This syndrome is inherited as an autosomal disease. It affects both males and females but the phenotype differs. In both sexes sensorineural deafness occurs but in females ovarian dysgenesis also occurs.

XX gonadal dysgenesis is a type of female hypogonadism in which no functional ovaries are present to induce puberty in an otherwise normal girl whose karyotype is found to be 46,XX. With nonfunctional "streak" ovaries she is low in estrogen levels (hypoestrogenic) and has high levels of FSH and LH. Estrogen and progesterone therapy is usually then commenced.

Although similar in some ways to true hermaphroditism, the conditions can be distinguished histologically and by karyotyping. The observable characteristics (phenotype) of this condition are highly variable, ranging from gonadal dysgenesis in males, to Turner-like females and phenotypically normal males. The phenotypical expression may be ambiguous, intersex, or male or female depending on the extent of the mosaicism. The most common presentation of 45,X/46,XY karyotype is phenotypically normal male, next being genital ambiguity.

There is a range of chromosomal anomalies within 45,X/46,XY where the variations are very complex, and the actual result in living individuals is often not a simple picture. Most patients with this karyotype are known to have abnormal gonadal histology and heights considerably below their genetic potential. High gonadotropin levels have been described in both male and female patients, as well as low levels of testosterone in male patients. Dosage loss of SHOX gene is commonly associated with short stature. Psychomotor development is normal.

As the gonads may not be symmetrical, the development of the Müllerian duct and Wolffian duct may be asymmetrical, too. Because of the presence of dysgenetic gonadal tissue and Y chromosome material, there is a high risk of the development of a gonadoblastoma.

People with Aarskog-Scott syndrome often have distinctive facial features, such as widely spaced eyes (hypertelorism), a small nose, a long area between the nose and mouth (philtrum), and a widow's peak hairline. They frequently have mild to moderate short stature during childhood, but their growth usually catches up with that of their peers during puberty. Hand abnormalities are common in this syndrome and include short fingers (brachydactyly), curved pinky fingers (fifth finger clinodactyly), webbing of the skin between some fingers (cutaneous syndactyly), and a single crease across the palm. Other abnormalities in people with Aarskog-Scott syndrome include heart defects and a split in the upper lip (cleft lip) with or without an opening in the roof of the mouth (cleft palate).

Most males with Aarskog-Scott syndrome have a shawl scrotum, in which the scrotum surrounds the penis instead of hanging below. Less often, they have undescended testes (cryptorchidism) or a soft out-pouching around the belly-button (umbilical hernia) or in the lower abdomen (inguinal hernia).

The intellectual development of people with Aarskog-Scott syndrome varies widely. Some may have mild learning and behavior problems, while others have normal intelligence. In rare cases, severe intellectual disability has been reported.

45,X/46,XY mosaicism, also known as X0/XY mosaicism and mixed gonadal dysgenesis, is a rare disorder of sex development in humans associated with sex chromosome aneuploidy and mosaicism of the Y chromosome. This is called a mosaic karyotype because, like tiles in mosaic floors or walls, there is more than one type of cell.

The clinical manifestations are highly variable, ranging from partial virilisation and ambiguous genitalia at birth, to patients with a completely male or female gonads. Most individuals with this karyotype have apparently normal male genitalia, and a minority with female genitalia, with a significant number of individuals showing genital abnormalities or intersex characteristics. A significantly higher than normal number of other developmental abnormalities are also found in individuals with X0/XY mosaicism. Psychomotor development is normal.

The term “pure gonadal dysgenesis” (PGD) has been used to distinguish a group of patients from gonadal dysgenesis related to Turner syndrome. In the latter a distinct chromosomal aberration is present, while in PGD the chromosomal constellation is either 46,XX or 46,XY. Thus XX gonadal dysgenesis is also referred to as "PGD, 46 XX", and XY gonadal dysgenesis as "PGD, 46,XY" or Swyer syndrome. Patients with PGD have a normal chromosomal constellation but may have localized genetic alterations.

Aneuploidy is often fatal, but in this case there is "X-inactivation" where the effect of the additional gene dosage due to the presence of extra X chromosomes is greatly reduced.

