- Microcephaly (HP:0000252): Head circumference below 2 standard deviations below the mean for age and gender. Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:96097)
- 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: Very frequent (HP:0040281). (ORPHA:96097)
- 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:96097)
- 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:96097)
- 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:96097)
- Thin vermilion border (HP:0000233): Height of the vermilion of the medial part of the lip more than 2 SD below the mean, or apparently reduced height of the vermilion of the lip in the frontal view. The vermilion is the red part of the lips (and confusingly, the vermilion itself is also often referred to as being equivalent the lips). Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:96097)
- Epicanthus (HP:0000286): A fold of skin starting above the medial aspect of the upper eyelid and arching downward to cover, pass in front of and lateral to the medial canthus. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:96097)
- Hypertelorism (HP:0000316): Interpupillary distance more than 2 SD above the mean (alternatively, the appearance of an increased interpupillary distance or widely spaced eyes). Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:96097)
- 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:96097)
- Micrognathia (HP:0000347): Developmental hypoplasia of the mandible. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:96097)
- Low-set ears (HP:0000369): Upper insertion of the ear to the scalp below an imaginary horizontal line drawn between the inner canthi of the eye and extending posteriorly to the ear. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:96097)
- Macrotia (HP:0000400): Median longitudinal ear length greater than two standard deviations above the mean and median ear width greater than two standard deviations above the mean (objective); or, apparent increase in length and width of the pinna (subjective). Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:96097)
- Prominent nasal bridge (HP:0000426): Anterior positioning of the nasal root in comparison to the usual positioning for age. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:96097)
- Downslanted palpebral fissures (HP:0000494): The palpebral fissure inclination is more than two standard deviations below the mean. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:96097)
- Carious teeth (HP:0000670): Caries is a multifactorial bacterial infection affecting the structure of the tooth. This term has been used to describe the presence of more than expected dental caries. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:96097)
- Delayed speech and language development (HP:0000750): A degree of language development that is significantly below the norm for a child of a specified age. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:96097)
- Brachydactyly (HP:0001156): Digits that appear disproportionately short compared to the hand/foot. The word brachydactyly is used here to describe a series distinct patterns of shortened digits (brachydactyly types A-E). This is the sense used here. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:96097)
- Craniosynostosis (HP:0001363): Craniosynostosis refers to the premature closure of the cranial sutures. Primary craniosynostosis refers to the closure of one or more sutures due to abnormalities in skull development, and secondary craniosynostosis results from failure of brain growth. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:96097)
- 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: Frequent (HP:0040282). (ORPHA:96097)
- 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:96097)
- Hypoplasia of the radius (HP:0002984): Underdevelopment of the radius. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:96097)
- Hypoplasia of the ulna (HP:0003022): Underdevelopment of the ulna. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:96097)
- Short nose (HP:0003196): Distance from nasion to subnasale more than two standard deviations below the mean, or alternatively, an apparently decreased length from the nasal root to the nasal tip. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:96097)
- Flat face (HP:0012368): Absence of concavity or convexity of the face when viewed in profile. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:96097)
- Hernia (HP:0100790). Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:96097)
- Chorioretinal coloboma (HP:0000567): Absence of a region of the retina, retinal pigment epithelium, and choroid. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:96097)
- Eczematoid dermatitis (HP:0000964): Eczema is a form of dermatitis that is characterized by scaly, pruritic, erythematous lesions located on flexural surfaces. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:96097)
- Dextrocardia (HP:0001651): The heart is located in the right hand sided hemithorax. That is, there is a left-right reversal (or "mirror reflection") of the anatomical location of the heart in which the heart is locate on the right side instead of the left. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:96097)
- Absent thumb (HP:0009777): Absent thumb, i.e., the absence of both phalanges of a thumb and the associated soft tissues. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:96097)
- Aplasia/Hypoplasia of the gallbladder (HP:0011466): Absence or underdevelopment of the gallbladder. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:96097)
These phenotypes are associated with the disease Distal duplication 5q syndrome (ORPHA:96097).