- Microphthalmia (HP:0000568): A developmental anomaly characterized by abnormal smallness of one or both eyes. Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:2166)
- Hypotelorism (HP:0000601): Interpupillary distance less than 2 SD below the mean (alternatively, the appearance of an decreased interpupillary distance or closely spaced eyes). Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:2166)
- Postaxial hand polydactyly (HP:0001162): Supernumerary digits located at the ulnar side of the hand (that is, on the side with the fifth finger). Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:2166)
- Hypoplasia of penis (HP:0008736). Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:2166)
- Hypoplasia of the premaxilla (HP:0010650): An abnormality of the premaxilla (the embryonic structure that forms the anterior part of the maxilla) causing it to appear relatively small in size compared to the other parts of the maxilla or other facial structures. Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:2166)
- 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:2166)
- 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:2166)
- 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:2166)
- Cleft palate (HP:0000175): Cleft palate is a developmental defect of the palate resulting from a failure of fusion of the palatine processes and manifesting as a separation of the roof of the mouth (soft and hard palate). Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:2166)
- 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: Frequent (HP:0040282). (ORPHA:2166)
- 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: Frequent (HP:0040282). (ORPHA:2166)
- Microcephaly (HP:0000252): Head circumference below 2 standard deviations below the mean for age and gender. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:2166)
- Adrenal hypoplasia (HP:0000835): Developmental hypoplasia of the adrenal glands. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:2166)
- Abnormality of the hypothalamus-pituitary axis (HP:0000864): Abnormality of the pituitary gland (also known as hypophysis), which is an endocrine gland that protrudes from the bottom of the hypothalamus at the base of the brain. The pituitary gland secretes the hormones ACTH, TSH, PRL, GH, endorphins, FSH, LH, oxytocin, and antidiuretic hormone. The secretion of hormones from the anterior pituitary is under the strict control of hypothalamic hormones, and the posterior pituitary is essentially an extension of the hypothalamus, so that hypothalamus and pituitary gland may be regarded as a functional unit. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:2166)
- Hypotonia (HP:0001252): Hypotonia is an abnormally low muscle tone (the amount of tension or resistance to movement in a muscle). Even when relaxed, muscles have a continuous and passive partial contraction which provides some resistance to passive stretching. Hypotonia thus manifests as diminished resistance to passive stretching. Hypotonia is not the same as muscle weakness, although the two conditions can co-exist. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:2166)
- Holoprosencephaly (HP:0001360): Holoprosencephaly is a structural anomaly of the brain in which the developing forebrain fails to divide into two separate hemispheres and ventricles. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:2166)
- Abnormal cardiac septum morphology (HP:0001671): An anomaly of the intra-atrial or intraventricular septum. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:2166)
- 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:2166)
- Abnormal lung lobation (HP:0002101): A developmental defect in the formation of pulmonary lobes. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:2166)
- Thyroid hypoplasia (HP:0005990): Developmental hypoplasia of the thyroid gland. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:2166)
- Aplasia/Hypoplasia of the corpus callosum (HP:0007370): Absence or underdevelopment of the corpus callosum. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:2166)
- Abnormal cardiovascular system morphology (HP:0030680): Any structural anomaly of the heart and blood vessels. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:2166)
- 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: Occasional (HP:0040283). (ORPHA:2166)
- Micrognathia (HP:0000347): Developmental hypoplasia of the mandible. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:2166)
- Cerebellar hypoplasia (HP:0001321): Cerebellar hypoplasia is a descriptive term implying a cerebellum with a reduced volume, but a normal shape and is stable over time. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:2166)
- 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: Frequent (HP:0040282). (ORPHA:2166)
- Umbilical hernia (HP:0001537): Protrusion of abdominal contents through a defect in the abdominal wall musculature around the umbilicus. Skin and subcutaneous tissue overlie the defect. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:2166)
- Omphalocele (HP:0001539): A midline anterior incomplete closure of the abdominal wall in which there is herniation of the abdominal viscera into the base of the abdominal cord. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:2166)
- Polyhydramnios (HP:0001561): The presence of excess amniotic fluid in the uterus during pregnancy. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:2166)
- Talipes (HP:0001883): A deformity of foot and ankle that has different subtypes that are talipes equinovarus, talipes equinovalgus, talipes calcaneovarus and talipes calcaneovalgus. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:2166)
- Encephalocele (HP:0002084): A neural tube defect characterized by sac-like protrusions of the brain and the membranes that cover it through openings in the skull. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:2166)
- Intestinal malrotation (HP:0002566): An abnormality of the intestinal rotation and fixation that normally occurs during the development of the gut. This can lead to volvulus, or twisting of the intestine that causes obstruction and necrosis. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:2166)
- Renal hypoplasia/aplasia (HP:0008678): Absence or underdevelopment of the kidney. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:2166)
- Cyclopia (HP:0009914): Cyclopia is a congenital abnormality in which there is only one eye. That eye is centrally placed in the area normally occupied by the root of the nose. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:2166)
- Abnormal localization of kidney (HP:0100542): An abnormal site of the kidney. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:2166)
- Absent nares (HP:0100596): The nostrils (the paired channels of the nose) are not present. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:2166)
These phenotypes are associated with the disease Holoprosencephaly-postaxial polydactyly syndrome (ORPHA:2166).