Much like Down syndrome, the mental effects of 49,XXXXY syndrome vary. Impaired speech and behavioral problems are typical. Those with 49,XXXXY syndrome tend to exhibit infantile secondary sex characteristics with sterility in adulthood and have some skeletal anomalies. Skeletal anomalies include:

- Genu valgum

- Pes cavus

- Fifth finger clinodactyly

The effects also include:

- Cleft palate

- Club feet

- Respiratory conditions

- Short or/and broad neck

- Low birth weight

- Hyperextensible joints

- Short stature

- Narrow shoulders

- Coarse features in older age

- Hypertelorism

- Epicanthal folds

- Prognathism

- Gynecomastia (rare)

- Muscular hypotonia

- Hypoplastic genitalia

- Cryptorchidism

- Congenital heart defects

- A very round face in infancy

The most notable features of Wilson-Turner Syndrome are intellectual disability, obesity, hypogonadism, gynecomastia, and distinct facial features. All of the symptoms are chronic. Affected females are known to have less severe signs and symptoms than males. Female carriers of the disorder may have none or mild symptoms.

- Intellectual Disability is the limitation in an individual's mental functioning and skills. Patients of Wilson-Turner Syndrome have mental disability generally ranging from mild to severe, more frequently on the former. This symptom often coincides with delay in speech development and the occurrence of mood swings. Most males were noted to have a quiet and a cheerful disposition. However, individuals who displayed aggression and became easily upset were also seen. Children will display a delay in speech development often combined with excessive drooling and low voice tone. Some of the studied male patients had speech impairment ranging from little or no speech to minor stuttering.

- Obesity is the accumulation of excess fat on the body. Individuals with Wilson-Turner Syndrome are characterized to have truncal obesity, meaning the fat has accumulated in one's middle. Truncal obesity is often related to heart disease, kidney disease, and lowered blood immune system. Truncal obesity in this disorder becomes more apparent around the age of puberty.

- Tapered fingers is when one end of the finger is diminished in thickness, causing the ends of the fingers to appear pointed. This deformity is not debilitating in any particular manner. In addition to tapered fingers, both hands and feet tend to be small. Some males were observed to have pes planus, also known as flat feet.

- Hypogonadism is a condition in which the gonads have a decrease in function. This condition may result from the lack of sex hormone synthesis, such as androgen and estrogen. Hormones produced by the gonads may also decrease. Hypogonadism also influences the onset of other conditions of the Wilson-Turner Syndrome, such as gynecomastia and decreased testes size in males. It can also cause short stature in men and women. In addition to little genital development, pubic and body hair are scant.

- Some of the facial features that are associated with Wilson-Turner Syndrome include small head circumference, high forehead, prominent ears, and nose with a flattened bridge. There have been cases of a moderately high palate. Low muscle tone and subcutaneous swelling in facial tissue has also been noted. Thick eyebrows are also common. However, there has been reported cases where individuals had none of the mentioned facial features, which shows phenotypic abnormalities have possible environmental influences.

- Gynecomastia is a non-cancerous increase in male breast tissue. It is believed that disturbances in the endocrine system leads to an increase in estrogen and androgen hormones lead to the development of gynecomastia. A key feature of gynecomastia is a rubbery or firm glandular subcutaneous chest tissue that is palpated under the areola of the nipple, instead of the soft fatty tissue. There can also be in increase in diameter of the areola asymmetry in the chest tissue. The breast enlargement can occur in one or both side. Similar to truncal obesity, gynecomastia becomes apparent around the age of puberty.

Genitopatellar syndrome is a rare condition characterized by genital abnormalities, missing or underdeveloped kneecaps (patellae), intellectual disability, and abnormalities affecting other parts of the body.

Genitopatellar syndrome is also associated with delayed development and intellectual disability, which are often severe. Affected individuals may have an unusually small head (microcephaly) and structural brain abnormalities, including underdeveloped or absent tissue connecting the left and right halves of the brain (agenesis of the corpus callosum).

Aarskog–Scott syndrome is a rare disease inherited as X-linked and characterized by short stature, facial abnormalities, skeletal and genital anomalies. This condition mainly affects males, although females may have mild features of the syndrome.

