- Thin upper lip vermilion (HP:0000219): Height of the vermilion of the upper lip in the midline more than 2 SD below the mean. Alternatively, an apparently reduced height of the vermilion of the upper lip in the frontal view (subjective). Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:163979)
- Microcephaly (HP:0000252): Head circumference below 2 standard deviations below the mean for age and gender. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:163979)
- Short philtrum (HP:0000322): Distance between nasal base and midline upper lip vermilion border more than 2 SD below the mean. Alternatively, an apparently decreased distance between nasal base and midline upper lip vermilion border. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:163979)
- Short chin (HP:0000331): Decreased vertical distance from the vermilion border of the lower lip to the inferior-most point of the chin. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:163979)
- 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:163979)
- Underdeveloped nasal alae (HP:0000430): Thinned, deficient, or excessively arched ala nasi. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:163979)
- 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: Frequent (HP:0040282). (ORPHA:163979)
- Bilateral ptosis (HP:0001488). Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:163979)
- Pes planus (HP:0001763): A foot where the longitudinal arch of the foot is in contact with the ground or floor when the individual is standing; or, in a patient lying supine, a foot where the arch is in contact with the surface of a flat board pressed against the sole of the foot by the examiner with a pressure similar to that expected from weight bearing; or, the height of the arch is reduced. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:163979)
- Toe clinodactyly (HP:0001863): Bending or curvature of a toe in the tibial direction (i.e., towards the big toe). Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:163979)
- 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:163979)
- Short 5th finger (HP:0009237): Hypoplasia (congenital reduction in size) of the fifth finger, also known as the little finger. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:163979)
- Overhanging nasal tip (HP:0011833): Positioning of the nasal tip inferior to the nasal base. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:163979)
- 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: Occasional (HP:0040283). (ORPHA:163979)
- 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:163979)
- 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:163979)
- Hydronephrosis (HP:0000126): Severe distention of the kidney with dilation of the renal pelvis and calices. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:163979)
- 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: Occasional (HP:0040283). (ORPHA:163979)
- 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: Occasional (HP:0040283). (ORPHA:163979)
- Broad forehead (HP:0000337): Width of the forehead or distance between the frontotemporales is more than two standard deviations above the mean (objective); or apparently increased distance between the two sides of the forehead. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:163979)
- Choanal atresia (HP:0000453): Absence or abnormal closure of the choana (the posterior nasal aperture). Most embryologists believe that posterior choanal atresia results from a failure of rupture between the 35th and 38th day of fetal life of the partition which separates the bucconasal or buccopharyngeal membranes. The resultant choanal atresia may be unilateral or bilateral, bony or membranous, complete or incomplete. In over 90 per cent of cases the obstruction is bony, while in the remainder it is membranous. The bony type of atresia is commonly located 1-2 mm. anterior to the posterior edge of the hard palate, and the osseous septum varies in thickness from 1 to 10 mm. In the membranous form of choanal atresia the obstruction usually occurs further posteriorly. In approximately one third of cases the atresia is bilateral. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:163979)
- Downslanted palpebral fissures (HP:0000494): The palpebral fissure inclination is more than two standard deviations below the mean. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:163979)
- Proptosis (HP:0000520): An eye that is protruding anterior to the plane of the face to a greater extent than is typical. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:163979)
- Upslanted palpebral fissure (HP:0000582): The palpebral fissure inclination is more than two standard deviations above the mean for age (objective); or, the inclination of the palpebral fissure is greater than typical for age. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:163979)
- Hyperextensibility of the finger joints (HP:0001187): The ability of the finger joints to move beyond their normal range of motion. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:163979)
- 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:163979)
- Ventricular septal defect (HP:0001629): A hole between the two bottom chambers (ventricles) of the heart. The defect is centered around the most superior aspect of the ventricular septum. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:163979)
- Atrial septal defect (HP:0001631): Atrial septal defect (ASD) is a congenital abnormality of the interatrial septum that enables blood flow between the left and right atria via the interatrial septum. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:163979)
- Patent ductus arteriosus (HP:0001643): In utero, the ductus arteriosus (DA) serves to divert ventricular output away from the lungs and toward the placenta by connecting the main pulmonary artery to the descending aorta. A patent ductus arteriosus (PDA) in the first 3 days of life is a physiologic shunt in healthy term and preterm newborn infants, and normally is substantially closed within about 24 hours after bith and completely closed after about three weeks. Failure of physiologcal closure is referred to a persistent or patent ductus arteriosus (PDA). Depending on the degree of left-to-right shunting, PDA can have clinical consequences. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:163979)
- Bulbous tips of toes (HP:0001782): An abnormality of the morphology of the toes, such that the tips of the toes are prominent and bulbous. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:163979)
- Rocker bottom foot (HP:0001838): The presence of both a prominent heel and a convex contour of the sole. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:163979)
- Thrombocytopenia (HP:0001873): A reduction in the number of circulating thrombocytes. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:163979)
- Anemia (HP:0001903): A reduction in erythrocytes volume or hemoglobin concentration. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:163979)
- Respiratory insufficiency (HP:0002093). Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:163979)
- Intracranial hemorrhage (HP:0002170): Hemorrhage occurring within the skull. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:163979)
- Broad skull (HP:0002682): Increased width of the skull. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:163979)
- Tracheal stenosis (HP:0002777). Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:163979)
- Hypocalcemia (HP:0002901): The concentration of calcium in the blood circulation is below the lower limit of normal. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:163979)
- Hyperbilirubinemia (HP:0002904): An increased amount of bilirubin in the blood. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:163979)
- 2-3 toe syndactyly (HP:0004691): Syndactyly with fusion of toes two and three. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:163979)
- Capillary hemangioma (HP:0005306): The presence of a capillary hemangioma, which are hemangiomas with small endothelial spaces. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:163979)
- Wide intermamillary distance (HP:0006610): A larger than usual distance between the left and right nipple. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:163979)
- Aplasia/Hypoplasia of the nails (HP:0008386): Aplasia or developmental hypoplasia of the nail. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:163979)
- Microtia (HP:0008551): Underdevelopment of the external ear. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:163979)
- Long toe (HP:0010511): Toes that appear disproportionately long compared to the foot. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:163979)
- Absent gallbladder (HP:0011467): A developmental defect in which the gallbladder fails to form. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:163979)
- Interrupted aortic arch (HP:0011611): Non-continuity of the arch of aorta with an atretic point or absent segment. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:163979)
- Heart murmur (HP:0030148): An extra or unusual sound heard during a heartbeat caused vibrations resulting from the flow of blood through the heart. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:163979)
These phenotypes are associated with the disease X-linked intellectual disability-craniofacioskeletal syndrome (ORPHA:163979).