Traits

Traits linked to SEMA3E

semaphorin 3E

The Human Phenotype Ontology links 99 traits to SEMA3E, by body system: features seen in people with one of the gene's rare conditions.

SEMA3E

Abnormality of head or neck

Trait	How often it is seen
Lost smell	Very often (80–99%)
Abnormal soft palate morphology	Often (30–79%)
Bell's palsy	Often (30–79%)
Blockage of the rear opening of the nasal cavity	Often (30–79%)
Delayed eruption of teeth	Often (30–79%)
Depressed nasal bridge	Often (30–79%)
Dimple chin	Often (30–79%)
Facial asymmetry	Often (30–79%)
Narrow face	Often (30–79%)
Narrow mouth	Often (30–79%)
Abnormally small head	Sometimes (5–29%)
Cheekbone underdevelopment	Sometimes (5–29%)
Cleft eyelid	Sometimes (5–29%)
Cleft palate	Sometimes (5–29%)
Cleft upper lip	Sometimes (5–29%)
Dandy-Walker malformation	Sometimes (5–29%)
Eye folds	Sometimes (5–29%)
Highly arched eyebrow	Sometimes (5–29%)
Skin tag in front of the ear	Sometimes (5–29%)
Webbed neck	Rarely (1–4%)

Abnormality of the eye

Trait	How often it is seen
Cat eye	Very often (80–99%)
Notched pupil	Very often (80–99%)
Abnormally small eyeball	Often (30–79%)
Absence of eyeballs	Often (30–79%)
Birth defect that causes a hole in the innermost layer at the back of the eye	Often (30–79%)
Cross-eyed	Often (30–79%)
Drooping upper eyelid	Often (30–79%)
Involuntary, rapid, rhythmic eye movements	Often (30–79%)
Optic atrophy	Often (30–79%)
Abnormality of tear production	Sometimes (5–29%)
Abnormality of the eye	Sometimes (5–29%)
Abnormality of vision	Sometimes (5–29%)
Wide-set eyes	Sometimes (5–29%)

Abnormality of the genitourinary system

Trait	How often it is seen
Decreased testicular size	Always
Primary amenorrhea	Always
Short penis	Always
Undescended testes	Very often (80–99%)
Abnormal morphology of female internal genitalia	Often (30–79%)
Cleft of scrotum	Often (30–79%)
Underdeveloped labia	Often (30–79%)
Horseshoe kidney	Sometimes (5–29%)
Hydronephrosis	Sometimes (5–29%)
Infertility	Sometimes (5–29%)
Vesicoureteral reflux	Sometimes (5–29%)

Abnormality of the nervous system

Trait	How often it is seen
Abnormal cranial nerve morphology	Very often (80–99%)
Global developmental delay	Very often (80–99%)
Attention deficit	Often (30–79%)
Autism	Often (30–79%)
Intellectual disability	Often (30–79%)
Obsessive compulsive behavior	Often (30–79%)
Absent/small cerebellum	Sometimes (5–29%)
Aqueductal stenosis	Sometimes (5–29%)
Cranial nerve paralysis	Sometimes (5–29%)
Holoprosencephaly	Sometimes (5–29%)

Abnormality of the ear

Trait	How often it is seen
Abnormality of the inner ear	Very often (80–99%)
Abnormally shaped ears	Very often (80–99%)
Absent/small ear lobes	Very often (80–99%)
Hearing impairment	Very often (80–99%)
Hypoplasia of the semicircular canal	Very often (80–99%)
Overfolded ears	Very often (80–99%)
Ears rotated toward back of head	Often (30–79%)
Small ears	Sometimes (5–29%)

Abnormality of the cardiovascular system

Trait	How often it is seen
Abnormal aortic valve morphology	Often (30–79%)
Abnormal cardiac septum morphology	Often (30–79%)
Abnormal cardiovascular system morphology	Often (30–79%)
Aortic arch aneurysm	Often (30–79%)
Interrupted aortic arch	Often (30–79%)
Patent ductus arteriosus	Often (30–79%)
Tetralogy of Fallot	Often (30–79%)

Abnormality of limbs

Trait	How often it is seen
Abnormality of the shankbone	Sometimes (5–29%)
Curvature of little finger	Sometimes (5–29%)
Notched thighbone	Sometimes (5–29%)
Short fingers or toes	Sometimes (5–29%)
Talipes	Sometimes (5–29%)
More than five fingers or toes on hands or feet	Rarely (1–4%)

Abnormality of the digestive system

Trait	How often it is seen
Feeding difficulties in infancy	Very often (80–99%)
Acid reflux	Often (30–79%)
Poor swallowing	Often (30–79%)
Abnormal connection between trachea and esophagus	Sometimes (5–29%)
Umbilical hernia	Sometimes (5–29%)
Omphalocele	Rarely (1–4%)

Abnormality of the musculoskeletal system

Trait	How often it is seen
Low muscle tone	Often (30–79%)
Abnormality of bone mineral density	Sometimes (5–29%)
Abnormality of the ribs	Sometimes (5–29%)
Missing part of vertebrae	Sometimes (5–29%)
Scoliosis	Sometimes (5–29%)

Abnormality of the endocrine system

Trait	How often it is seen
Hypogonadotropic hypogonadism	Always
Delayed puberty	Very often (80–99%)
Anterior hypopituitarism	Often (30–79%)
Adrenal abnormalities	Sometimes (5–29%)

Growth abnormality

Trait	How often it is seen
Growth delay as children	Often (30–79%)
Short stature	Often (30–79%)
Prenatal growth deficiency	Sometimes (5–29%)

Abnormality of the integument

Trait	How often it is seen
Limited armpit hair	Always
Sparse pubic hair	Always

Abnormality of the respiratory system

Trait	How often it is seen
Respiratory function loss	Sometimes (5–29%)
Softening of voice box tissue	Sometimes (5–29%)

Abnormality of prenatal development or birth

Trait	How often it is seen
High levels of amniotic fluid	Often (30–79%)

Abnormality of the immune system

Trait	How often it is seen
Abnormality of immune system physiology	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 SEMA3E and how often each is seen. Find out more at hpo.jax.org.

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