The Aarskog–Scott syndrome (AAS) is also known as the Aarskog syndrome, faciodigitogenital syndrome, shawl scrotum syndrome and faciogenital dysplasia.

People with Renpenning's typically begin learning language at an ordinary pace, but by the age of 3–4 they experience a regression in mental and physical development, such as mild low muscle tone resulting in elongated faces and rapid loss in the normal growth of the head (microcephaly). Small testes and short stature are also known to commonly occur.

Manifestations include enlarged viscera, hepatomegaly, diabetes, short stature and cranial hyperostosis.

Males with 48, XXXY can have average or tall stature, which becomes more prominent in adulthood. Facial dysmorphism is common in males with 48, XXXY and can include increased distance between the eyes (hypertelorism), skin folds of the upper eyelid (epicanthal folds), up-slanting opening between the eyelids (palpebral fissures) and hooded eyelids. Other physical features include the fifth finger or "pinky" to be bent inwards towards the fourth finger (clinodactyly), short nail beds, flat feet, double jointedness (hyperextensibility) and prominent elbows with cubitus varus where the arm rests closer to the body. Musculoskeletal features may include congentical elbow dislocation and the limited ability of the feet to roll inwards while walking and upon landing. Micropenis is another common symptom of this syndrome.

Individuals affected with XXXY are also prone to developing Taurodontism, which often presents early in life, and can be an early indicator of XXY syndrome. Those with this syndrome are also prone to hip dysplasia, and other joint abnormalities. An individual’s symptoms vary due to differing androgen deficiencies, and also with alter with age. Prepubescent boys with XXXY syndrome may not differ in physical appearance from a child without the syndrome. This is likely because androgen levels do not differ among pre-pubescent boys, but a difference does arise as puberty progresses. Those with XXXY syndrome may also experience feminine distribution of adipose tissue, and gynecomastia may also be present. Tall stature is more likely to appear in adolescence, when androgen levels begin to differ between those with XXXY syndrome and those that do not have it.

Wilson-Turner Syndrome (WTS), also known as Mental Retardation X Linked Syndromic 6 (MRXS6), or Mental Retardation X Linked with Gynecomastia and Obesity is a congenital condition characterized by intellectual disability and associated with childhood-onset obesity. It is found to be linked to the X chromosome and caused by a mutation in the HDAC8 gene, which is located on the q arm at locus 13.1. Individuals with Wilson–Turner syndrome have a spectrum of physical characteristics including dysmorphic facial feature, hypogonadism, and short stature. Females generally have milder phenotype than males. The study of X-linked mental retardation began in 1943 when Martin and Bell reported a family exhibiting sex-linked mental retardation. However, this syndrome was not recognized until 1991. Wilson studied 14 males from 3 successive generations that presented hypogonadism, mental retardation, gynecomastia, short stature, among other symptoms. Eventually, this disorder was ruled distinct from a syndrome presented by Prader and Willi (Prader-Willi syndrome) because of its mode of inheritance, gynecomastia, and presence of small hands and feet. However, there are some speculations that this syndrome is in the same spectrum as the Cornelia de Lange syndrome. This disorder affects all demographics equally and is seen in less than one in one million people.

Children with the Sanjad Sakati syndrome have a triad of:

a) hypoparathyroidism (with episodes of hypocalcemia, hypocalcemic tetany and hypocalcemic seizures.

b) severe mental retardation and

c) dysmorphism.

Typically, children with this syndrome are born low-birth-weight due to intrauterine growth retardation. At birth, there is dysmorphism, which is later typified into the features described below. The child is stunted, often with demonstrable growth hormone deficiency and has moderate to severe mental retardation, mainly as a consequence of repeated seizures brought on by the low blood ionic calcium levels. The immuno-reactive parathormone levels are low to undetectable, with low calcium and high phosphate levels in the blood.

"Dysmorphism" is most evident on the face, with the following features:

- Long narrow face

- Deep-set, small eyes

- Beaked nose

- Large, floppy ears

- Small head (microcephaly) and

- Thin lips with a long philtrum.

Those with XXXY syndrome can have testicular dysgenesis and hypergonadotrophic hypogonadism. Testicular dygenesis is a condition in which a male has incomplete or complete loss of spermatogenesis, so that the individual produces very low levels, or no sperm. This results in infertility of that individual. Hypergonadotrophic hypogonadism is a condition in which the function of the testes in males is reduced and can result in low levels of sex steroids produced like testosterone.

