SFMS affects the skeletal and nervous system. This syndrome's external signs would be an unusual facial appearance with their heads being slightly smaller and unusually shaped, a narrow face which is also called dolichocephaly, a large mouth with a drooping lower lip that are held open, protruding upper jaw, widely spaced upper front teeth, an underdeveloped chin, cleft palate and exotropied-slanted eyes with drooping eyelids.

Males who have SFMS have short stature and a thin body build. Also skin is lightly pigmented with multiple freckles. They may have scoliosis and chest abnormalities.

Affected boys have reduced muscle tone as infants and young children. X-rays sometimes show that their bones are underdeveloped and show characteristics of younger bones of children. Boys usually under the age of 10 have reduced muscle tone but later, patients with SFMS over the age of 10 have increased muscle tone and reflexes that cause spasticity. Their hands are short with unusual palm creases with short, shaped fingers and foot abnormalities are shortened and have fused toes and usually mild.

They have an absent of a spleen and the genitals may also show undescended testes ranging from mild to severe that leads to female gender assignment.

People who have SFMS have severe mental retardation. They are sometimes restless, behavior problems, seizures and severe delay in language development. They are self-absorbed with reduced ability to socialize with others around them. They also have psychomotor retardation which is the slowing-down of thoughts and a reduction of physical movements. They have cortical atrophy or degeneration of the brain's outer layer. Cortical atrophy is usually founded in older affected people.

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.

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.

Not all of the DOOR symptoms are consistently present. They can vary in severity, and additional features can be noted in individuals affected by DOOR syndrome.

Some of these additional features are:

- Polyhydramnios (increased amniotic fluid during pregnancy) and increased nuchal fold during pregnancy

- Specific facial features such as a large nose

- Severe and sometimes refractory seizures, abnormalities on the magnetic resonance imaging of the brain

- Increased 2-oxoglutaric acid in the blood and urine - this compound is made or used by several enzymes

- Finger-like thumbs

- Visual impairment

- Peripheral neuropathy (nerves conducting sensation from extremities to the brain) and insensivity to pain

Intellectual impairment is present in all reported cases, but the severity can vary widely. The prognosis in terms of survival also varies greatly from early childhood till adulthood.

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.

Coffin–Lowry syndrome is a severe mental retardation associated with abnormalities of:

- Growth

- "In utero" growth is normal but post natal growth is retarded. Patients are sometimes microcephalic.

- Cardio-vascular

- Cardiac abnormalities affect 15% of the patients.

- Skeleton

- Progressive kyphoscoliosis affects 1 in 2 patients. Micrognathia is also associated with this syndrome.

- Patients may also have an underdeveloped upper jaw bone, abnormally prominent brows, or widely spaced eyes.

- Vision and audition

- Auditory abnormalities are frequent and often present. Vision abnormalities are not often present.

Other features include:

- Stunting

- Small hands and feet with long, tapering fingers and clinodactyly

- Dental anomalies in the form of malalignment and malocclusion

In another study of six patients, the patients were investigated further. They were found to have low levels of IGF-1 and markedly retarded bone age.

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.

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.

The acronym "MASA" describes the four major symptoms - Mental retardation, Aphasia, Shuffling gait, and Adducted thumbs. Another name for this syndrome is "L1 syndrome".

The term "CRASH", for "corpus callosum hypoplasia, retardation, adducted thumbs, spastic paraplegia, and hydrocephalus" has also been used to describe L1CAM-related disorders.

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.

DOOR (deafness, onychdystrophy, osteodystrophy, and mental retardation) syndrome is a genetic disease which is inherited in an autosomal recessive fashion. DOOR syndrome is characterized by mental retardation, sensorineural deafness, abnormal nails and phalanges of the hands and feet, and variable seizures. A similar deafness-onychodystrophy syndrome is transmitted as an autosomal dominant trait and has no mental retardation. Some authors have proposed that it may be the same as Eronen Syndrome, but since both disorders are extremely rare it is hard to make a determination.

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.

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.

