Traits

Traits linked to KMT2D

lysine methyltransferase 2D

The Human Phenotype Ontology links 242 traits to KMT2D, 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
Blockage of the rear opening of the nasal cavity	Always
Blocked tear duct	Always
Corners of eye widely separated	Always
Decreased volume of lip	Always
Deformity of the skull	Always
Dimple chin	Always
Downward slanting of the opening between the eyelids	Always
Failure of development of more than six teeth	Always
Full lower lip	Always
High, narrow palate	Always
Limited hair on end of eyebrow	Always
Midface retrusion	Always
Nasal tip, upturned	Always
Receding chin	Always
Short nose	Always
Smooth philtrum	Always
Tented mouth	Always
Wide nose	Always
Broad opening between the eyelids	Very often (80–99%)
Eversion of lateral third of lower eyelids	Very often (80–99%)
High palate	Very often (80–99%)
Highly arched eyebrow	Very often (80–99%)
Long eyelashes	Very often (80–99%)
Short columella	Very often (80–99%)
Wide nasal bridge	Very often (80–99%)
Abnormal dentition	Often (30–79%)
Abnormality of dental shape	Often (30–79%)
Abnormally small head	Often (30–79%)
Bifid uvula	Often (30–79%)
Bilateral blockage of the rear opening of the nasal cavity	Often (30–79%)
Branchial sinus	Often (30–79%)
Central cleft upper lip	Often (30–79%)
Cleft lip	Often (30–79%)
Cleft of the mouth	Often (30–79%)
Cleft palate	Often (30–79%)
Decreased size of tooth	Often (30–79%)
Delayed loss of baby teeth	Often (30–79%)
Depressed nasal bridge	Often (30–79%)
Depressed nasal tip	Often (30–79%)
Failure of development of between one and six teeth	Often (30–79%)
Flat nose	Often (30–79%)
High forehead	Often (30–79%)
Little lower jaw	Often (30–79%)
Pit in front of the ear	Often (30–79%)
Proboscis	Often (30–79%)
Sparse eyebrow	Often (30–79%)
Thin red part of the upper lip	Often (30–79%)
Underdeveloped tissue around nostril	Often (30–79%)
Widely spaced teeth	Often (30–79%)
Absent tear duct	Sometimes (5–29%)
Bad bite	Sometimes (5–29%)
Bell's palsy	Sometimes (5–29%)
Born with teeth	Sometimes (5–29%)
Branchial cyst	Sometimes (5–29%)
Broad philtrum	Sometimes (5–29%)
Bulbous nose	Sometimes (5–29%)
Dental cavities	Sometimes (5–29%)
Downturned corners of mouth	Sometimes (5–29%)
Eye folds	Sometimes (5–29%)
Eyelids stay open	Sometimes (5–29%)
Facial asymmetry	Sometimes (5–29%)
Lip pit	Sometimes (5–29%)
Long, narrow head	Sometimes (5–29%)
Low hairline at back of neck	Sometimes (5–29%)
Low hanging columella	Sometimes (5–29%)
Narrow face	Sometimes (5–29%)
Narrowing of the rear opening of the nasal cavity	Sometimes (5–29%)
Prominent forehead	Sometimes (5–29%)
Skin tag in front of the ear	Sometimes (5–29%)
Tongue tied	Sometimes (5–29%)
Prominent eyelashes	Not recorded

Abnormality of the ear

Trait	How often it is seen
Large earlobe	Always
Prominent ear	Always
Sensorineural hearing impairment	Always
Small ears	Always
Abnormality of the outer ear	Very often (80–99%)
Large ears	Very often (80–99%)
Aplasia of the semicircular canal	Often (30–79%)
Chronic infections of the middle ear	Often (30–79%)
Conductive deafness	Often (30–79%)
Cupped ear	Often (30–79%)
Hearing impairment	Often (30–79%)
Low-set ears	Often (30–79%)
Recurrent middle ear infection	Often (30–79%)
Absent ear canal	Sometimes (5–29%)
Bilateral conductive hearing impairment	Sometimes (5–29%)
Cholesteatoma	Sometimes (5–29%)
Ears rotated toward back of head	Sometimes (5–29%)
Mixed hearing impairment	Sometimes (5–29%)
Overfolded ears	Sometimes (5–29%)
Progressive sensorineural hearing impairment	Sometimes (5–29%)
Severe sensorineural hearing impairment	Sometimes (5–29%)