Genitopatellar syndrome is a rare disorder with characteristic craniofacial features, congenital flexion contractures of the lower limbs, absent or abnormal patellae, urogenital anomalies, and severe psychomotor retardation.

In 2012, it was shown that mutations in the gene KAT6B cause the syndrome.

While inclusion criteria for Rud syndrome have varied considerably, the major manifestations includes congenital ichthyosis, hypogonadism, small stature, mental retardation, and epilepsy. Ocular findings were inconsistently reported and included strabismus, blepharoptosis, blepharospasm, glaucoma, cataract, nystagmus, and retinitis pigmentosa. Other systemic includes metabolic, bony, neurologic, and muscular abnormalities.

49,XXXXY syndrome is an extremely rare aneuploidic sex chromosomal abnormality. It occurs in approximately 1 out of 85,000 to 100,000 males.

Renpenning's syndrome is a neurodevelopmental disorder recognised in males that causes intellectual disability, mild growth retardation with examples in the testes and head, and a somewhat short stature. The condition only affects males, starting at birth, and was first characterized in 1962. but first described by Hans Renpenning in 1963 after he documented these traits on many children in one family alone.

It can be associated with "PQBP1".

Different areas of deletion are associated with different symptoms. Deletions from the centromere to 13q32 or any deletions including the 13q32 band are associated with slow growth, intellectual disability, and congenital malformations. Deletions from 13q33 to the end of the chromosome are associated with intellectual disability. Intellectual disabilities range from very mild to very severe, and can co-occur with behavioral disorders and/or autism spectrum disorders.

At birth, the main symptoms include low weight (due to intrauterine growth restriction), hypotonia, and feeding difficulties. Infants may also have cleft palate.

13q deletion syndrome gives a characteristic appearance to affected individuals, potentially including microphthalmia (small eyes), hypertelorism (wide-set eyes), thin forehead, high palate, underdeveloped midface, small mouth, small nose, broad, flat nasal bridge, short neck, low hairline, irregular or wrongly positioned teeth, low-set ears, micrognathia (small jaw), tooth enamel defects, short stature, microcephaly (small head), a prominent, long philtrum, and earlobes turned inwards.

Congenital heart disease is associated with 13q deletion syndrome. Common defects include atrial septal defect, tetralogy of Fallot, ventricular septal defect, patent ductus arteriosus, pulmonary stenosis, and coarctation of the aorta. Defects of the endocrine system, digestive system, and genitourinary system are also common. These include underdevelopment or agenesis of the pancreas, adrenal glands, thymus, gallbladder, and thyroid; Hirschsprung's disease; gastric reflux, imperforate anus, retention testis, ectopic kidney, renal agenesis, and hydronephrosis.

A variety of brain abnormalities are also associated with 13q deletion. They can include epilepsy, craniosynostosis (premature closing of the skull bones), spastic diplegia, cerebral hypotrophy, underdevelopment or agenesis of the corpus callosum, cerebellar hypoplasia, deafness, and, rarely, hydrocephalus, Dandy–Walker syndrome, and spina bifida. The eyes can be severely damaged and affected individuals may be blind. They may also have coloboma of the iris or choroid, strabismus, nystagmus, glaucoma, or cataracts.

Other skeletal malformations are found with 13q deletion syndrome, including syndactyly, clubfoot, clinodactyly, and malformations of the vertebrae and/or thumbs.

Deletions that include the 13q32 band, which contains the brain development gene ZIC2, are associated with holoprosencephaly; they are also associated with hand and foot malformations. Deletions that include the 13q14 band, which contains the tumor suppressor gene Rb, are associated with a higher risk of developing retinoblastoma, which is more common in XY children. Deletion of the 13q33.3 band is associated with hypospadias. Other genes in the potentially affected region include NUFIP1, HTR2A, PDCH8, and PCDH17.

XYY syndrome is a genetic condition in which a male has an extra Y chromosome. Symptoms are usually few. They may include being taller than average, acne, and an increased risk of learning problems. The person is generally otherwise normal, including normal fertility.

