- Aplasia/Hypoplasia involving the nose (HP:0009924): Underdevelopment or absence of the nose or parts thereof. Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:3301)
- Multicystic kidney dysplasia (HP:0000003): Multicystic dysplasia of the kidney is characterized by multiple cysts of varying size in the kidney and the absence of a normal pelvicaliceal system. The condition is associated with ureteral or ureteropelvic atresia, and the affected kidney is nonfunctional. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:3301)
- 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:3301)
- Small scrotum (HP:0000046): Apparently small scrotum for age. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:3301)
- Vaginal atresia (HP:0000148): Congenital occlusion of the vagina or adhesion of the walls of the vagina causing occlusion. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:3301)
- Narrow mouth (HP:0000160): Distance between the commissures of the mouth more than 2 SD below the mean. Alternatively, an apparently decreased width of the oral aperture (subjective). Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:3301)
- Full cheeks (HP:0000293): Increased prominence or roundness of soft tissues between zygomata and mandible. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:3301)
- Micrognathia (HP:0000347): Developmental hypoplasia of the mandible. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:3301)
- Microcornea (HP:0000482): A congenital abnormality of the cornea in which the cornea and the anterior segment of the eye are smaller than normal. The horizontal diameter of the cornea does not reach 10 mm even in adulthood. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:3301)
- Cataract (HP:0000518): A cataract is an opacity or clouding that develops in the crystalline lens of the eye or in its capsule. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:3301)
- Microphthalmia (HP:0000568): A developmental anomaly characterized by abnormal smallness of one or both eyes. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:3301)
- Iris coloboma (HP:0000612): A coloboma of the iris. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:3301)
- Optic atrophy (HP:0000648): Atrophy of the optic nerve. Optic atrophy results from the death of the retinal ganglion cell axons that comprise the optic nerve and manifesting as a pale optic nerve on fundoscopy. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:3301)
- Abnormal rib morphology (HP:0000772): An anomaly of the rib. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:3301)
- Missing ribs (HP:0000921): A developmental anomaly with absence of one or more ribs. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:3301)
- Agenesis of corpus callosum (HP:0001274): Absence of the corpus callosum as a result of the failure of the corpus callosum to develop, which can be the result of a failure in any one of the multiple steps of callosal development including cellular proliferation and migration, axonal growth or glial patterning at the midline. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:3301)
- Abnormality of the larynx (HP:0001600): An abnormality of the larynx. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:3301)
- Abnormal cardiac septum morphology (HP:0001671): An anomaly of the intra-atrial or intraventricular septum. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:3301)
- 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:3301)
- Abnormal lung lobation (HP:0002101): A developmental defect in the formation of pulmonary lobes. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:3301)
- Tracheal stenosis (HP:0002777). Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:3301)
- Aplasia/Hypoplasia of the nipples (HP:0006709). Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:3301)
- Hypoplasia of penis (HP:0008736). Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:3301)
- Amelia involving the upper limbs (HP:0009812): Amelia of one or both upper limbs. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:3301)
- Acromelia of the lower limbs (HP:0010494): Shortening of the legs predominantly affecting terminal parts of the leg in relation to the upper and middle arm segments. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:3301)
- Non-midline cleft of the upper lip (HP:0100335): Clefting (gap or groove) of the upper lip affecting the lateral portions of the upper lip rather than the midline/median region. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:3301)
- Abnormally ossified vertebrae (HP:0100569): An abnormality of the formation and mineralization of one or more vertebrae. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:3301)
- Septo-optic dysplasia (HP:0100842): Underdevelopment of the optic nerve and absence of the septum pellucidum. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:3301)
- Orofacial cleft (HP:0000202): The presence of a cleft (gap, opening, or groove) in the oral cavity, including cleft of the upper lip and/or cleft of the palate. Cleft of the upper lip is visible as a groove or fissure in the lip, most frequently due to a congenital failure of the maxillary and median nasal processes to fuse. Cleft palate is characterized by a grooved depression or fissure in the roof of the mouth, most often resulting from a congenital failure of the palate to fuse properly. Clefts of the lip and palate can occur individually or together. It is preferable to code each defect separately. Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:3301)
- Hydrocephalus (HP:0000238): Hydrocephalus is an active distension of the ventricular system of the brain resulting from inadequate passage of CSF from its point of production within the cerebral ventricles to its point of absorption into the systemic circulation. Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:3301)
- Polyhydramnios (HP:0001561): The presence of excess amniotic fluid in the uterus during pregnancy. Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:3301)
- Tetraamelia (HP:0003057): Amelia of all four limbs. Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:3301)
- Aplasia/Hypoplasia of the lungs (HP:0006703). Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:3301)
- Microtia (HP:0008551): Underdevelopment of the external ear. Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:3301)
- Aplasia/Hypoplasia involving the pelvis (HP:0009103). Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:3301)
These phenotypes are associated with the disease Tetraamelia-multiple malformations syndrome (ORPHA:3301).