Symptoms of M2DS include infantile hypotonia and failure to thrive, delayed psychomotor development, impaired speech, abnormal or absent gait, epilepsy, spasticity, gastrointestinal motility problems, recurrent infections, and genitourinary abnormalities. Many of those affected by M2DS also fit diagnostic criteria for autism. M2DS can be associated with syndromic facies, namely an abnormally flat back of the head, underdevelopment of the midface, ear anomalies, deep-set eyes, prominent chin, pointed nose, and a flat nasal bridge.

Alopecia contractures dwarfism mental retardation syndrome or (ACD mental retardation syndrome) is a developmental disorder which causes mainly baldness and dwarfism in combination with intellectual disability; skeletal anomalies, caries and nearsightedness are also typical.

The ACD mental retardation syndrome was first described in 1980 by Albert Schinzel and only few cases have since been identified in the world. At the time Dr. Schinzel made no conclusion of the hereditary pattern of this syndrome but similarities between cases reported by year 2000 seem to suggest autosomal or x-linked recessive inheritance or possibly a dominant mutation caused by mosaicism as causes of this syndrome.

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.

The combination of muscular hypotonia and fixed dilated pupils in infancy is suspicious of Gillespie syndrome. Early onset partial aniridia, cerebellar ataxia, and mental retardation are hallmark of syndrome. The iris abnormality is specific and seems pathognomonic of Gillespie syndrome. The aniridia consisting of a superior coloboma and inferior iris hypoplasia, foveomacular dysplasia.

Atypical Gillespie syndrome associated with bilateral ptosis, exotropia, correctopia, iris hypoplasia, anterior capsular lens opacities, foveal hypoplasia, retinal vascular tortuosity, and retinal hypopigmentation.

Neurological signs ar nystagmus, mild craniofacial asymmetry, axial hypotonia, developmental delay, and mild mental retardation. Mariën P did not support the prevailing view of a global mental retardation as a cardinal feature of Gillespie syndrome but primarily reflect cerebellar induced neurobehavioral dysfunctions following disruption of the cerebrocerebellar anatomical circuitry that closely resembles the "cerebellar cognitive and affective syndrome" (CeCAS).

Congenital pulmonary stenosis and helix dysplasia can be associated.

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

Psychopathology and related behavioral abnormalities are typically seen in LFS, and they may be considered in the diagnosis of the disorder. The most common of these in LFS is an autism-like spectrum disorder, and LFS is considered as one of a number of genetic disorders associated with autism. Additional alterations of psychopathology with behavioral manifestations that have been observed in LFS include: psychotic behavior, schizophrenia, hyperactivity and attention-deficit hyperactivity disorder, aggression, oppositional defiant disorder, obsessive compulsive disorder, extreme shyness, learning disability, cognitive impairment, short-term memory deficit, low frustration tolerance, social dysfunction, lack of impulse control, eating disorder and associated malnutrition, attributed to psychogenic loss of appetite; and pyromania.

While psychiatric conditions like these are to be expected with LFS, there have also been cases of the disorder with some preservation of mental and behavioral abilities, such as problem solving, reasoning and normal intelligence.

The psychopathology of LFS usually exhibits schizophrenia. When schizophrenia is diagnosed in an individual known to be affected by intellectual disability, LFS may be considered in the differential diagnosis of schizophrenia, with confirmation of cause through appropriate psychiatric and genetic evaluation methods.

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.

Associated symptoms range from things such as colobomas of the eyes, heart defects, ichthyosiform dermatosis, intellectual disability, and ear abnormalities. Further symptoms that may be suggested include characteristic facies, hearing loss, and cleft palate.

There is a wide range of congenital problems associated with kabuki syndrome with large differences between affected individuals. Some of the common problems are heart defects, urinary tract anomalies, hearing loss, hypotonia, recurrent ear infections and postnatal growth deficiency. Other characteristics include skeletal abnormality, joint laxity, short stature, and unusual dermatoglyphic patterns.

In terms of development, mild to moderate intellectual disability is a common feature. Also, children with kabuki syndrome often have distinctive behavioral features. A few have normal intelligence, most of whom have learning difficulties such as struggling with fine motor, speech skills, and memory.

There is no indication that the life expectancy of individuals with kabuki syndrome is shortened. Most medical issues are resolved with medical intervention. The fact that there are relatively few adults known with this syndrome is probably related to its recent discovery in 1980 in Japan and around 1990 in Europe and America.