Abnormality of the nervous system

Trait	How often it is seen
Bilateral tonic-clonic seizure with focal onset	Always
Difficulty articulating speech	Always
Focal impaired awareness seizure	Always
Lateral ventricle dilatation	Always
Lobar holoprosencephaly	Always
Delayed speech and language development	Very often (80–99%)
Global developmental delay	Very often (80–99%)
Intellectual disability	Very often (80–99%)
Neurodevelopmental delay	Very often (80–99%)
Alobar holoprosencephaly	Often (30–79%)
Decrease in size of the outer layer of the brain due to loss of brain cells	Often (30–79%)
Intellectual disability, mild	Often (30–79%)
Motor delay	Often (30–79%)
Too much cerebrospinal fluid in the brain	Often (30–79%)
Ventriculomegaly	Often (30–79%)
Autism spectrum disorder	Sometimes (5–29%)
Communication delay	Sometimes (5–29%)
EEG abnormality	Sometimes (5–29%)
Epilepsy	Sometimes (5–29%)

Abnormality of the genitourinary system

Trait	How often it is seen
Bilateral renal hypoplasia	Always
Renal failure	Always
Undescended testes	Always
Ureteropelvic junction obstruction	Always
Urinary tract abnormalities	Often (30–79%)
Abnormal kidney location	Sometimes (5–29%)
Abnormal localisation of kidneys	Sometimes (5–29%)
Absent/small kidney	Sometimes (5–29%)
Crossed fused renal ectopia	Sometimes (5–29%)
Double ureter	Sometimes (5–29%)
Duplicated collecting system	Sometimes (5–29%)
Hydrocele testis	Sometimes (5–29%)
Hydronephrosis	Sometimes (5–29%)
Hypospadias	Sometimes (5–29%)
Multicystic kidney dysplasia	Sometimes (5–29%)
Underdeveloped penis	Sometimes (5–29%)
Short penis	Not recorded

Abnormality of the cardiovascular system

Trait	How often it is seen
Abnormal cardiac septum morphology	Often (30–79%)
Abnormality of the heart	Often (30–79%)
An opening in the wall separating the top two chambers of the heart	Often (30–79%)
Increased blood pressure in blood vessels of lungs	Often (30–79%)
Narrowing of aorta	Often (30–79%)
Absent thymus	Sometimes (5–29%)
Aortic valve has two leaflets rather than three	Sometimes (5–29%)
Hole in heart wall separating two lower heart chambers	Sometimes (5–29%)
Increased spleen size	Sometimes (5–29%)
Patent ductus arteriosus	Sometimes (5–29%)
Patent foramen ovale	Sometimes (5–29%)
Right ventricular hypertrophy	Sometimes (5–29%)
Interrupted aortic arch	Rarely (1–4%)
Narrowing of aortic valve	Rarely (1–4%)
Scimitar anomaly	Rarely (1–4%)
Underdeveloped left heart	Rarely (1–4%)

Abnormality of the eye

Trait	How often it is seen
Abnormally close eyes	Always
Drooping of both upper eyelids	Always
Blue outer white part of eyeball	Often (30–79%)
Cross-eyed	Often (30–79%)
Drooping upper eyelid	Often (30–79%)
Marcus Gunn jaw winking synkinesis	Often (30–79%)
Peters anomaly	Often (30–79%)
Abnormally small eyeball	Sometimes (5–29%)
Cat eye	Sometimes (5–29%)
Cornea of eye less than 10mm in diameter	Sometimes (5–29%)
Involuntary, rapid, rhythmic eye movements	Sometimes (5–29%)
Lazy eye	Sometimes (5–29%)
Notched pupil	Sometimes (5–29%)
Optic disc coloboma	Sometimes (5–29%)
Wide-set eyes	Sometimes (5–29%)
Optic nerve hypoplasia	Rarely (1–4%)

Abnormality of limbs

Trait	How often it is seen
Curvature of finger	Always
Short 5th finger	Always
Short fingers or toes	Always
Short middle bone of finger	Very often (80–99%)
Curvature of little finger	Often (30–79%)
Prominent fingertip pads	Often (30–79%)
Single transverse palmar crease	Often (30–79%)
Broad big toe	Sometimes (5–29%)
Curvature of digit	Sometimes (5–29%)
Dislocated hip since birth	Sometimes (5–29%)
Hip dislocation	Sometimes (5–29%)
Small hand	Sometimes (5–29%)

