Traits

Traits linked to SYNGAP1

synaptic Ras GTPase activating protein 1

The Human Phenotype Ontology links 119 traits to SYNGAP1, 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
IQ between 34 and 49	Always
Motor delay	Always
Abnormality of pain sensation	Very often (80–99%)
Delayed speech and language development	Very often (80–99%)
EEG with focal spike waves	Very often (80–99%)
Encephalopathy	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%)
Abnormal eating behavior	Often (30–79%)
Abnormal gait	Often (30–79%)
Abnormality of coordination	Often (30–79%)
Ataxia	Often (30–79%)
Attention deficit	Often (30–79%)
Autism spectrum disorder	Often (30–79%)
Behavioral abnormality	Often (30–79%)
Bilateral tonic-clonic seizure with generalized onset	Often (30–79%)
Brain degeneration	Often (30–79%)
Brief seizures with staring spells	Often (30–79%)
Decreased reflex response	Often (30–79%)
Difficulty sleeping	Often (30–79%)
Eating-induced seizure	Often (30–79%)
EEG with multifocal slow activity	Often (30–79%)
EEG with polyspike wave complexes	Often (30–79%)
Epilepsy	Often (30–79%)
Generalized myoclonic seizure	Often (30–79%)
Grand mal seizures	Often (30–79%)
Incoordination	Often (30–79%)
Intellectual disability, severe	Often (30–79%)
Lack of peer relationships	Often (30–79%)
Loss of developmental milestones	Often (30–79%)
More active than typical	Often (30–79%)
Myoclonic absence seizure	Often (30–79%)
Poor speech	Often (30–79%)
Sudden loss of muscle tone	Often (30–79%)
Abnormal corpus callosum morphology	Sometimes (5–29%)
Abnormal emotional state	Sometimes (5–29%)
Abnormal myelination	Sometimes (5–29%)
Abnormal subarachnoid space morphology	Sometimes (5–29%)
Absent speech development	Sometimes (5–29%)
Autism	Sometimes (5–29%)
Brain imaging abnormality	Sometimes (5–29%)
Degeneration of cerebrum	Sometimes (5–29%)
Diminished deep tendon reflex	Sometimes (5–29%)
Disorder of involuntary muscle movements	Sometimes (5–29%)
EEG with generalized slow activity	Sometimes (5–29%)
EEG with irregular generalized spike and wave complexes	Sometimes (5–29%)
Hypsarrhythmia	Sometimes (5–29%)
Impulsivity	Sometimes (5–29%)
Interictal epileptiform activity	Sometimes (5–29%)
Involuntary movements	Sometimes (5–29%)
Jerking	Sometimes (5–29%)
Mental deterioration	Sometimes (5–29%)
Obsessive-compulsive trait	Sometimes (5–29%)
Poor social interactions	Sometimes (5–29%)
Recurrent hand flapping	Sometimes (5–29%)
Simple febrile seizure	Sometimes (5–29%)
Tremor	Sometimes (5–29%)
Unsteady walk	Sometimes (5–29%)
Abnormal pyramidal sign	Rarely (1–4%)
Epileptic encephalopathy	Rarely (1–4%)
Repeated seizures without recovery between them	Rarely (1–4%)
Seizure affecting one half of brain	Rarely (1–4%)
EEG abnormality	Not recorded
Epileptic spasm	Not recorded
Language impairment	Not recorded

Abnormality of head or neck

Trait	How often it is seen
Abnormal facial shape	Often (30–79%)
Abnormally small head	Often (30–79%)
Congenital muscular torticollis	Often (30–79%)
Drooling	Often (30–79%)
Wry neck	Often (30–79%)
Abnormal tongue physiology	Sometimes (5–29%)
Decreased volume of lip	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%)
High palate	Sometimes (5–29%)
Long face	Sometimes (5–29%)
Narrow mouth	Sometimes (5–29%)
Triangular face	Sometimes (5–29%)
Wide mouth	Sometimes (5–29%)
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 nasal bridge	Rarely (1–4%)

Abnormality of the eye

Trait	How often it is seen
Cross-eyed	Often (30–79%)
Deeply set eye	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%)
Abnormally small eyeball	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%)

Abnormality of limbs

Trait	How often it is seen
Postaxial polydactyly	Sometimes (5–29%)
Increased muscle tone of arm or leg	Rarely (1–4%)
Webbed fingers or toes	Rarely (1–4%)

Abnormality of the digestive system

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

Abnormality of the integument

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

Abnormality of the ear

Trait	How often it is seen
Anteverted ears	Sometimes (5–29%)
Large ears	Sometimes (5–29%)

Growth abnormality

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

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 genitourinary system

Trait	How often it is seen
Hypospadias	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 SYNGAP1 and how often each is seen. Find out more at hpo.jax.org.

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