Smith–Fineman–Myers syndrome (SFMS1), congenital disorder that causes birth defects. This syndrome was named after 3 men, Richard D. Smith, Robert M. Fineman and Gart G. Myers who discovered it around 1980.

At birth, there is no sign that a child will develop symptoms of aspartylglucosaminuria. Typically, signs and symptoms become apparent between two and four years of age and become progressively worse as the individual ages. The following signs and symptoms may appear:

- Individuals are more prone to respiratory infections

- Development of scoliosis

- Seizures or difficulty with movement

- Skin and joints may become loose

- Facial features change progressively; this may include:

- Progression of developmental and mental disabilities, including:

- An intellectual peak occurs in the mid-teens and allows a plateau for the disease. Once an individual hits the age of 25-30 the decrease begins again, including:

(Children are physically uncoordinated, but remain able to play sports and do everyday activities until they reach adulthood.)

- During the first year of life inguinal and umbilical hernias are common.

- Less severe symptoms include:

- People with aspartylglucosaminuria may have lower than average height, because they tend to go through puberty earlier.

- Epilepsy may develop in adulthood.

- Finnish studies have shown that life expectancy is shorter than average.

Alpha-thalassemia mental retardation syndrome (ATRX), also called alpha-thalassemia X-linked mental retardation, nondeletion type or ATR-X syndrome, is a condition caused by a mutated gene. Females with this mutated gene have no specific signs or features, but may demonstrate skewed X chromosome inactivation. Hemizygous males tend to be moderately intellectually disabled and have physical characteristics including coarse facial features, microcephaly (small head size), hypertelorism (widely spaced eyes), a depressed nasal bridge, a tented upper lip, and an everted lower lip. Mild or moderate anemia, associated with alpha-thalassemia, is part of the condition.

It is associated with "ATRX".

The incidence of this condition is <1 per million population. It is found only in females as all affected males die before birth. Teeth with large roots (radiculomegaly), heart defects, and small eyes (microphthalmia) are the characteristic triad found in this syndrome.

Typical features of the condition include:

- Face

- Deep set eyes

- Broad nasal tip divided by a cleft

- Eyes

- Microphthalmia (small eyes)

- Early cataracts

- Glaucoma

- Teeth

- Radiculomegaly (teeth with very large roots)

- Delayed loss of primary teeth

- Missing (oligodontia) or abnormally small teeth

- Misaligned teeth

- Defective tooth enamel.

- Heart defects

- Atrial and/or ventricular defects

- Mitral valve prolapse

- Mild mental retardation and conductive or sensorineural hearing loss may occur.

MASA syndrome, also called CRASH syndrome, Gareis-Mason syndrome, L1 syndrome, spastic paraplegia 1 is a rare X-linked recessive neurological disorder.

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

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.

Clinical manifestations similar to all five described cases of Kapur–Toriello syndrome severe neurodevelopment delay, microphthalmia and/or coloboma, low set and malformed ears, bilateral cleft lip and palate, and constipation. Out of the five cases, two cases presented with imperforated anus/rectal stenosis. Both cases were described in females and, although not definitive, may describe clinical manifestations that differ between sexes.

Along with the four aspects of the disorder that give it its name, there are also other common symptoms:

- A downward slant of the forehead

- Delayed bone maturation

- Mental retardation

The ocular abnormalities are generally retinal coloboma and nystagmus.

The main symptoms are given by its name: dry, scaly skin (ichthyosis), absence of hair (atrichia) and excessive sensitivity to light (photophobia). Additional features include short stature, mental retardation, seizures and a tendency for respiratory infections.

X-linked intellectual disability (previously known as X-linked mental retardation) refers to forms of intellectual disability which are specifically associated with X-linked recessive inheritance.

As with most X-linked disorders, males are more heavily affected than females. Females with one affected X chromosome and one normal X chromosome tend to have milder symptoms.

Unlike many other types of intellectual disability, the genetics of these conditions are relatively well understood. It has been estimated there are ~200 genes involved in this syndrome; of these ~100 have been identified.

X-linked intellectual disability accounts for ~16% of all cases of intellectual disability in males.