Abnormality of the digestive system

Trait	How often it is seen
Anteriorly placed anus	Always
Feeding difficulties in infancy	Very often (80–99%)
Feeding difficulties	Often (30–79%)
Absent anus	Sometimes (5–29%)
Acid reflux	Sometimes (5–29%)
Extra kidney	Sometimes (5–29%)
Prolonged yellowing of skin in newborn	Sometimes (5–29%)
Anorectal anomaly	Rarely (1–4%)
Anoperineal fistula	Not recorded
Intestinal malrotation	Not recorded
Malabsorption	Not recorded
Narrowing of anal opening	Not recorded

Abnormality of the musculoskeletal system

Trait	How often it is seen
Abnormal formation of the hip	Always
Butterfly vertebrae	Always
Thoracic scoliosis	Always
Abnormal vertebral body morphology	Very often (80–99%)
Missing part of vertebrae	Very often (80–99%)
Vertebral clefting	Very often (80–99%)
Decreased muscle tone in infant	Often (30–79%)
Double-Jointed	Often (30–79%)
Joint dislocation	Often (30–79%)
Low muscle tone	Often (30–79%)
Scoliosis	Often (30–79%)
Congenital diaphragmatic hernia	Sometimes (5–29%)

Abnormality of the integument

Trait	How often it is seen
Abnormal fingerprints	Very often (80–99%)
Spinal dimple	Often (30–79%)
Excessive hair growth	Sometimes (5–29%)
Poor nail formation	Sometimes (5–29%)
Small nail	Sometimes (5–29%)
Sparse hair	Sometimes (5–29%)
Pilomatrixoma	Rarely (1–4%)
Birthmark	Not recorded
Excessive hairiness	Not recorded

Abnormality of the endocrine system

Trait	How often it is seen
Decreased parathyroid hormone secretion	Always
Decreased response to growth hormone stimulation test	Always
Underactive thyroid	Always
Premature breast development	Often (30–79%)
Underactive thyroid gland from birth	Often (30–79%)
Early onset of puberty	Sometimes (5–29%)
Reduced circulating growth hormone concentration	Sometimes (5–29%)
Small thyroid gland	Sometimes (5–29%)

Growth abnormality

Trait	How often it is seen
Growth delay	Always
Obesity	Always
Prenatal growth deficiency	Always
Growth delay as children	Very often (80–99%)
Severe short stature	Very often (80–99%)
Absent pubertal growth spurt	Often (30–79%)
Faltering weight	Often (30–79%)
Short stature	Often (30–79%)

Abnormality of blood and blood-forming tissues

Trait	How often it is seen
Decreased memory B cell proportion	Very often (80–99%)
Decreased CD4+ memory T cell proportion	Often (30–79%)
Autoimmune thrombocytopenia	Not recorded
Hemolytic anemia	Not recorded

Abnormality of the immune system

Trait	How often it is seen
Unusual bronchiolitis	Always
Recurrent infections	Often (30–79%)
Recurrent respiratory infections	Sometimes (5–29%)
Recurrent aspiration pneumonia	Not recorded

Abnormal cellular phenotype

Trait	How often it is seen
Decreased circulating IgA concentration	Often (30–79%)
Decreased circulating IgG2 concentration	Sometimes (5–29%)
Decreased circulating total IgG concentration	Sometimes (5–29%)

Laboratory abnormality

Trait	How often it is seen
Low blood sugar	Sometimes (5–29%)
Unconjugated hyperbilirubinemia	Sometimes (5–29%)
Hyperinsulinemic hypoglycemia	Rarely (1–4%)

Abnormality of prenatal development or birth

Trait	How often it is seen
High levels of amniotic fluid	Often (30–79%)
Echogenic fetal bowel	Sometimes (5–29%)

Abnormality of the breast

Trait	How often it is seen
Absent nipple	Often (30–79%)
Small nipples	Often (30–79%)

Abnormality of the respiratory system

Trait	How often it is seen
Subpleural honeycombing	Always
Type II pneumocyte hyperplasia	Always

Abnormality of the voice

Trait	How often it is seen
Weak cry	Always

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 KMT2D and how often each is seen. Find out more at hpo.jax.org.

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