Traits

Traits linked to SIX6

SIX homeobox 6

The Human Phenotype Ontology links 52 traits to SIX6, by body system: features seen in people with one of the gene's rare conditions.

Abnormality of the eye

Trait	How often it is seen
Abnormally small eyeball	Always
Optic nerve aplasia	Always
Abnormal choroid morphology	Very often (80–99%)
Absence of eyeballs	Very often (80–99%)
Cross-eyed	Very often (80–99%)
Glaucoma	Very often (80–99%)
Severe farsightedness	Very often (80–99%)
Corneal scarring	Often (30–79%)
Enlarged eyeball	Often (30–79%)
Retinal detachment	Often (30–79%)
Abnormal retinal pigmentation	Sometimes (5–29%)
Birth defect that causes a hole in the innermost layer at the back of the eye	Sometimes (5–29%)
Cat eye	Sometimes (5–29%)
Clouding of the lens of the eye	Sometimes (5–29%)
Hardening of skin and connective tissue	Sometimes (5–29%)
Notched pupil	Sometimes (5–29%)
Breakdown of light-sensitive cells in back of eye	Not recorded
Constricted pupils	Not recorded
Horizontal nystagmus	Not recorded
Involuntary, rapid, rhythmic eye movements	Not recorded
Macular atrophy	Not recorded
Optic nerve hypoplasia	Not recorded

Abnormality of the musculoskeletal system

Trait	How often it is seen
Butterfly vertebrae	Not recorded
Extra ribs	Not recorded
Generalized decreased muscle tone	Not recorded
Low muscle tone	Not recorded
Missing part of vertebrae	Not recorded
Missing ribs	Not recorded
Rib fusion	Not recorded
Spastic diplegia	Not recorded
Spastic tetraplegia	Not recorded
Underdeveloped vertebrae	Not recorded
Vertebral fusion	Not recorded

Abnormality of the nervous system

Trait	How often it is seen
Global developmental delay	Always
Agenesis of corpus callosum	Not recorded
Hypothalamic hamartoma	Not recorded
Specific learning disability	Not recorded
Underdevelopment of part of brain called corpus callosum	Not recorded

Abnormality of the genitourinary system

Trait	How often it is seen
Hypospadias	Not recorded
Short penis	Not recorded
Undescended testes	Not recorded

Abnormality of head or neck

Trait	How often it is seen
Abnormally small head	Not recorded
Frontal bossing	Not recorded

Abnormality of the cardiovascular system

Trait	How often it is seen
Hole in heart wall separating two lower heart chambers	Not recorded
Patent ductus arteriosus	Not recorded

Abnormality of the ear

Trait	How often it is seen
Bilateral sensorineural hearing impairment	Always
Sensorineural hearing impairment	Not recorded

Abnormality of the endocrine system

Trait	How often it is seen
Hypogonadotropic hypogonadism	Not recorded
Underdeveloped pituitary gland	Not recorded

Growth abnormality

Trait	How often it is seen
Short stature	Sometimes (5–29%)
Growth delay as children	Not recorded

Abnormality of the digestive system

Trait	How often it is seen
Birth defect in which part of esophagus did not develop	Not recorded

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 SIX6 and how often each is seen. Find out more at hpo.jax.org.

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