Traits

Traits linked to SMCHD1

structural maintenance of chromosomes flexible hinge domain containing 1

The Human Phenotype Ontology links 90 traits to SMCHD1, 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
Abnormal dental position	Very often (80–99%)
Abnormality of the midface	Very often (80–99%)
Absent nose	Very often (80–99%)
Expressionless face	Very often (80–99%)
Hyposmia	Very often (80–99%)
Lost smell	Very often (80–99%)
Missing nostrils	Very often (80–99%)
Mono nostril	Very often (80–99%)
Unerupted adult teeth	Very often (80–99%)
Blockage of the rear opening of the nasal cavity	Often (30–79%)
Decreased facial expression	Often (30–79%)
Decreased nasal size	Often (30–79%)
Decreased size of maxilla	Often (30–79%)
Eyelids stay open at night	Often (30–79%)
High palate	Often (30–79%)
Midface retrusion	Often (30–79%)
Paranasal sinus hypoplasia	Often (30–79%)
Pink eye	Often (30–79%)
Unopened tear duct	Often (30–79%)
Weakness of facial musculature	Often (30–79%)
Bad bite	Sometimes (5–29%)
Bell's palsy	Sometimes (5–29%)
Bifid uvula	Sometimes (5–29%)
Cleft lip	Sometimes (5–29%)
Cleft palate	Sometimes (5–29%)
Dacryocystocele	Sometimes (5–29%)
Decreased size of teeth	Sometimes (5–29%)
Monobrow	Sometimes (5–29%)
Submucous cleft hard palate	Sometimes (5–29%)

Abnormality of the eye

Trait	How often it is seen
Clouding of the lens of the eye	Very often (80–99%)
Abnormally small eyeball	Often (30–79%)
Absence of eyeballs	Often (30–79%)
Blindness	Often (30–79%)
Cat eye	Often (30–79%)
Corneal inflammation	Often (30–79%)
Lazy eye	Often (30–79%)
Notched pupil	Often (30–79%)
Visual loss	Often (30–79%)
Optic atrophy	Sometimes (5–29%)
Retinal detachment	Sometimes (5–29%)
Serous retinal detachment	Sometimes (5–29%)
Wide-set eyes	Not recorded

Abnormality of the musculoskeletal system

Trait	How often it is seen
Muscle degeneration	Very often (80–99%)
Progressive muscle weakness	Very often (80–99%)
Prominent swayback	Very often (80–99%)
Abdominal wall muscle weakness	Often (30–79%)
Beevor's sign	Often (30–79%)
Camptocormia	Often (30–79%)
EMG: myopathic abnormalities	Often (30–79%)
Frequent falls	Often (30–79%)
Funnel chest	Often (30–79%)
Scoliosis	Often (30–79%)
Straight collarbone	Often (30–79%)
Wasting of pec muscles	Often (30–79%)
Scapulohumeral muscular dystrophy	Not recorded

Abnormality of the genitourinary system

Trait	How often it is seen
Underdeveloped penis	Very often (80–99%)
Underdevelopment of external reproductive organs	Very often (80–99%)
Undescended testes	Often (30–79%)
Hypospadias	Sometimes (5–29%)
Small labia majora	Sometimes (5–29%)
Primary amenorrhea	Not recorded
Short penis	Not recorded

Abnormality of the ear

Trait	How often it is seen
Sensorineural hearing impairment	Often (30–79%)
Absent ear canal	Sometimes (5–29%)
Conductive deafness	Sometimes (5–29%)
Hearing impairment	Sometimes (5–29%)
Abnormally shaped ears	Rarely (1–4%)
Absent tragus	Rarely (1–4%)

Abnormality of limbs

Trait	How often it is seen
Winged shoulder blade	Always
Distal upper limb muscle weakness	Often (30–79%)
Foot drop	Often (30–79%)
Limb-girdle muscle weakness	Often (30–79%)
Pelvic girdle muscle weakness	Sometimes (5–29%)

Abnormality of the nervous system

Trait	How often it is seen
Hypoplasia of the olfactory bulb	Very often (80–99%)
Abnormal gait	Often (30–79%)
High stepping	Often (30–79%)
Epilepsy	Sometimes (5–29%)
Intellectual disability	Sometimes (5–29%)

Abnormality of the cardiovascular system

Trait	How often it is seen
Abnormality of retina blood vessels	Often (30–79%)
Complete right bundle branch block	Often (30–79%)
Supraventricular arrhythmia	Sometimes (5–29%)

Abnormality of the digestive system

Trait	How often it is seen
Inguinal hernia	Very often (80–99%)
Belly sticks out	Often (30–79%)

Abnormality of the endocrine system

Trait	How often it is seen
Decreased activity of gonads	Very often (80–99%)
Hypogonadotropic hypogonadism	Often (30–79%)

Abnormality of the respiratory system

Trait	How often it is seen
Stiff lung or chest wall causing decreased lung volume	Often (30–79%)
Respiratory function loss	Sometimes (5–29%)

Abnormality of the breast

Trait	How often it is seen
Enlarged male breast	Often (30–79%)

Constitutional symptom

Trait	How often it is seen
Chronic pain	Often (30–79%)

Laboratory abnormality

Trait	How often it is seen
Elevated blood creatine phosphokinase	Very often (80–99%)

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 SMCHD1 and how often each is seen. Find out more at hpo.jax.org.

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