- Male hypogonadism (HP:0000026, a Human Phenotype Ontology term): Decreased functionality of the male gonad, i.e., of the testis, with reduced spermatogenesis or testosterone synthesis. Evidence: TAS. Frequency: Very frequent (HP:0040281, a Human Phenotype Ontology term). (ORPHA:163971)
- Cryptorchidism (HP:0000028, a Human Phenotype Ontology term): 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: Very frequent (HP:0040281, a Human Phenotype Ontology term). (ORPHA:163971)
- Hypospadias (HP:0000047, a Human Phenotype Ontology term): Abnormal position of urethral meatus on the ventral penile shaft (underside) characterized by displacement of the urethral meatus from the tip of the glans penis to the ventral surface of the penis, scrotum, or perineum. Evidence: TAS. Frequency: Occasional (HP:0040283, a Human Phenotype Ontology term). (ORPHA:163971)
- Microcephaly (HP:0000252, a Human Phenotype Ontology term): Head circumference below 2 standard deviations below the mean for age and gender. Evidence: TAS. Frequency: Frequent (HP:0040282, a Human Phenotype Ontology term). (ORPHA:163971)
- Prominent supraorbital ridges (HP:0000336, a Human Phenotype Ontology term): Greater than average forward and/or lateral protrusion of the supraorbital portion of the frontal bones. Evidence: TAS. Frequency: Very frequent (HP:0040281, a Human Phenotype Ontology term). (ORPHA:163971)
- Macrotia (HP:0000400, a Human Phenotype Ontology term): Median longitudinal ear length greater than two standard deviations above the mean and median ear width greater than two standard deviations above the mean (objective); or, apparent increase in length and width of the pinna (subjective). Evidence: TAS. Frequency: Very frequent (HP:0040281, a Human Phenotype Ontology term). (ORPHA:163971)
- Prominent nasal bridge (HP:0000426, a Human Phenotype Ontology term): Anterior positioning of the nasal root in comparison to the usual positioning for age. Evidence: TAS. Frequency: Very frequent (HP:0040281, a Human Phenotype Ontology term). (ORPHA:163971)
- Deeply set eye (HP:0000490, a Human Phenotype Ontology term): An eye that is more deeply recessed into the plane of the face than is typical. Evidence: TAS. Frequency: Very frequent (HP:0040281, a Human Phenotype Ontology term). (ORPHA:163971)
- Psychosis (HP:0000709, a Human Phenotype Ontology term): A condition characterized by changes in personality and thought patterns, often accompanied by hallucinations and delusional beliefs, is known as psychosis. Evidence: TAS. Frequency: Occasional (HP:0040283, a Human Phenotype Ontology term). (ORPHA:163971)
- Hypergonadotropic hypogonadism (HP:0000815, a Human Phenotype Ontology term): Reduced function of the gonads (testes in males or ovaries in females) associated with excess pituitary gonadotropin secretion and resulting in delayed sexual development and growth delay. Evidence: TAS. Frequency: Very frequent (HP:0040281, a Human Phenotype Ontology term). (ORPHA:163971)
- Increased circulating gonadotropin level (HP:0000837, a Human Phenotype Ontology term): Overproduction of gonadotropins (FSH, LH) by the anterior pituitary gland. Evidence: TAS. Frequency: Very frequent (HP:0040281, a Human Phenotype Ontology term). (ORPHA:163971)
- Delayed skeletal maturation (HP:0002750, a Human Phenotype Ontology term): A decreased rate of skeletal maturation. Delayed skeletal maturation can be diagnosed on the basis of an estimation of the bone age from radiographs of specific bones in the human body. Evidence: TAS. Frequency: Very frequent (HP:0040281, a Human Phenotype Ontology term). (ORPHA:163971)
- Clinodactyly of the 5th finger (HP:0004209, a Human Phenotype Ontology term): Clinodactyly refers to a bending or curvature of the fifth finger in the radial direction (i.e., towards the 4th finger). Evidence: TAS. Frequency: Very frequent (HP:0040281, a Human Phenotype Ontology term). (ORPHA:163971)
- Mild intellectual disability (HP:0001256, a Human Phenotype Ontology term): 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: Very frequent (HP:0040281, a Human Phenotype Ontology term). (ORPHA:163971)
- Failure to thrive (HP:0001508, a Human Phenotype Ontology term): Failure to thrive (FTT) refers to a child whose physical growth is substantially below the norm. Evidence: TAS. Frequency: Very frequent (HP:0040281, a Human Phenotype Ontology term). (ORPHA:163971)
- Short stature (HP:0004322, a Human Phenotype Ontology term): 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: Very frequent (HP:0040281, a Human Phenotype Ontology term). (ORPHA:163971)
- Small nail (HP:0001792, a Human Phenotype Ontology term): A nail that is diminished in length and width, i.e., underdeveloped nail. Evidence: TAS. Frequency: Very frequent (HP:0040281, a Human Phenotype Ontology term). (ORPHA:163971)
- Abnormal facial shape (HP:0001999, a Human Phenotype Ontology term): An abnormal morphology (form) of the face or its components. Evidence: TAS. Frequency: Very frequent (HP:0040281, a Human Phenotype Ontology term). (ORPHA:163971)
- Absence of secondary sex characteristics (HP:0008187, a Human Phenotype Ontology term): No secondary sexual characteristics are present at puberty. Evidence: TAS. Frequency: Very frequent (HP:0040281, a Human Phenotype Ontology term). (ORPHA:163971)
- Decreased testicular size (HP:0008734, a Human Phenotype Ontology term): Reduced volume of the testicle (the male gonad). Evidence: TAS. Frequency: Very frequent (HP:0040281, a Human Phenotype Ontology term). (ORPHA:163971)
- Coronal craniosynostosis (HP:0004440, a Human Phenotype Ontology term): Premature closure of the coronal suture of skull. Evidence: TAS. Frequency: Very frequent (HP:0040281, a Human Phenotype Ontology term). (ORPHA:163971)
- Paranoia (HP:0011999, a Human Phenotype Ontology term): The feeling and belief that one is being targeted or is a focus of negative or untoward actions, overt or covert, from others. The affected individual expresses a concern that people are in general against the individual and are engaging in subtle behaviors to make things difficult for them. The origins of such thinking may arise from real events and become amplified over time. Paranoia may also arise in the absence of any action or interaction between the person and their environment. Evidence: TAS. Frequency: Occasional (HP:0040283, a Human Phenotype Ontology term). (ORPHA:163971)
- Decreased serum testosterone concentration (HP:0040171, a Human Phenotype Ontology term). Evidence: TAS. Frequency: Very frequent (HP:0040281, a Human Phenotype Ontology term). (ORPHA:163971)
- Excessive shyness (HP:0100962, a Human Phenotype Ontology term): Atypically high degree of awkwardness or apprehension experienced when approaching or being approached by others. Evidence: TAS. Frequency: Occasional (HP:0040283, a Human Phenotype Ontology term). (ORPHA:163971)
- Small hand (HP:0200055, a Human Phenotype Ontology term): Disproportionately small hand. Evidence: TAS. Frequency: Very frequent (HP:0040281, a Human Phenotype Ontology term). (ORPHA:163971)
These phenotypes are associated with the disease X-linked intellectual disability, Cilliers type (ORPHA:163971, an Orphanet rare-disease identifier).