- Small scrotum (HP:0000046): Apparently small scrotum for age. Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:2234)
- Hypogonadism (HP:0000135): A decreased functionality of the gonad. Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:2234)
- Decreased fertility (HP:0000144). Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:2234)
- Atypical behavior (HP:0000708): Atypical behavior is an abnormality in a person's actions that can be controlled or modulated by the will of the individual. While abnormal behaviors can be difficult to control, they are distinct from other abnormal actions that cannot be affected by the individual's will. Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:2234)
- Gynecomastia (HP:0000771): Abnormal development of large mammary glands in males resulting in breast enlargement. Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:2234)
- 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:2234)
- Hemivertebrae (HP:0002937): Absence of one half of the vertebral body. Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:2234)
- Abnormal vertebral body morphology (HP:0003312): Abnormal form of vertebral body, which is the central cylindrical portion of the vertebra that together with other structures such as the vertebral arch, pedicles, laminae, spinous process, transverse processes, and articular facets makes up a vertebra. Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:2234)
- Eunuchoid habitus (HP:0003782): A body habitus that is tall, slim and underweight, with long legs and long arms (i.e., arm span exceeds height by 5 cm or more). Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:2234)
- Type II diabetes mellitus (HP:0005978): A type of diabetes mellitus initially characterized by insulin resistance and hyperinsulinemia and subsequently by glucose interolerance and hyperglycemia. Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:2234)
- Decreased testicular size (HP:0008734): Reduced volume of the testicle (the male gonad). Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:2234)
- Hypoplasia of penis (HP:0008736). Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:2234)
- Short neck (HP:0000470): Diminished length of the neck. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:2234)
- Abnormal rib morphology (HP:0000772): An anomaly of the rib. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:2234)
- Abnormality of the thyroid gland (HP:0000820): An abnormality of the thyroid gland. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:2234)
- Obesity (HP:0001513): Accumulation of substantial excess body fat. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:2234)
- Sparse body hair (HP:0002231): Sparseness of the body hair. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:2234)
- 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:2234)
- Abnormality of the humeroulnar joint (HP:0100745): An anomaly of the joint between the trochlear notch of ulna and the trochlea of humerus, which is part of the elbow joint. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:2234)
These phenotypes are associated with the disease Male hypergonadotropic hypogonadism-intellectual disability-skeletal anomalies syndrome (ORPHA:2234).