Traits

Traits linked to SETD1A

SET domain containing 1A, histone lysine methyltransferase

The Human Phenotype Ontology links 40 traits to SETD1A, 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
Delayed speech and language development	Always
Grand mal seizures	Always
Global developmental delay	Very often (80–99%)
Intellectual disability	Very often (80–99%)
Motor delay	Very often (80–99%)
Aggressive behavior	Often (30–79%)
Difficulty sleeping	Often (30–79%)
Short attention span	Often (30–79%)
Anxiety	Sometimes (5–29%)
Autism spectrum disorder	Sometimes (5–29%)
Delayed CNS myelination	Sometimes (5–29%)
Epilepsy	Sometimes (5–29%)
Schizophrenia	Sometimes (5–29%)

Abnormality of head or neck

Trait	How often it is seen
Downward slanting of the opening between the eyelids	Often (30–79%)
Drooping upper lip	Often (30–79%)
Eye folds	Often (30–79%)
High forehead	Often (30–79%)
Wide nose	Often (30–79%)
Big calvaria	Sometimes (5–29%)
Deformity of the skull	Sometimes (5–29%)
Full cheeks	Sometimes (5–29%)
Nasal tip, upturned	Sometimes (5–29%)
Wide mouth	Sometimes (5–29%)
Widely spaced teeth	Sometimes (5–29%)

Abnormality of the ear

Trait	How often it is seen
Hearing impairment	Sometimes (5–29%)
Low-set ears	Sometimes (5–29%)
Small ears	Sometimes (5–29%)

Abnormality of the eye

Trait	How often it is seen
Visual impairment	Often (30–79%)
Wide-set eyes	Often (30–79%)
Deeply set eye	Sometimes (5–29%)

Abnormality of the digestive system

Trait	How often it is seen
Chronic constipation	Often (30–79%)
Feeding difficulties	Often (30–79%)

Abnormality of the musculoskeletal system

Trait	How often it is seen
Double-Jointed	Often (30–79%)
Generalized decreased muscle tone	Often (30–79%)

Growth abnormality

Trait	How often it is seen
Obesity	Sometimes (5–29%)
Short stature	Sometimes (5–29%)

Abnormality of prenatal development or birth

Trait	How often it is seen
Low levels of amniotic fluid	Sometimes (5–29%)

Abnormality of the cardiovascular system

Trait	How often it is seen
Patent foramen ovale	Sometimes (5–29%)

Abnormality of the genitourinary system

Trait	How often it is seen
Hydrocele testis	Often (30–79%)

Abnormality of the immune system

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

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 SETD1A and how often each is seen. Find out more at hpo.jax.org.

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