- Hypoplasia of the uterus (HP:0000013): Underdevelopment of the uterus. Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:90796)
- Hypospadias (HP:0000047): 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: Very frequent (HP:0040281). (ORPHA:90796)
- 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: Very frequent (HP:0040281). (ORPHA:90796)
- Decreased fertility (HP:0000144). Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:90796)
- Polycystic ovaries (HP:0000147). Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:90796)
- Primary amenorrhea (HP:0000786). Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:90796)
- Hypergonadotropic hypogonadism (HP:0000815): 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). (ORPHA:90796)
- Delayed puberty (HP:0000823): Passing the age when puberty normally occurs with no physical or hormonal signs of the onset of puberty. Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:90796)
- Osteoporosis (HP:0000939): Osteoporosis is a systemic skeletal disease characterized by low bone density and microarchitectural deterioration of bone tissue with a consequent increase in bone fragility. According to the WHO criteria, osteoporosis is defined as a BMD that lies 2.5 standard deviations or more below the average value for young healthy adults (a T-score below -2.5 SD). Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:90796)
- Sparse axillary hair (HP:0002215): Reduced number or density of axillary hair. Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:90796)
- Sparse pubic hair (HP:0002225): Reduced number or density of pubic hair. Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:90796)
- Sparse body hair (HP:0002231): Sparseness of the body hair. Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:90796)
- Delayed skeletal maturation (HP:0002750): 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). (ORPHA:90796)
- Reduced bone mineral density (HP:0004349): A reduction of bone mineral density, that is, of the amount of matter per cubic centimeter of bones. Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:90796)
- Absence of secondary sex characteristics (HP:0008187): No secondary sexual characteristics are present at puberty. Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:90796)
- Primary gonadal insufficiency (HP:0008193). Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:90796)
- Decreased serum estradiol (HP:0008214): A reduction below normal concentration of estradiol in the circulation. Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:90796)
- Elevated circulating follicle stimulating hormone level (HP:0008232): An elevated concentration of follicle-stimulating hormone in the blood. Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:90796)
- Enlarged polycystic ovaries (HP:0008675). Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:90796)
- Elevated circulating luteinizing hormone level (HP:0011969): An elevated concentration of luteinizing hormone in the blood. Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:90796)
- Abnormal circulating corticosterone level (HP:0012112): An abnormality of the concentration of corticosterone in the blood. Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:90796)
- Decreased circulating androgen concentration (HP:0030349): A reduction in the blood concentration of an androgen, that is, of a steroid hormone that controls development and maintenance of masculine characteristics. The androgens include testosterone and Dehydroepiandrosterone. Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:90796)
- Decreased serum testosterone concentration (HP:0040171). Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:90796)
- Dysmenorrhea (HP:0100607): Pain during menstruation that interferes with daily activities. Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:90796)
- 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: Frequent (HP:0040282). (ORPHA:90796)
- Decreased fertility in females (HP:0000868). Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:90796)
- 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:90796)
- Hypoplasia of the vagina (HP:0008726): Developmental hypoplasia of the vagina. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:90796)
- Decreased testicular size (HP:0008734): Reduced volume of the testicle (the male gonad). Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:90796)
- Decreased fertility in males (HP:0012041). Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:90796)
- Ambiguous genitalia, male (HP:0000033): Ambiguous genitalia in an individual with XY genetic gender. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:90796)
- Male pseudohermaphroditism (HP:0000037): Hermaphroditism refers to a discrepancy between the morphology of the gonads and that of the external genitalia. In male pseudohermaphroditism, the genotype is male (XY) and the external genitalia are imcompletely virilized, ambiguous, or complete female. If gonads are present, they are testes. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:90796)
- Gynecomastia (HP:0000771): Abnormal development of large mammary glands in males resulting in breast enlargement. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:90796)
- Failure to thrive (HP:0001508): Failure to thrive (FTT) refers to a child whose physical growth is substantially below the norm. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:90796)
- Female external genitalia in individual with 46,XY karyotype (HP:0008730): The presence of female external genitalia in a person with a male karyotype. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:90796)
- Abnormal sex determination (HP:0012244): Anomaly of primary or secondary sexual development or characteristics. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:90796)
These phenotypes are associated with the disease 46,XY difference of sex development due to isolated 17,20-lyase deficiency (ORPHA:90796).