal sharp waves	Rarely (1–4%)
Epileptic encephalopathy	Rarely (1–4%)
Repeated seizures without recovery between them	Rarely (1–4%)
Motor delay	Not recorded
Visually-induced seizure	Not recorded

Abnormality of head or neck

Trait	How often it is seen
Abnormally small head	Often (30–79%)
Facial tics	Often (30–79%)
Limited neck range of motion	Often (30–79%)
Tongue twitching	Often (30–79%)
Downward slanting of the opening between the eyelids	Sometimes (5–29%)
Drooling	Sometimes (5–29%)
Facial paralysis	Sometimes (5–29%)
Failure of development of between one and six teeth	Sometimes (5–29%)
High forehead	Sometimes (5–29%)
Narrow mouth	Sometimes (5–29%)
Nuchal rigidity	Sometimes (5–29%)
Abnormal facial shape	Rarely (1–4%)
Broad philtrum	Rarely (1–4%)
Full lower lip	Rarely (1–4%)
Long philtrum	Rarely (1–4%)
Nasal tip, upturned	Rarely (1–4%)
Prominent forehead	Rarely (1–4%)
Thick nasal alae	Rarely (1–4%)
Thin red part of the upper lip	Rarely (1–4%)
Wide mouth	Rarely (1–4%)
Wide nasal bridge	Rarely (1–4%)
Development of small head that was not present at birth	Not recorded

Abnormality of the eye

Trait	How often it is seen
Extreme sensitivity of the eyes to light	Very often (80–99%)
Blind spot	Often (30–79%)
Double vision	Often (30–79%)
Metamorphopsia	Often (30–79%)
Photopsia	Often (30–79%)
Drooping upper eyelid	Sometimes (5–29%)
Gaze-evoked horizontal nystagmus	Sometimes (5–29%)
Involuntary, rapid, rhythmic eye movements	Sometimes (5–29%)
Seesaw nystagmus	Sometimes (5–29%)
Spasmus nutans	Sometimes (5–29%)
Vertical nystagmus	Sometimes (5–29%)
Visual impairment	Sometimes (5–29%)
Wide-set eyes	Sometimes (5–29%)
Abnormal involuntary eye movements	Rarely (1–4%)
Abnormality of vision	Rarely (1–4%)
Abnormally small eyeball	Rarely (1–4%)
Amaurosis fugax	Rarely (1–4%)
Optic atrophy	Rarely (1–4%)
Retina degeneration	Rarely (1–4%)
Blindness	Not recorded
Cerebral visual impairment	Not recorded

Abnormality of the musculoskeletal system

Trait	How often it is seen
Low muscle tone	Always
Functional motor deficit	Very often (80–99%)
Muscle weakness	Very often (80–99%)
Cogwheel rigidity	Often (30–79%)
Generalized decreased muscle tone	Often (30–79%)
Low muscle tone in trunk	Often (30–79%)
Rigidity	Often (30–79%)
Decreased muscle tone in infant	Sometimes (5–29%)
Involuntary muscle stiffness, contraction, or spasm	Sometimes (5–29%)
Poor head control	Sometimes (5–29%)
Scoliosis	Sometimes (5–29%)
Spasticity and rigidity of muscles	Sometimes (5–29%)
First dorsal interossei muscle weakness	Rarely (1–4%)

Abnormality of limbs

Trait	How often it is seen
Distal upper limb muscle weakness	Sometimes (5–29%)
Dropped arches	Sometimes (5–29%)
Limited knee straightening	Sometimes (5–29%)
Pes valgus	Sometimes (5–29%)
Tibial torsion	Sometimes (5–29%)
Increased muscle tone of arm or leg	Rarely (1–4%)
Talipes valgus	Rarely (1–4%)
Webbed fingers or toes	Rarely (1–4%)

Abnormality of the integument

Trait	How often it is seen
Cyanotic episode	Sometimes (5–29%)
Paleness	Sometimes (5–29%)
Frontal balding	Rarely (1–4%)
Premature skin wrinkling	Rarely (1–4%)

Abnormality of the digestive system

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

Abnormality of the ear

Trait	How often it is seen
Dizziness	Often (30–79%)
Hearing impairment	Often (30–79%)
Ringing in ears	Sometimes (5–29%)

Growth abnormality

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

Laboratory abnormality

Trait	How often it is seen
Brain swelling	Often (30–79%)
Increased CSF protein concentration	Often (30–79%)

Abnormality of prenatal development or birth

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

Abnormality of the cardiovascular system

Trait	How often it is seen
Aortopulmonary collateral arteries	Sometimes (5–29%)

Abnormality of the endocrine system

Trait	How often it is seen
Early onset of puberty	Rarely (1–4%)

Constitutional symptom

Trait	How often it is seen
Sudden unexpected death in epilepsy	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 SCN1A and how often each is seen. Find out more at hpo.jax.org.

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