- 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:370930)
- 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:370930)
- Myopia (HP:0000545): An abnormality of refraction characterized by the ability to see objects nearby clearly, while objects in the distance appear blurry. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:370930)
- Hirsutism (HP:0001007): Abnormally increased hair growth referring to a male pattern of body hair (androgenic hair). Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:370930)
- Truncal obesity (HP:0001956): Obesity located preferentially in the trunk of the body as opposed to the extremities. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:370930)
- Relative macrocephaly (HP:0004482): A relatively mild degree of macrocephaly in which the head circumference is not above two standard deviations from the mean, but appears dysproportionately large when other factors such as body stature are taken into account. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:370930)
- Microcephaly (HP:0000252): Head circumference below 2 standard deviations below the mean for age and gender. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:370930)
- Long philtrum (HP:0000343): Distance between nasal base and midline upper lip vermilion border more than 2 SD above the mean. Alternatively, an apparently increased distance between nasal base and midline upper lip vermilion border. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:370930)
- Synophrys (HP:0000664): Meeting of the medial eyebrows in the midline. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:370930)
- Broad ribs (HP:0000885): Increased width of ribs. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:370930)
- Short clavicles (HP:0000894): Reduced length of the clavicles. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:370930)
- Soft, doughy skin (HP:0001027): A skin texture that is unusually soft (and may feel silky), and has a malleable consistency resembling that of dough. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:370930)
- Acne (HP:0001061): A skin condition in which there is an increase in sebum secretion by the pilosebaceous apparatus associated with open comedones (blackheads), closed comedones (whiteheads), and pustular nodules (papules, pustules, and cysts). Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:370930)
- Joint dislocation (HP:0001373): Displacement or malalignment of joints. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:370930)
- Joint hypermobility (HP:0001382): The capability that a joint (or a group of joints) has to move, passively and/or actively, beyond normal limits along physiological axes. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:370930)
- Growth delay (HP:0001510): A deficiency or slowing down of growth pre- and postnatally. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:370930)
- 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:370930)
- Hepatomegaly (HP:0002240): Abnormally increased size of the liver. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:370930)
- Moderate intellectual disability (HP:0002342): Moderate intellectual disability (ID) is defined as a type of ID characterized by moderately sub-average adaptive functioning and intellectual functioning, with an intelligence quotient (IQ) the range of 35-49. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:370930)
- Coxa valga (HP:0002673): Coxa valga is a deformity of the hip in which the angle between the femoral shaft and the femoral neck is increased compared to age-adjusted values (about 150 degrees in newborns gradually reducing to 120-130 degrees in adults). Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:370930)
- Flared metaphysis (HP:0003015): The presence of a splayed (i.e.,flared) metaphyseal segment of one or more long bones. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:370930)
- Short long bone (HP:0003026): One or more abnormally short long bone. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:370930)
- 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:370930)
- Accelerated skeletal maturation (HP:0005616): An abnormally increased rate of skeletal maturation. Accelerated 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: Frequent (HP:0040282). (ORPHA:370930)
- Broad thumb (HP:0011304): Increased thumb width without increased dorso-ventral dimension. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:370930)
- Thick vermilion border (HP:0012471): Increased width of the skin of vermilion border region of upper lip. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:370930)
- Clinodactyly (HP:0030084): An angulation of a digit at an interphalangeal joint in the plane of the palm (finger) or sole (toe). Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:370930)
- Short femoral neck (HP:0100864): An abnormally short femoral neck (which is the process of bone, connecting the femoral head with the femoral shaft). Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:370930)
- Moon facies (HP:0500011): A rounded, puffy face with fat deposits in the temporal fossa and cheeks, a double chin. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:370930)
These phenotypes are associated with the disease XYLT1-CDG (ORPHA:370930).