Traits

Traits linked to SLC6A1

solute carrier family 6 member 1

The Human Phenotype Ontology links 88 traits to SLC6A1, 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
Generalized myoclonic-atonic seizure	Always
Intellectual disability	Always
Brief seizures with staring spells	Very often (80–99%)
EEG with focal spike waves	Very often (80–99%)
Global developmental delay	Very often (80–99%)
Motor delay	Very often (80–99%)
Absent speech development	Often (30–79%)
Attention deficit	Often (30–79%)
Autism spectrum disorder	Often (30–79%)
Bilateral tonic-clonic seizure with generalized onset	Often (30–79%)
Delayed speech and language development	Often (30–79%)
EEG with polyspike wave complexes	Often (30–79%)
Eyelid myoclonus	Often (30–79%)
Generalized myoclonic seizure	Often (30–79%)
Lack of peer relationships	Often (30–79%)
More active than typical	Often (30–79%)
Repetitive movements	Often (30–79%)
Sudden loss of muscle tone	Often (30–79%)
Abnormal emotional state	Sometimes (5–29%)
Abnormal thalamus morphology	Sometimes (5–29%)
Ataxia	Sometimes (5–29%)
Brain imaging abnormality	Sometimes (5–29%)
Cerebral white matter atrophy	Sometimes (5–29%)
Delayed CNS myelination	Sometimes (5–29%)
EEG with generalized slow activity	Sometimes (5–29%)
EEG with irregular generalized spike and wave complexes	Sometimes (5–29%)
Grand mal seizures	Sometimes (5–29%)
Interictal epileptiform activity	Sometimes (5–29%)
Myoclonic seizure	Sometimes (5–29%)
Poor social interactions	Sometimes (5–29%)
Simple febrile seizure	Sometimes (5–29%)
Tremor	Sometimes (5–29%)
Abnormal pyramidal sign	Rarely (1–4%)
Epileptic encephalopathy	Rarely (1–4%)
Seizure affecting one half of brain	Rarely (1–4%)
Unsteady walk	Rarely (1–4%)
Epileptic spasm	Not recorded

Abnormality of head or neck

Trait	How often it is seen
Deep philtrum	Often (30–79%)
Depressed nasal bridge	Often (30–79%)
Downward slanting of the opening between the eyelids	Often (30–79%)
Prominent nose	Often (30–79%)
Big lower jaw	Sometimes (5–29%)
Broad head shape	Sometimes (5–29%)
Cleft palate	Sometimes (5–29%)
Downturned corners of mouth	Sometimes (5–29%)
Eye folds	Sometimes (5–29%)
High, narrow palate	Sometimes (5–29%)
Little lower jaw	Sometimes (5–29%)
Narrow forehead	Sometimes (5–29%)
Narrow opening between the eyelids	Sometimes (5–29%)
Nasal tip, upturned	Sometimes (5–29%)
Short philtrum	Sometimes (5–29%)
Thin red part of the upper lip	Sometimes (5–29%)
Abnormal facial shape	Rarely (1–4%)
Abnormally small head	Rarely (1–4%)
Broad philtrum	Rarely (1–4%)
Full lower lip	Rarely (1–4%)
Long philtrum	Rarely (1–4%)
Prominent forehead	Rarely (1–4%)
Thick nasal alae	Rarely (1–4%)
Wide mouth	Rarely (1–4%)
Wide nasal bridge	Rarely (1–4%)

Abnormality of limbs

Trait	How often it is seen
Acromesomelia	Sometimes (5–29%)
Attachment of thumb close to wrist	Sometimes (5–29%)
Broad big toe	Sometimes (5–29%)
Broad thumb	Sometimes (5–29%)
Inability to straighten knee	Sometimes (5–29%)
Overlapping toe	Sometimes (5–29%)
Postaxial polydactyly	Sometimes (5–29%)
Tapered finger	Sometimes (5–29%)
Webbed 2nd-3rd fingers	Sometimes (5–29%)
Webbed fingers or toes	Rarely (1–4%)

Abnormality of the cardiovascular system

Trait	How often it is seen
An opening in the wall separating the top two chambers of the heart	Sometimes (5–29%)
Hole in heart wall separating two lower heart chambers	Sometimes (5–29%)
Narrowing of pulmonic valve	Sometimes (5–29%)
Patent ductus arteriosus	Sometimes (5–29%)
Plaque build-up in arteries supplying blood to heart	Sometimes (5–29%)

Abnormality of the musculoskeletal system

Trait	How often it is seen
Low muscle tone	Often (30–79%)
Congenital pseudoarthrosis of the clavicle	Sometimes (5–29%)
Muscle degeneration	Sometimes (5–29%)
Scoliosis	Sometimes (5–29%)

Abnormality of the integument

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

Abnormality of the ear

Trait	How often it is seen
Abnormality of the outer ear	Often (30–79%)
Sensorineural hearing impairment	Sometimes (5–29%)

Abnormality of the digestive system

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

Abnormality of the eye

Trait	How often it is seen
Abnormally small eyeball	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 SLC6A1 and how often each is seen. Find out more at hpo.jax.org.

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