- 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: Very frequent (HP:0040281). (ORPHA:1772)
- 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: Very frequent (HP:0040281). (ORPHA:1772)
- Muscle hypertrophy of the lower extremities (HP:0008968): Muscle hypertrophy primarily affecting the legs. Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:1772)
- Unilateral cryptorchidism (HP:0012741): Absence of a testis from the scrotum on one side owing to failure of the testis or testes to descend through the inguinal canal to the scrotum. Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:1772)
- Azoospermia (HP:0000027): Absence of any measurable level of sperm,whereby spermatozoa cannot be observed even after centrifugation of the semen pellet. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:1772)
- Ambiguous genitalia, male (HP:0000033): Ambiguous genitalia in an individual with XY genetic gender. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:1772)
- 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: Frequent (HP:0040282). (ORPHA:1772)
- 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: Frequent (HP:0040282). (ORPHA:1772)
- Ambiguous genitalia, female (HP:0000061): Ambiguous genitalia in an individual with XX genetic gender. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:1772)
- Ambiguous genitalia (HP:0000062): A genital phenotype that is not clearly assignable to a single gender. Ambiguous genitalia can be evaluated using the Prader scale: Prader 0: Normal female external genitalia. Prader 1: Female external genitalia with clitoromegaly. Prader 2: Clitoromegaly with partial labial fusion forming a funnel-shaped urogenital sinus. Prader 3: Increased phallic enlargement. Complete labioscrotal fusion forming a urogenital sinus with a single opening. Prader 4: Complete scrotal fusion with urogenital opening at the base or on the shaft of the phallus. Prader 5: Normal male external genitalia. The diagnosis of ambiguous genitalia is made for Prader 1-4. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:1772)
- Penoscrotal hypospadias (HP:0000808): A severe form of hypospadias in which the urethral opening is located at the junction of the penis and scrotum. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:1772)
- Abnormal internal genitalia (HP:0000812): An anomaly of the adnexa, uterus, and vagina (in female) or seminal tract and prostate (in male). Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:1772)
- Increased circulating gonadotropin level (HP:0000837): Overproduction of gonadotropins (FSH, LH) by the anterior pituitary gland. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:1772)
- Male infertility (HP:0003251). Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:1772)
- Bilateral cryptorchidism (HP:0008689): Absence of 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:1772)
- Urogenital sinus anomaly (HP:0100779): A rare birth defect in women where the urethra and vagina both open into a common channel. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:1772)
- Epispadias (HP:0000039): Epispadias is a urogenital malformation characterized by the failure of the urethral tube to tubularize on the dorsal aspect. Unlike in hypospadias, where the meatus is on the ventral aspect, children with epispadias have a wide-open urethral plate on the dorsum. It is commonly seen as a component in the spectrum of bladder exstrophy-epispadias-complex. Isolated epispadias constitutes less than 10 percent of the total cases of epispadias. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:1772)
- Chordee (HP:0000041): A congenital anomaly of the penis characterized by ventral (i.e., downward), lateral, or ventrolateral curvature of the shaft and glans penis of more than 30 degrees. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:1772)
- Abnormal scrotum morphology (HP:0000045): Any structural abnormality of the scrotum, i.e., the sac that contains the testes, epididymis, and the lower part of the spermatic cord. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:1772)
- Bifid scrotum (HP:0000048): Midline indentation or cleft of the scrotum. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:1772)
- Abnormality of the kidney (HP:0000077): An abnormality of the kidney. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:1772)
- Horseshoe kidney (HP:0000085): A connection of the right and left kidney by an isthmus of functioning renal parenchyma or fibrous tissue that crosses the midline. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:1772)
- Gonadoblastoma (HP:0000150): The presence of a gonadoblastoma, a neoplasm of a gonad that consists of aggregates of germ cells and sex cord elements. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:1772)
- High palate (HP:0000218): Height of the palate more than 2 SD above the mean (objective) or palatal height at the level of the first permanent molar more than twice the height of the teeth (subjective). Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:1772)
- Epicanthus (HP:0000286): A fold of skin starting above the medial aspect of the upper eyelid and arching downward to cover, pass in front of and lateral to the medial canthus. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:1772)
- Micrognathia (HP:0000347): Developmental hypoplasia of the mandible. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:1772)
- Hearing impairment (HP:0000365): A decreased magnitude of the sensory perception of sound. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:1772)
- Recurrent otitis media (HP:0000403): Increased susceptibility to otitis media, as manifested by recurrent episodes of otitis media. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:1772)
- Webbed neck (HP:0000465): Pterygium colli is a congenital skin fold that runs along the sides of the neck down to the shoulders. It involves an ectopic fibrotic facial band superficial to the trapezius muscle. Excess hair-bearing skin is also present and extends down the cervical region well beyond the normal hairline. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:1772)
