Traits

Traits linked to SOX2

SRY-box transcription factor 2

The Human Phenotype Ontology links 73 traits to SOX2, 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
Optic nerve aplasia	Always
Abnormal choroid morphology	Very often (80–99%)
Abnormally small eyeball	Very often (80–99%)
Absence of eyeballs	Very often (80–99%)
Cross-eyed	Very often (80–99%)
Glaucoma	Very often (80–99%)
Optic nerve hypoplasia	Very often (80–99%)
Septo-optic dysplasia	Very often (80–99%)
Severe farsightedness	Very often (80–99%)
Visual impairment	Very often (80–99%)
Involuntary, rapid, rhythmic eye movements	Often (30–79%)
Visual loss	Often (30–79%)
Abnormal retinal pigmentation	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%)

Abnormality of the nervous system

Trait	How often it is seen
Global developmental delay	Always
Absent septum pellucidum	Often (30–79%)
Agenesis of corpus callosum	Often (30–79%)
Epilepsy	Often (30–79%)
Paralysis or weakness of one side of body	Often (30–79%)
Absent/small cerebellum	Sometimes (5–29%)
Autism	Sometimes (5–29%)
Difficulty sleeping	Sometimes (5–29%)
Extreme thirst	Sometimes (5–29%)
Holoprosencephaly	Sometimes (5–29%)
Intellectual disability	Sometimes (5–29%)
Too much cerebrospinal fluid in the brain	Sometimes (5–29%)
Hypothalamic hamartoma	Not recorded
Specific learning disability	Not recorded
Underdevelopment of part of brain called corpus callosum	Not recorded

Abnormality of the musculoskeletal system

Trait	How often it is seen
11 pairs of ribs	Sometimes (5–29%)
Abnormal vertebral morphology	Sometimes (5–29%)
Missing part of vertebrae	Sometimes (5–29%)
Butterfly vertebrae	Not recorded
Extra ribs	Not recorded
Generalized decreased muscle tone	Not recorded
Low muscle tone	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 head or neck

Trait	How often it is seen
Cleft palate	Often (30–79%)
Lost smell	Sometimes (5–29%)
Abnormally small head	Not recorded
Frontal bossing	Not recorded

Abnormality of the endocrine system

Trait	How often it is seen
Abnormality of the hypothalamus-pituitary axis	Often (30–79%)
Underdeveloped pituitary gland	Often (30–79%)
Diabetes insipidus	Sometimes (5–29%)
Hypogonadotropic hypogonadism	Not recorded

Abnormality of the genitourinary system

Trait	How often it is seen
Underdeveloped penis	Often (30–79%)
Undescended testes	Often (30–79%)
Hypospadias	Sometimes (5–29%)
Short penis	Not recorded

Growth abnormality

Trait	How often it is seen
Short stature	Often (30–79%)
Growth delay	Sometimes (5–29%)
Obesity	Sometimes (5–29%)
Growth delay as children	Not recorded

Abnormality of the cardiovascular system

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

Abnormality of the digestive system

Trait	How often it is seen
Abnormal connection between trachea and esophagus	Very often (80–99%)
Birth defect in which part of esophagus did not develop	Very often (80–99%)
Constipation	Sometimes (5–29%)

Abnormality of the ear

Trait	How often it is seen
Bilateral sensorineural hearing impairment	Always
Hearing impairment	Often (30–79%)
Sensorineural hearing impairment	Sometimes (5–29%)

Abnormality of the integument

Trait	How often it is seen
Decreased ability to sweat	Sometimes (5–29%)
Dry skin	Sometimes (5–29%)

Constitutional symptom

Trait	How often it is seen
Fatigue	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 SOX2 and how often each is seen. Find out more at hpo.jax.org.

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