Most children with Allan–Herndon–Dudley syndrome have weak muscle tone (hypotonia) and underdevelopment of many muscles (muscle hypoplasia). As they get older, they usually develop joint deformities called contractures, which restrict the movement of certain joints. Abnormal muscle stiffness (spasticity), muscle weakness, and involuntary movements of the arms and legs also limit mobility. As a result, many people with Allan–Herndon–Dudley syndrome are unable to walk independently and become wheelchair-bound by adulthood.

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.

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.

Affected newborns generally have striking neurological defects and seizures. Severely impaired development is common, but disturbances in motor functions may not appear until later in life.

Infants with microcephaly are born with either a normal or reduced head size. Subsequently, the head fails to grow, while the face continues to develop at a normal rate, producing a child with a small head and a receding forehead, and a loose, often wrinkled scalp. As the child grows older, the smallness of the skull becomes more obvious, although the entire body also is often underweight and dwarfed. Development of motor functions and speech may be delayed. Hyperactivity and intellectual disability are common occurrences, although the degree of each varies. Convulsions may also occur. Motor ability varies, ranging from in some to spastic quadriplegia in others.

The three most common symptoms of Opitz G/BBB syndrome (both type I & II) are hypertelorism (exceptionally wide-spaced eyes), laryngo-tracheo-esophalgeal defects (including clefts and holes in the palate, larynx, trachea and esophagus) and hypospadias (urinary openings in males not at the tip of the penis) (Meroni, Opitz G/BBB syndrome, 2012). Abnormalities in the larynx, trachea and esophagus can cause significant difficulty breathing and/or swallowing and can result in reoccurring pneumonia and life-threatening situations. Commonly, there may be a gap between the trachea and esophagus, referred to as a laryngeal cleft; which can allow food or fluid to enter the airway and make breathing and eating a difficult task.

Genital abnormalities like a urinary opening under the penis (hypospadias), undescended testes (cryptorchidism), underdeveloped scrotum and a scrotum divided into two lobes (bifid scrotum) can all be commonplace for males with the disease.

Developmental delays of the brain and nervous system are also common in both types I and II of the disease. 50% of people with Opitz G/BBB Syndrome will experience developmental delay and mild intellectual disability. This can impact motor skills, speech and learning capabilities. Some of these instances are likened to autistic spectrum disorders. Close to half of the people with Opitz G/BBB Syndrome also have a cleft lip (hole in the lip opening) and possibly a cleft palate (hole in the roof of the mouth), as well. Less than half of the people diagnosed have heart defects, imperforate anus (obstructed anal opening), and brain defects. Of all the impairments, female carriers of X-linked Type I Opitz G/BBB Syndrome usually only have ocular hypertelorism.

The facial appearance of individuals with this syndrome include long eyelids with turning up of the lateral third of the lower eyelid, a broad and depressed nasal tip, large prominent earlobes, and a cleft or high-arched palate.

Other clinical features often include scoliosis, short fifth finger, persistence of fingerpads, and X-ray abnormalities of the vertebrae, hands, and hip joints.

Common signs of Say–Meyer syndrome are trigonocephaly as well as head and neck symptoms. The head and neck symptoms come in the form of craniosynostosis affecting the metopic suture (the dense connective tissue structure that divides the two halves of the skull in children which usually fuse together by the age of six). Symptoms of Say–Meyer syndrome other than developmental delay and short stature include

- Intellectual disability.

- Low-set ears/posteriorly rotated ears

- Intellectual deficit as well as learning disability

- Intrauterine growth retardation (poor growth of a baby while it is in the mother's womb)

- Posterior fontanel

- Premature synostosis of the lambdoid suture (the fusion of the bones to the joint is premature)

- Narrow forehead

- Trigonocephaly (a frontal bone anomaly that is characterized by a premature fusion of the bones which gives the forehead a triangular shape)

- Hypotelorism or hypertelorism (reduced or increased width between the eyes)

- Craniosynostosis (when one or more seam-like junctions between two bones fuses by turning into bone. This changes the growth pattern of the skull)

- Low birth weight and height

The affected patients sometimes show a highly arched palate, clinodactyly (a defect in which toes or fingers are positioned abnormally) and ventricular septal defect (a heart defect that allows blood to pass directly from left to the right ventricle which is caused by an opening in the septum). Overall, Say–Meyer syndrome impairs growth, motor function, and mental state.

MECP2 Duplication Syndrome (M2DS) is a rare disease that is characterized by severe intellectual disability and impaired motor function. It is an X-linked genetic disorder caused by the overexpression of MeCP2 protein.

