- 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:83628)
- 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: Occasional (HP:0040283). (ORPHA:83628)
- Bifid scrotum (HP:0000048): Midline indentation or cleft of the scrotum. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:83628)
- 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:83628)
- Hypoplastic labia majora (HP:0000059): Undergrowth of the outer labia. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:83628)
- 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:83628)
- Renal duplication (HP:0000075): A congenital anomaly of the urinary tract, in which the kidney is duplicated and is drained via two separate renal pelves and ureters. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:83628)
- Vesicoureteral reflux (HP:0000076): Abnormal (retrograde) movement of urine from the bladder into ureters or kidneys related to inadequacy of the valvular mechanism at the ureterovesicular junction or other causes. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:83628)
- Renal agenesis (HP:0000104): Agenesis, that is, failure of the kidney to develop during embryogenesis and development. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:83628)
- Bifid uterus (HP:0000136): The presence of a bifid uterus. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:83628)
- Hemangioma (HP:0001028): A hemangioma is a benign tumor characterized by blood-filled spaces lined by benign endothelial cells. A hemangioma characterized by large endothelial spaces (caverns) is called a cavernous hemangioma (in contrast to a hemangioma with small endothelial spaces, which is called capillary hemangioma). Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:83628)
- Anal atresia (HP:0002023): Congenital absence of the anus, i.e., the opening at the bottom end of the intestinal tract. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:83628)
- Spina bifida (HP:0002414): Incomplete closure of the embryonic neural tube, whereby some vertebral arches remain unfused and open. The mildest form is spina bifida occulta, followed by meningocele and meningomyelocele. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:83628)
- Myelomeningocele (HP:0002475): Protrusion of the meninges and portions of the spinal cord through a defect of the vertebral column. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:83628)
- Bladder exstrophy (HP:0002836): Eversion of the posterior bladder wall through the congenitally absent lower anterior abdominal wall and anterior bladder wall. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:83628)
- Ectopic anus (HP:0004397): Abnormal displacement or malposition of the anus. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:83628)
- Skin tags (HP:0010609): Cutaneous skin tags also known as acrochorda or fibroepithelial polyps are small benign tumors that may either form secondarily over time primarily in areas where the skin forms creases, such as the neck, armpit or groin or may also be present at birth, in which case they usually occur in the periauricular region. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:83628)
These phenotypes are associated with the disease LUMBAR syndrome (ORPHA:83628).