Traits

Traits linked to PNKP

polynucleotide kinase 3'-phosphatase

The Human Phenotype Ontology links 103 traits to PNKP, by body system: features seen in people with one of the gene's rare conditions.

PNKP

Abnormality of the nervous system

Trait	How often it is seen
Absent reflexes	Always
Ataxia	Always
Degeneration of cerebellum	Always
Epilepsy	Always
Global developmental delay	Always
More active than typical	Always
Peripheral neuropathy	Always
Ventriculomegaly	Always
Epileptic encephalopathy	Very often (80–99%)
Focal motor seizure	Very often (80–99%)
Generalized myoclonic seizure	Very often (80–99%)
Intellectual disability	Very often (80–99%)
Cognitive impairment	Often (30–79%)
Difficulty sleeping	Often (30–79%)
Dystonia	Often (30–79%)
EEG abnormality	Often (30–79%)
EEG with burst suppression	Often (30–79%)
Focal tonic seizure	Often (30–79%)
Hypsarrhythmia	Often (30–79%)
Impaired vibratory sensation	Often (30–79%)
Increased reflexes	Often (30–79%)
Lethargy	Often (30–79%)
Abnormal pyramidal sign	Sometimes (5–29%)
Atrophy/Degeneration affecting the brainstem	Sometimes (5–29%)
Autism spectrum disorder	Sometimes (5–29%)
Balance impairment	Sometimes (5–29%)
Brief seizures with staring spells	Sometimes (5–29%)
Choreoathetosis	Sometimes (5–29%)
Decreased reflex response	Sometimes (5–29%)
Delayed myelination	Sometimes (5–29%)
Difficulty articulating speech	Sometimes (5–29%)
Difficulty making arithmetical calculations	Sometimes (5–29%)
Diffuse cerebral atrophy	Sometimes (5–29%)
Diffuse white matter abnormalities	Sometimes (5–29%)
Disorder of involuntary muscle movements	Sometimes (5–29%)
EEG with spike-wave complexes	Sometimes (5–29%)
Episodic ataxia	Sometimes (5–29%)
Febrile seizure (within the age range of 3 months to 6 years)	Sometimes (5–29%)
Fewer and broader ridges in brain	Sometimes (5–29%)
Generalized clonic seizure	Sometimes (5–29%)
Generalized tonic seizure	Sometimes (5–29%)
Grand mal seizures	Sometimes (5–29%)
Infantile spasms	Sometimes (5–29%)
Jerking	Sometimes (5–29%)
Loss of developmental milestones	Sometimes (5–29%)
Nerve damage causing decreased feeling and movement	Sometimes (5–29%)
Reading disability	Sometimes (5–29%)
Seizure affecting one half of brain	Sometimes (5–29%)
Self-injurious behavior	Sometimes (5–29%)
Short attention span	Sometimes (5–29%)
Somatic sensory dysfunction	Sometimes (5–29%)
Sudden loss of muscle tone	Sometimes (5–29%)
Tremor	Sometimes (5–29%)
Underdevelopment of part of brain called corpus callosum	Sometimes (5–29%)
Uni- and bilateral multifocal epileptiform discharges	Sometimes (5–29%)
Decreased motor nerve conduction velocity	Not recorded
Decreased sensation in extremities	Not recorded
Intellectual disability, severe	Not recorded
Motor delay	Not recorded
Paralysis of all four limbs	Not recorded
Simplified gyral pattern	Not recorded

Abnormality of the musculoskeletal system

Trait	How often it is seen
Decreased muscle tone in infant	Often (30–79%)
Poor head control	Often (30–79%)
Involuntary muscle stiffness, contraction, or spasm	Sometimes (5–29%)
Kyphoscoliosis	Sometimes (5–29%)
Muscular dystrophy	Sometimes (5–29%)
Progressive distal muscular atrophy	Sometimes (5–29%)
Distal muscle wasting	Not recorded
Low muscle tone	Not recorded
Muscle degeneration	Not recorded
Weakness of outermost muscles	Not recorded

Abnormality of head or neck

Trait	How often it is seen
Abnormally small head	Always
Cleft palate	Rarely (1–4%)
Depressed nasal bridge	Rarely (1–4%)
Nasal tip, upturned	Rarely (1–4%)
Sloping forehead	Rarely (1–4%)
Progressively abnormally small cranium	Not recorded

Abnormality of limbs

Trait	How often it is seen
Abnormalities of the toes	Sometimes (5–29%)
Distal lower limb muscle weakness	Sometimes (5–29%)
High-arched foot	Sometimes (5–29%)
Broad finger	Rarely (1–4%)
Short finger	Rarely (1–4%)
Wide toe bones	Rarely (1–4%)

Abnormality of the digestive system

Trait	How often it is seen
Feeding difficulties	Often (30–79%)
Poor suck	Often (30–79%)
Poor swallowing	Often (30–79%)
Umbilical hernia	Rarely (1–4%)

Abnormality of the eye

Trait	How often it is seen
Oculomotor apraxia	Always
Abnormal saccadic eye movements	Sometimes (5–29%)
Cross-eyed	Rarely (1–4%)

Abnormality of the genitourinary system

Trait	How often it is seen
Renal dysplasia	Rarely (1–4%)
Short penis	Rarely (1–4%)
Ureterocele	Rarely (1–4%)

Laboratory abnormality

Trait	How often it is seen
Elevated circulating alpha-fetoprotein concentration	Often (30–79%)
Elevated serum cholesterol	Often (30–79%)
Low albumin	Often (30–79%)

Abnormality of the cardiovascular system

Trait	How often it is seen
Hole in heart wall separating two lower heart chambers	Rarely (1–4%)
Spider veins	Not recorded

Growth abnormality

Trait	How often it is seen
Obesity	Often (30–79%)
Faltering weight	Rarely (1–4%)

Abnormality of the endocrine system

Trait	How often it is seen
Early onset of puberty	Rarely (1–4%)

Abnormality of the immune system

Trait	How often it is seen
Recurrent respiratory infections	Often (30–79%)

Abnormality of the integument

Trait	How often it is seen
Absent thumbnail	Rarely (1–4%)

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

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