- Cryptorchidism (HP:0000028): Testis in inguinal canal. That is, absence of one or both testes from the scrotum owing to failure of the testis or testes to descend through the inguinal canal to the scrotum. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:85274)
- Micropenis (HP:0000054): Abnormally small penis. At birth, the normal penis is about 3 cm (stretched length from pubic tubercle to tip of penis) with micropenis less than 2.0-2.5 cm. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:85274)
- Hypogonadism (HP:0000135): A decreased functionality of the gonad. Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:85274)
- Visual loss (HP:0000572): Loss of visual acuity (implying that vision was better at a certain time point in life). Otherwise the term reduced visual acuity should be used (or a subclass of that). Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:85274)
- Tooth malposition (HP:0000692): Abnormal alignment, positioning, or spacing of the teeth, i.e., misaligned teeth. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:85274)
- Tapered finger (HP:0001182): The gradual reduction in girth of the finger from proximal to distal. Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:85274)
- Intellectual disability (HP:0001249): The term intellectual disability or intellectual developmental disorder is used to describe significantly sub-average intellectual and adaptive functioning based on clinical assessment and as measured by individually administered, appropriately normed, standardized and validated tests of intellectual functioning and adaptive behavior, with onset during the developmental period from infancy through adolescence. Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:85274)
- Muscle weakness (HP:0001324): Reduced strength of muscles. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:85274)
- Obesity (HP:0001513): Accumulation of substantial excess body fat. Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:85274)
- Sparse body hair (HP:0002231): Sparseness of the body hair. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:85274)
- 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: Very frequent (HP:0040281). (ORPHA:85274)
- Incomprehensible speech (HP:0002546). Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:85274)
- Short stature (HP:0004322): A height below that which is expected according to age and gender norms. Although there is no universally accepted definition of short stature, many refer to "short stature" as height more than 2 standard deviations below the mean for age and gender (or below the 3rd percentile for age and gender dependent norms). Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:85274)
- Abnormal dental morphology (HP:0006482): An abnormality of the morphology of the tooth. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:85274)
- Hypoplasia of penis (HP:0008736). Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:85274)
These phenotypes are associated with the disease Syndromic X-linked intellectual disability 7 (ORPHA:85274).