Traits

Traits linked to SHANK3

SH3 and multiple ankyrin repeat domains 3

The Human Phenotype Ontology links 77 traits to SHANK3, by body system: features seen in people with one of the gene's rare conditions.

SHANK3

Abnormality of the nervous system

Trait	How often it is seen
Delayed speech and language development	Always
Global developmental delay	Always
Schizophrenia	Always
Behavioral abnormality	Very often (80–99%)
Autism	Often (30–79%)
Epilepsy	Often (30–79%)
Hyperorality	Often (30–79%)
Impaired pain sensation	Often (30–79%)
Intellectual disability	Often (30–79%)
Poor eye contact	Often (30–79%)
Poor social interactions	Often (30–79%)
Repetitive movements	Often (30–79%)
Teeth grinding	Often (30–79%)
Unsteady walk	Often (30–79%)
Wide based walk	Often (30–79%)
Abnormal periventricular white matter morphology	Sometimes (5–29%)
Aggressive behavior	Sometimes (5–29%)
Delayed CNS myelination	Sometimes (5–29%)
Difficulty sleeping	Sometimes (5–29%)
Fluid-filled sac located in membrane surrounding brain or spinal cord	Sometimes (5–29%)
More active than typical	Sometimes (5–29%)
Tongue thrusting	Sometimes (5–29%)
Ventriculomegaly	Sometimes (5–29%)
Decreased reflex response	Not recorded
IQ between 34 and 49	Not recorded
Motor delay	Not recorded

Abnormality of head or neck

Trait	How often it is seen
Bad bite	Often (30–79%)
Big calvaria	Often (30–79%)
Bulbous nose	Often (30–79%)
Eye folds	Often (30–79%)
Full cheeks	Often (30–79%)
Fullness of eyelids	Often (30–79%)
High palate	Often (30–79%)
Long eyelashes	Often (30–79%)
Long, narrow head	Often (30–79%)
Thick eyebrow	Often (30–79%)
Zygomatic flattening	Often (30–79%)
Little lower jaw	Sometimes (5–29%)
Long philtrum	Sometimes (5–29%)
Pointed chin	Sometimes (5–29%)
Wide nasal bridge	Sometimes (5–29%)
Widely spaced teeth	Sometimes (5–29%)
Abnormally small head	Rarely (1–4%)
Boxer's nasal deformity	Not recorded
Prominent brow	Not recorded
Short chin	Not recorded

Abnormality of the eye

Trait	How often it is seen
Cross-eyed	Often (30–79%)
Deeply set eye	Often (30–79%)
Drooping upper eyelid	Often (30–79%)
Cerebral visual impairment	Sometimes (5–29%)
Wide-set eyes	Sometimes (5–29%)

Abnormality of the integument

Trait	How often it is seen
Decreased ability to sweat	Often (30–79%)
Spinal dimple	Often (30–79%)
Underdeveloped toenails	Often (30–79%)
Abnormal toenail development	Not recorded

Abnormality of the musculoskeletal system

Trait	How often it is seen
Low muscle tone, in neonatal onset	Very often (80–99%)
Generalized decreased muscle tone	Often (30–79%)
Bacterial infection of skin	Sometimes (5–29%)
Double-Jointed	Sometimes (5–29%)

Abnormality of limbs

Trait	How often it is seen
Curvature of little finger	Often (30–79%)
Large hands	Often (30–79%)
Webbed 2nd and 3rd toes	Often (30–79%)

Abnormality of the digestive system

Trait	How often it is seen
Acid reflux	Often (30–79%)
Episodic vomiting	Often (30–79%)
Feeding difficulties	Often (30–79%)

Abnormality of the ear

Trait	How often it is seen
Large ears	Often (30–79%)
Hearing impairment	Sometimes (5–29%)
Prominent ear	Not recorded

Abnormality of the genitourinary system

Trait	How often it is seen
Abnormality of the kidney	Often (30–79%)
Polycystic kidney dysplasia	Sometimes (5–29%)
Vesicoureteral reflux	Sometimes (5–29%)

Abnormality of the cardiovascular system

Trait	How often it is seen
Hole in heart wall separating two lower heart chambers	Sometimes (5–29%)
Patent ductus arteriosus	Sometimes (5–29%)

Laboratory abnormality

Trait	How often it is seen
Heat intolerance	Often (30–79%)
Swelling caused by excess lymph fluid under skin	Often (30–79%)

Abnormality of the immune system

Trait	How often it is seen
Recurrent infections	Often (30–79%)

Growth abnormality

Trait	How often it is seen
Tall stature	Very often (80–99%)

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 SHANK3 and how often each is seen. Find out more at hpo.jax.org.

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