Several X-linked syndromes include intellectual disability as part of the presentation. These include:

- Coffin–Lowry syndrome

- MASA syndrome

- MECP2 duplication syndrome

- X-linked alpha thalassemia mental retardation syndrome

- mental retardation and microcephaly with pontine and cerebellar hypoplasia

ATR-16 syndrome affects the blood, development, and brain; symptoms vary based on the specific genes deleted on chromosome 16. Because it is so rare, it is difficult to determine the "core" symptoms of the disease. People with ATR-16 have alpha-thalassemia, a blood disorder where there is less normal hemoglobin in the blood than there should be, and the red blood cells are smaller than they should be (microcytic anemia). Affected children have various characteristic physical features, including clubfoot, "locked" little fingers, microcephaly (small head), hypertelorism (widely spaced eyes), broad, prominent nose bridge, downward-slanted palpebral fissures, small ears, retrognathia, and short neck. Children with ATR-16 syndrome also have mild to moderate intellectual disabilities, developmental delays/growth delays, and speech delays. Some children with ATR-16 have seizures, cryptorchidism (undescended testes), or hypospadias.

Gillespie syndrome, also called aniridia, cerebellar ataxia and mental deficiency. is a rare genetic disorder. The disorder is characterized by partial aniridia (meaning that part of the iris is missing), ataxia (motor and coordination problems), and, in most cases, intellectual disability. It is heterogeneous, inherited in either an autosomal dominant or autosomal recessive manner. Gillespie syndrome was first described by American ophthalmologist Fredrick Gillespie in 1965.

The syndrome is characterized by alopecia, hypogonadism, hypothyroidism, hearing loss, intellectual disability and diabetes mellitus. Electrocardiogram anomalies have also been reported.

Dental features:

- small teeth in males

- pointed (screwdriver shaped or conical) incisors (sometimes called Hutchinson teeth)

- incisors with an irregulal incisal edge

- canines: enlarged and globular; may be dome or bud shaped with trilobed edge

- premolars and molars: small, round and globular; may have supernumary lobes (mulberry or lotus flower shape)

- widely separated teeth (diastemma)

- hypoplastic enamel

- dental agenesis

- presence of mesiodents (median incisor behind normal upper incisors)

- pulp chamber anomalies

Facial features:

- anteverted pinnae

- long face

- prominent nasal bridge and nose

- prognathism occasionally

Ophthalmic features:

- bilateral congenital nuclear opacities (100%)

- severe amblyopia

- nystagmus (93%)

- strabismus (43%)

- microcornea (96%)

- congenital glaucoma

- scleral staphylomas

- retinal cystoid degeneration

- microphthalmia

These lead to severe visual impairment in affected males.

Other:

- The fourth metacarpal may be shortened

30% of patients also have some degree of intellectual impairment: of these 80% are mildly to moderately affected: the other 20% may have developmental delays and behavior problems.

Carrier females display milder variable symptoms of disease. Ocular signs are present in 90% of heterozygous females. These are typically lens opacities often involving the posterior Y sutures. More rarely dental anomalies and the characteristic facial features may also occur.

Allan–Herndon–Dudley syndrome is a rare X-linked inherited disorder of brain development that causes moderate to severe intellectual disability and problems with movement. This condition, which occurs almost exclusively in males, disrupts development from before birth.

Allan–Herndon–Dudley syndrome, which is named eponymously for William Allan, Florence C. Dudley, and C. Nash Herndon, results from a mutation of the thyroid hormone transporter MCT8 (also referred to as SLC16A2). Consecutively, thyroid hormones are unable to enter the nervous system, which depends on thyroid signaling for proper function and development.

FG syndrome's major clinical features include intellectual disability, usually severe; hyperactive behavior, often with an outgoing personality; severe constipation, with or without structural anomalies in the anus such as imperforate anus; macrocephaly; severe hypotonia; a characteristic facial appearance due to hypotonia, giving a droopy, "open-mouthed" expression, a thin upper lip, a full or pouting lower lip, and partial or complete loss of the corpus callosum. About a third of reported cases of individuals with FG syndrome die in infancy, usually due to respiratory infection; premature death is rare after infancy.

Zamzam–Sheriff–Phillips syndrome is a rare autosomal recessive congenital disorder. It is characterized by aniridia, ectopia lentis, abnormal upper incisors and intellectual disability. Not a lot of research has been undertaken of this particular disease so thus far there is no known gene that affects this condition. However it has been hypothesised that the symptoms described are found at a particular gene, though intellectual disability is believed to be due to a different genetic cause.

Consanguinuity (intermarrying among relatives such as cousins), often associated with autosomal recessive inheritance, has been attributed to the inheritance of this disease.