- Spastic paraplegia (HP:0001258): Complete loss of the ability to move the lower limbs accompanied by spasticity of the lower limbs. Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:306617)
- Mild intellectual disability (HP:0001256): Mild intellectual disability (ID) is defined as a type of ID characterized by mildly sub-average adaptive functioning and intellectual functioning, with an intelligence quotient (IQ) the range of 50-69. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:306617)
- Moderate intellectual disability (HP:0002342): Moderate intellectual disability (ID) is defined as a type of ID characterized by moderately sub-average adaptive functioning and intellectual functioning, with an intelligence quotient (IQ) the range of 35-49. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:306617)
- Upper motor neuron dysfunction (HP:0002493): A functional anomaly of the upper motor neuron. The upper motor neurons are neurons of the primary motor cortex which project to the brainstem and spinal chord via the corticonuclear, corticobulbar and corticospinal (pyramidal) tracts. They are involved in control of voluntary movements. Dysfunction leads to weakness, impairment of fine motor movements, spasticity, hyperreflexia and abnormal pyramidal signs. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:306617)
- Lower limb muscle weakness (HP:0007340): Weakness of the muscles of the legs. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:306617)
- Cognitive impairment (HP:0100543): Abnormal cognition is characterized by deficits in thinking, reasoning, or remembering. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:306617)
- Adducted thumb (HP:0001181): In the resting position, the tip of the thumb is on, or near, the palm, close to the base of the fourth or fifth finger. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:306617)
- Ataxia (HP:0001251): Ataxia refers to impaired coordination of voluntary muscle movement. Cerebellar ataxia refers to ataxia due to dysfunction of the cerebellum. This causes a variety of elementary neurological deficits including asynergy (lack of coordination between muscles, limbs and joints), dysmetria (lack of ability to judge distances that can lead to under- or overshoot in grasping movements), and dysdiadochokinesia (inability to perform rapid movements requiring antagonizing muscle groups to be switched on and off repeatedly). Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:306617)
- Mental deterioration (HP:0001268): Loss of previously present mental abilities, generally in adults. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:306617)
These phenotypes are associated with the disease X-linked complicated spastic paraplegia type 1 (ORPHA:306617).