The condition is generally not inherited from a person's parents but rather occurs as a result of a random event during sperm cell development. Diagnosis is by a chromosomal analysis. There are 47 chromosomes, instead of the usual 46, giving a 47,XYY karyotype.

Treatment may include speech therapy or extra help with schoolwork. Outcomes are generally good. Prevention is not possible. The condition occurs in about 1 in 1,000 male births. Many people with the condition are unaware that they have it. The condition was first described in 1961.

It causes facial abnormalities, skeletal malformation and occasionally neural tube defects; the skeletal disfigurements resolve to a degree in the course of development.

Mutations in different parts of the gene may lead to deafness or Stickler syndrome type III (eye problems: myopia, retinal detachment and skeletal abnormalities).

Infants and children: Infants that are born with Weissenbacher-Zweymüller syndrome usually have short bones in their arms and legs. The thigh and upper arm bones are wider than usual resulting in a dumbbell-shape while the bones of the vertebrae may be abnormal. Typical abnormal facial features can be wide-set protruding eyes (hypertelorism), a small and upturned nose with a flat bridge, small jaw (micrognathia) and a cleft palate. Some infants have high-frequency hearing loss. Infants may also exhibit a psychomotor delay. After the period of growth deficiency the individual makes improvements in bone growth leading to a normal physical development around age 5 or 6.

Adults: Many with Weissenbacher-Zweymüller syndrome have a catch-up growth phase causing the adults to not be unusually short. Many adults still will have hearing loss and typical abnormal facial features of Weissenbacher-Zweymüller syndrome.

Craniofacial and other features of LFS include: maxillary hypoplasia (underdevelopment of the upper jaw bone), a small mandible (lower jaw bone) and receding chin, a high-arched palate (the roof of the mouth), with crowding and misalignment of the upper teeth; macrocephaly (enlarged skull) with a prominent forehead, hypernasal speech (voice), a long nose with a high, narrow nasal bridge; a deep, short philtrum (the indentation in the upper lip, beneath the nose), low-set ears with some apparent retroversion, hypotonia (decreased muscle tone), pectus excavatum (a malformity of the chest), slightly enlarged to normal testicular size in males, and seizures.

Hypernasal speech, or "hypernasality", is primarily the result of velopharyngeal insufficiency, a sometimes congenital aberration in which the velopharyngeal sphincter allows too much air into the nasal cavity during speech. In LFS, hypernasality may also be caused by failure of the soft palate and uvula to reach the back wall of the pharynx (the interior cavity of the throat where swallowing generally occurs) during speech, a condition that can be associated with a submucosal cleft palate.

LFS is clinically distinguished from other X-linked forms of intellectual disability by the accompanying presence of marfanoid habitus. Marfanoid habitus describes a group of physical features common to Marfan syndrome. Including Marfan syndrome and LFS, marfanoid features of this type have also been observed with several other disorders, one of which is multiple endocrine neoplasia type 2.

In LFS, specific features identified as marfanoid include: a long, narrow face; tall, thin stature; long, slender limbs, fingers and toes (not unlike arachnodactyly) with joint hyperextensibility, shortened halluces (the big toes) and long second toes.

The diagnosis of marfanoid habitus in LFS is often delayed because many of the physical features and characteristics associated with it are usually not evident until adolescence.

People with the 47,XYY karyotype have an increased growth velocity from early childhood, with an average final height approximately 7 cm (3") above expected final height. In Edinburgh, Scotland, eight 47,XYY boys born 1967–1972 and identified in a newborn screening programme had an average height of 188.1 cm (6'2") at age 18—their fathers' average height was 174.1 cm (5'8½"), their mothers' average height was 162.8 cm (5'4"). The increased gene dosage of three X/Y chromosome pseudoautosomal region (PAR1) SHOX genes has been postulated as a cause of the increased stature seen in all three sex chromosome trisomies: 47,XXX, 47,XXY, and 47,XYY.

Severe acne was noted in a very few early case reports, but dermatologists specializing in acne now doubt the existence of a relationship with 47,XYY.

Testosterone levels (prenatally) are normal in 47,XYY males. Most 47,XYY males have normal sexual development and have normal fertility.