- Visual impairment (HP:0000505): Visual impairment (or vision impairment) is vision loss (of a person) to such a degree as to qualify as an additional support need through a significant limitation of visual capability resulting from either disease, trauma, or congenital or degenerative conditions that cannot be corrected by conventional means, such as refractive correction, medication, or surgery. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:1772)
- Nystagmus (HP:0000639): Rhythmic, involuntary oscillations of one or both eyes related to abnormality in fixation, conjugate gaze, or vestibular mechanisms. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:1772)
- Autistic behavior (HP:0000729): Persistent deficits in social interaction and communication and interaction as well as a markedly restricted repertoire of activity and interest as well as repetitive patterns of behavior. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:1772)
- Pectus excavatum (HP:0000767): A defect of the chest wall characterized by a depression of the sternum, giving the chest ("pectus") a caved-in ("excavatum") appearance. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:1772)
- Gynecomastia (HP:0000771): Abnormal development of large mammary glands in males resulting in breast enlargement. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:1772)
- Hypothyroidism (HP:0000821): Deficiency of thyroid hormone. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:1772)
- 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: Occasional (HP:0040283). (ORPHA:1772)
- Developmental glaucoma (HP:0001087): Glaucoma which forms during the early years of a child's life is called developmental or congenital glaucoma. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:1772)
- 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: Occasional (HP:0040283). (ORPHA:1772)
- Obesity (HP:0001513): Accumulation of substantial excess body fat. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:1772)
- Bicuspid aortic valve (HP:0001647): The presence of an aortic valve with two instead of the normal three cusps (flaps). Bicuspid aortic valvue is a malformation of a commissure (small space between the attachment of each cusp to the aortic wall) and the adjacent parts of the two corresponding cusps forming a raphe (the fused area of the two underdeveloped cusps turning into a malformed commissure between both cusps; the raphe is a fibrous ridge that extends from the commissure to the free edge of the two underdeveloped, conjoint cusps). Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:1772)
- Tachycardia (HP:0001649): A rapid heartrate that exceeds the range of the normal resting heartrate for age. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:1772)
- Prolonged QT interval (HP:0001657): Increased time between the start of the Q wave and the end of the T wave as measured by the electrocardiogram (EKG). Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:1772)
- Coarctation of aorta (HP:0001680): Coarctation of the aorta is a narrowing or constriction of a segment of the aorta. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:1772)
- Hallux valgus (HP:0001822): Lateral deviation of the great toe (i.e., in the direction of the little toe). Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:1772)
- Low posterior hairline (HP:0002162): Hair on the neck extends more inferiorly than usual. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:1772)
- Nail dysplasia (HP:0002164): The presence of developmental dysplasia of the nail. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:1772)
- Dyscalculia (HP:0002442): A specific learning disability involving mathematics and arithmetic. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:1772)
- Scoliosis (HP:0002650): The presence of an abnormal lateral curvature of the spine. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:1772)
- 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: Occasional (HP:0040283). (ORPHA:1772)
- Cubitus valgus (HP:0002967): Abnormal positioning in which the elbows are turned out. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:1772)
- Wide intermamillary distance (HP:0006610): A larger than usual distance between the left and right nipple. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:1772)
- Short 4th metacarpal (HP:0010044): Short fourth metacarpal bone. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:1772)
- Streak ovary (HP:0010464): A developmental disorder characterized by the progressive loss of primordial germ cells in the developing ovaries of an embryo, leading to hypoplastic ovaries composed of wavy connective tissue with occasional clumps of granulosa cells, and frequently mesonephric or hilar cells. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:1772)
- Short metatarsal (HP:0010743): Diminished length of a metatarsal bone, with resultant proximal displacement of the associated toe. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:1772)
- Ovotestis (HP:0012861): A gonad that contains both ovarian follicles and testicular tubular elements. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:1772)
- Ovarian serous cystadenoma (HP:0012887): A cystic tumor of the ovary, containing thin, clear, yellow serous fluid and varying amounts of solid tissue. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:1772)
- Cervix cancer (HP:0030079): A tumor of the uterine cervix. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:1772)
- Abnormal cardiovascular system morphology (HP:0030680): Any structural anomaly of the heart and blood vessels. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:1772)
- Decreased serum testosterone concentration (HP:0040171). Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:1772)
- Posteriorly rotated ears (HP:0000358): A type of abnormal location of the ears in which the position of the ears is characterized by posterior rotation (the superior part of the ears is rotated towards the back of the head, and the inferior part of the ears towards the front). Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:1772)
These phenotypes are associated with the disease 45,X/46,XY mixed gonadal dysgenesis (ORPHA:1772).