Traits

Traits linked to MSX2

msh homeobox 2

The Human Phenotype Ontology links 44 traits to MSX2, by body system: features seen in people with one of the gene's rare conditions.

Abnormality of head or neck

Trait	How often it is seen
Deformity of the skull	Always
Holes in parietal bones	Always
Abnormal posterior cranial fossa morphology	Sometimes (5–29%)
Bicoronal synostosis	Sometimes (5–29%)
Big calvaria	Sometimes (5–29%)
Broad head shape	Sometimes (5–29%)
Cleft soft palate	Sometimes (5–29%)
Extra bones within cranial sutures	Sometimes (5–29%)
Extra teeth	Sometimes (5–29%)
Metopic synostosis	Sometimes (5–29%)
Scalp tenderness	Sometimes (5–29%)
Tall shaped head	Sometimes (5–29%)
Triangular head shape	Sometimes (5–29%)
Unicoronal synostosis	Sometimes (5–29%)
Brain tissue sticks out through back of skull	Rarely (1–4%)
Cleft lip	Rarely (1–4%)
Cleft palate	Rarely (1–4%)
Congenital craniofacial dysostosis	Rarely (1–4%)
Cleft upper lip	Not recorded
Cranium bifidum occultum	Not recorded
Encephalocele	Not recorded
Frontal bossing	Not recorded
Widely patent fontanelles and sutures	Not recorded

Abnormality of the eye

Trait	How often it is seen
Abnormally close eyes	Sometimes (5–29%)
Blue outer white part of eyeball	Sometimes (5–29%)
Close sighted	Sometimes (5–29%)
Farsightedness	Sometimes (5–29%)
Partial loss of field of vision	Sometimes (5–29%)

Abnormality of the nervous system

Trait	How often it is seen
Epilepsy	Sometimes (5–29%)
Headache	Sometimes (5–29%)
Encephalomalacia	Rarely (1–4%)
Intellectual disability	Rarely (1–4%)
Myelomeningocele	Rarely (1–4%)

Abnormality of limbs

Trait	How often it is seen
Finger-like thumb	Sometimes (5–29%)
Short fingers or toes	Sometimes (5–29%)
Broad thumb	Rarely (1–4%)

Abnormality of the cardiovascular system

Trait	How often it is seen
Venous malformation	Sometimes (5–29%)
Abnormal cerebral vein morphology	Rarely (1–4%)

Abnormality of the integument

Trait	How often it is seen
Focal absence of scalp tissue	Rarely (1–4%)
Dermoid cyst	Not recorded

Abnormality of the musculoskeletal system

Trait	How often it is seen
Multiple exostoses	Rarely (1–4%)
Short collarbone	Rarely (1–4%)

Abnormality of the digestive system

Trait	How often it is seen
Vomiting	Sometimes (5–29%)

Abnormality of the ear

Trait	How often it is seen
Small ears	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 MSX2 and how often each is seen. Find out more at hpo.jax.org.

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