Traits

Traits linked to MSX1

msh homeobox 1

The Human Phenotype Ontology links 84 traits to MSX1, 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
Absence of adult teeth	Always
Failure of development of more than six teeth	Always
Abnormal dentition	Very often (80–99%)
Abnormality of dental shape	Very often (80–99%)
Abnormality of tooth eruption	Very often (80–99%)
Chewing difficulties	Very often (80–99%)
Cone shaped tooth	Very often (80–99%)
Delayed eruption of teeth	Very often (80–99%)
Failure of development of between one and six teeth	Very often (80–99%)
Lip pit	Very often (80–99%)
Abnormal of nasal shape	Often (30–79%)
Abnormality of masticatory muscle	Often (30–79%)
Abnormality of the face	Often (30–79%)
Absence of premolar	Often (30–79%)
Absence of six year molar	Often (30–79%)
Absence of upper lateral incisor	Often (30–79%)
Absent central incisor	Often (30–79%)
Bad bite	Often (30–79%)
Cleft of the mouth	Often (30–79%)
Cleft palate	Often (30–79%)
Decreased length of dental roots	Often (30–79%)
Decreased size of tooth	Often (30–79%)
Delayed eruption of permanent teeth	Often (30–79%)
Disturbance of facial expression	Often (30–79%)
Drooping lower lip	Often (30–79%)
Non-midline cleft of the upper lip	Often (30–79%)
One sided cleft palate	Often (30–79%)
Velopharyngeal incompetence	Often (30–79%)
Widely spaced teeth	Often (30–79%)
Abnormal number of permanent teeth	Sometimes (5–29%)
Abnormality of canine	Sometimes (5–29%)
Abnormality of septum of nose	Sometimes (5–29%)
Abnormality of shape of baby molar	Sometimes (5–29%)
Absence of lower premolar	Sometimes (5–29%)
Both sided cleft lip	Sometimes (5–29%)
Decreased size of teeth	Sometimes (5–29%)
Extra upper front tooth	Sometimes (5–29%)
Hole in roof of mouth	Sometimes (5–29%)
Increased size of tooth	Sometimes (5–29%)
Missing lateral incisor	Sometimes (5–29%)
Outward turned lips	Sometimes (5–29%)
Peg-shaped maxillary lateral incisors	Sometimes (5–29%)
Right and left cleft palate	Sometimes (5–29%)
Short face	Sometimes (5–29%)
Taurodontia	Sometimes (5–29%)
Thin dental enamel	Sometimes (5–29%)
Decreased size of maxilla	Rarely (1–4%)
Absence of a tooth	Not recorded
Cleft upper lip	Not recorded
Decreased width of baby teeth	Not recorded

Abnormality of the integument

Trait	How often it is seen
Small fifth toenail	Always
Spoon-shaped nails	Always
Abnormal fingernails	Very often (80–99%)
Abnormality of the nail	Very often (80–99%)
Brittle nails	Very often (80–99%)
Ridged fingernail	Very often (80–99%)
Small fingernail	Very often (80–99%)
Thin toenail	Very often (80–99%)
Underdeveloped toenails	Very often (80–99%)
Fine hair	Often (30–79%)
Grooved nails	Not recorded
Nail pits	Not recorded

Abnormality of the digestive system

Trait	How often it is seen
Feeding difficulties in infancy	Often (30–79%)
Oral-pharyngeal dysphagia	Often (30–79%)
Poor suck	Often (30–79%)
Malnutrition	Sometimes (5–29%)
Poor swallowing	Sometimes (5–29%)
Umbilical hernia	Rarely (1–4%)

Abnormality of the nervous system

Trait	How often it is seen
Delayed speech and language development	Often (30–79%)
Speech articulation difficulties	Often (30–79%)
Behavioral abnormality	Sometimes (5–29%)
Low self-esteem	Sometimes (5–29%)
Specific learning disability	Rarely (1–4%)

Abnormality of the ear

Trait	How often it is seen
Chronic infections of the middle ear	Often (30–79%)
Recurrent middle ear infection	Often (30–79%)
Abnormal Eustachian tube morphology	Sometimes (5–29%)
Conductive deafness	Sometimes (5–29%)

Abnormality of limbs

Trait	How often it is seen
Club feet	Rarely (1–4%)

Abnormality of prenatal development or birth

Trait	How often it is seen
High levels of amniotic fluid	Rarely (1–4%)

Abnormality of the cardiovascular system

Trait	How often it is seen
All organs on wrong side of body	Rarely (1–4%)

Abnormality of the genitourinary system

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

Abnormality of the respiratory system

Trait	How often it is seen
Abnormal pattern of respiration	Often (30–79%)

Abnormality of the voice

Trait	How often it is seen
Nasal speech	Often (30–79%)

Growth abnormality

Trait	How often it is seen
Small for gestational age	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 MSX1 and how often each is seen. Find out more at hpo.jax.org.

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