- 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: Very frequent (HP:0040281). (ORPHA:293967)
- Hypogonadotropic hypogonadism (HP:0000044): Hypogonadotropic hypogonadism is characterized by reduced function of the gonads (testes in males or ovaries in females) and results from the absence of the gonadal stimulating pituitary hormones: follicle stimulating hormone (FSH) and luteinizing hormone (LH). Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:293967)
- 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: Very frequent (HP:0040281). (ORPHA:293967)
- Bifid uvula (HP:0000193): Uvula separated into two parts most easily seen at the tip. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:293967)
- Microcephaly (HP:0000252): Head circumference below 2 standard deviations below the mean for age and gender. Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:293967)
- 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: Very frequent (HP:0040281). (ORPHA:293967)
- Micrognathia (HP:0000347): Developmental hypoplasia of the mandible. Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:293967)
- Protruding ear (HP:0000411): Angle formed by the plane of the ear and the mastoid bone greater than the 97th centile for age (objective); or, outer edge of the helix more than 2 cm from the mastoid at the point of maximum distance (objective). Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:293967)
- Convex nasal ridge (HP:0000444): Nasal ridge curving anteriorly to an imaginary line that connects the nasal root and tip. The nose appears often also prominent, and the columella low. Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:293967)
- 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: Very frequent (HP:0040281). (ORPHA:293967)
- Global developmental delay (HP:0001263): A delay in the achievement of motor or mental milestones in the domains of development of a child, including motor skills, speech and language, cognitive skills, and social and emotional skills. This term should only be used to describe children younger than five years of age. Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:293967)
- Gynecomastia (HP:0000771): Abnormal development of large mammary glands in males resulting in breast enlargement. Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:293967)
- Primary amenorrhea (HP:0000786). Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:293967)
- Delayed puberty (HP:0000823): Passing the age when puberty normally occurs with no physical or hormonal signs of the onset of puberty. Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:293967)
- Insulin-resistant diabetes mellitus (HP:0000831): A type of diabetes mellitus related not to lack of insulin but rather to lack of response to insulin on the part of the target tissues of insulin such as muscle, fat, and liver cells. This type of diabetes is typically associated with increases both in blood glucose concentrations as well as in fasting and postprandial serum insulin levels. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:293967)
- Sprengel anomaly (HP:0000912): A congenital skeletal deformity characterized by the elevation of one scapula (thus, one scapula is located superior to the other). Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:293967)
- Hirsutism (HP:0001007): Abnormally increased hair growth referring to a male pattern of body hair (androgenic hair). Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:293967)
- Visual field defect (HP:0001123). Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:293967)
- Seizure (HP:0001250): A seizure is an intermittent abnormality of nervous system physiology characterized by a transient occurrence of signs and/or symptoms due to abnormal excessive or synchronous neuronal activity in the brain. Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:293967)
- Motor delay (HP:0001270): A type of Developmental delay characterized by a delay in acquiring motor skills. Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:293967)
- Hypertonia (HP:0001276): A condition in which there is increased muscle tone so that arms or legs, for example, are stiff and difficult to move. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:293967)
- Specific learning disability (HP:0001328): Impairment of certain skills such as reading or writing, coordination, self-control, or attention that interfere with the ability to learn. The impairment is not related to a global deficiency of intelligence. Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:293967)
- 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:293967)
- Oligohydramnios (HP:0001562): Diminished amniotic fluid volume in pregnancy. Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:293967)
- Pes cavus (HP:0001761): An increase in height of the medial longitudinal arch of the foot that does not flatten on weight bearing (i.e., a distinctly hollow form of the sole of the foot when it is bearing weight). Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:293967)
- Overlapping toe (HP:0001845): Describes a foot digit resting on the dorsal surface of an adjacent digit when the foot is at rest. Initially clawing may be dynamic and only noticeable on walking. Over time the plantar plate tears, subluxation occurs at the metatarsophalangeal joint (MTPJ), and the deformity becomes permanent. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:293967)
- Microcytic anemia (HP:0001935): A kind of anemia in which the volume of the red blood cells is reduced. Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:293967)
- Lower limb spasticity (HP:0002061): Spasticity (velocity-dependent increase in tonic stretch reflexes with increased muscle tone and hyperexcitable tendon reflexes) in the muscles of the lower limbs, hips, and pelvis. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:293967)
- Highly arched eyebrow (HP:0002553): Increased height of the central portion of the eyebrow, forming a crescent, semicircular, or inverted U shape. Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:293967)
- Delayed skeletal maturation (HP:0002750): A decreased rate of skeletal maturation. Delayed 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: Very frequent (HP:0040281). (ORPHA:293967)
- Genu valgum (HP:0002857): The legs angle inward, such that the knees are close together and the ankles far apart. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:293967)
- Broad hallux (HP:0010055): Visible increase in width of the hallux without an increase in the dorso-ventral dimension. Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:293967)
- Congenital sensorineural hearing impairment (HP:0008527): A type of hearing impairment caused by an abnormal functionality of the cochlear nerve with congenital onset. Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:293967)
- Contracture of the proximal interphalangeal joint of the 5th finger (HP:0009185): Proximal interphalangeal (PIP) flexion deformity of the little finger. That is, the PIP joint of a little finger is bent (flexed) and cannot be straightened actively or passively. It is thus a chronic loss of joint motion due to structural changes in muscle, tendons, ligaments, or skin that prevents normal movement. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:293967)
- Marked delay in bone age (HP:0003799). Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:293967)
- Hypoplasia of the tooth germ (HP:0006353): Developmental hypoplasia of the tooth germ, i.e., of the structure that forms in odontogenesis that will develop into a tooth. Evidence: TAS. Frequency: Occasional (HP:0040283). (ORPHA:293967)
- Cerebral dysmyelination (HP:0007266): Defective structure and function of myelin sheaths of the white matter of the brain. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:293967)
- Early-onset non-progressive night blindness (HP:0007642): A usually nonprogressive (i.e., stationary) form of night blindness with early (presumed to be congenital) onset. Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:293967)
- Decreased testicular size (HP:0008734): Reduced volume of the testicle (the male gonad). Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:293967)
- Severe postnatal growth retardation (HP:0008850): Severely slow or limited growth after birth, being four standard deviations or more below age- and sex-related norms. Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:293967)
- Underdeveloped superior crus of antihelix (HP:0011246): Decreased protrusion of the superior crus relative to the prominence of a normal antihelix stem. Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:293967)
- Broad thumb (HP:0011304): Increased thumb width without increased dorso-ventral dimension. Evidence: TAS. Frequency: Frequent (HP:0040282). (ORPHA:293967)
- Moderate global developmental delay (HP:0011343): A moderate delay in the achievement of motor or mental milestones in the domains of development of a child. Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:293967)
- Moderate intrauterine growth retardation (HP:0011408): Intrauterine growth retardation that is at least 3 standard deviations (SD) below average, but not as low as 4 SD, corrected for sex and gestational age. Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:293967)
- Feeding difficulties (HP:0011968): Impaired ability to eat related to problems gathering food and getting ready to suck, chew, or swallow it. Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:293967)
- Abnormal optic disc morphology (HP:0012795): A morphological abnormality of the optic disc, i.e., of the portion of the optic nerve clinically visible on fundoscopic examination. Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:293967)
- Decreased corneal thickness (HP:0100689): A decreased anteroposterior thickness of the cornea. Evidence: TAS. Frequency: Very frequent (HP:0040281). (ORPHA:293967)
These phenotypes are associated with the disease Hypogonadotropic hypogonadism-severe microcephaly-sensorineural hearing loss-dysmorphism syndrome (ORPHA:293967).