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.

The clinical manifestations present at birth are generalized hypotonia, muscle weakness, developmental delay with mental retardation and occasional seizures. The congenital muscular dystrophy is characterized by hypoglycosylation of α-dystroglycan.

Those born with the disease also experience severe ocular and brain defects. Half of all children with WWS are born with encephalocele, which is a gap in the skull that will not seal. The meninges of the brain protrude through this gap due to the neural tube failing to close during development. A malformation of the a baby's cerebellum is often a sign of this disease.Common ocular issues associated with WWS are abnormally small eyes and retinal abnormalities cause by an underdeveloped light-sensitive area in the back of the eye.

Individuals with this syndrome typically develop normally until reaching the second decade of their lives but the onset of symptoms has been observed as early as age seven. The first defect observed in individuals who suffer from this condition affects the auditory system and is known as bilateral nerve deafness. Another early symptom is the development of myopia (nearsightedness). In addition to bilateral nerve deafness and myopia, other symptoms that plague infected individuals early in disease progression include ataxia, muscle wasting, severe peripheral neuritic pain sometimes accompanied by elevated spinal fluid protein, and joint stiffness.

The central nervous system (CNS) is affected with deficits in the cerebral cortex which indicate signs of mental retardation even though psychological observations appear relatively normal for individuals studied. Atypical epilepsy is also a common feature of CNS malfunctioning including aphasia expressions, blurred vision, and numbness of the face and limbs.

In the third decade of the condition, individuals develop further visual problems including retinitis pigmentosa, and bilateral cataracts. Sufferers endure the restriction of visual fields, night blindness, and eventually severe or complete blindness.

Individuals with this syndrome exhibit many physical deformities including skeletal, epidermal, and subcutaneous abnormalities. The skeletal problems are characterized by scoliosis and muscle weakness indicative of the kyphoscoliotic type which follow muscle wasting and peripheral neuritis (nerve inflammation). Osteoporosis is also observed in many cases. Skin and subcutaneous atrophy is common as well as skin ulcerations due to inability of the skin to heal. One of the final manifestations of disease is baldness.There is no evidence that the progression of Flynn–Aird syndrome shortens the patient's life-span, but the terrible conditions certainly increase morbidity.

The syndrome causes cerebellar ataxia (balance and coordination problems), mental retardation, congenital cataracts in early childhood, muscle weakness, inability to chew food, thin brittle fingernails, and sparse hair.

Small stature, mild to severe mental retardation and dysarthria (slow, imprecise speech) are usually present.

Various skeletal abnormalities (e.g., curvature of the spine) and hypergonadotropic hypogonadism often occur.

Muscle weakness is progressive, but life expectancy is near normal.

Flynn–Aird syndrome is a rare, hereditary, neurological disease that is inherited in an autosomal dominant fashion. The syndrome involves defects in the nervous, auditory, skeletal, visual, and endocrine systems and encompasses numerous symptoms, bearing striking similarity to other known syndromes of neuroectodermal nature such as: Werner syndrome, Cockayne syndrome and Refsum syndrome.

The onset of Flynn–Aird syndrome typically occurs between ten and twenty years of age, however, the earliest case was diagnosed at age seven. As the syndrome progresses, initial symptoms tend to intensify and new symptoms become apparent. Unlike related syndromes and despite the intensity of symptoms in the disease progression, Flynn–Aird syndrome does not appear to shorten life expectancy.

The disease is characterized by early-onset dementia, ataxia, muscle wasting, skin atrophy, and eye abnormalities. In addition, patients have the potential of developing a number of other related symptoms such as: cataracts, retinitis pigmentosa, myopia (nearsightedness), dental caries, peripheral neuropathy (peripheral nerve damage), deafness, and cystic bone changes. This syndrome was first discovered in the early 1950s by American neurologists P. Flynn and Robert B. Aird who analyzed one family lineage inheritance pattern of this disease.

Males show more serious symptoms than females affected by this disorder.

The symptoms for males are:

1. Profound sensorineural hearing loss i.e, a complete or almost complete loss of hearing caused by abnormalities in the inner ear.

2. Weak muscle tone - Hypotonia.

3. Impaired muscle coordination - Ataxia.

4. Developmental delay.

5. Intellecual disability.

6. Vision loss caused by optic nerve atrophy in early childhood.

7. Peripheral neuropathy.

8. Recurrent infections, especially in the respiratory system.

9. Muscle weakness caused by recurrent infections.

Symptoms for females:

Very rarely seen hearing loss that begins in adulthood (age > 20 years) combined with ataxia and neuropathy. Optic atrophy and retinitis pigmentosa observed in some cases too.

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.

Walker–Warburg syndrome (WWS), also called Warburg syndrome, Chemke syndrome, HARD syndrome (Hydrocephalus, Agyria and Retinal Dysplasia), Pagon syndrome, cerebroocular dysgenesis (COD) or cerebroocular dysplasia-muscular dystrophy syndrome (COD-MD), is a rare form of autosomal recessive congenital muscular dystrophy. It is associated with brain (lissencephaly, hydrocephalus, cerebellar malformations) and eye abnormalities. This condition has a worldwide distribution. The overall incidence is unknown but a survey in North-eastern Italy has reported an incidence rate of 1.2 per 100,000 live births. It is the most severe form of congenital muscular dystrophy with most children dying before the age of three years.

Cohen syndrome is diagnosed by clinical examination, but often difficult due to variation in expression.

Ocular complications, though rare, are listed as optic atrophy, microphthalmia, pigmentary chorioretinitis, hemeralopia (decreased vision in bright light), myopia, strabismus, nystagmus and iris/retinal coloboma.

General appearance is obesity with thin/elongated arms and legs. Micrognathia, short philtrum, and high vaulted palate are common. Variable mental retardation with occasional seizure and deafness also is characteristic of Cohen syndrome.

Diagnosis of MSS is based on clinical symptoms, magnetic resonance imaging (MRI) of the brain (cerebellar atrophy particularly involving the cerebellar vermis), and muscle biopsy.

It can be associated with mutations of the SIL1 gene, and a mutation can be found in about 50% of cases.

Differential diagnosis includes Congenital Cataracts Facial Dysmorphism Neuropathy (CCFDN), Marinesco–Sjögren like syndrome with chylomicronemia, carbohydrate deficient glycoprotein syndromes, Lowe syndrome, and mitochondrial disease.

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.

VLDLR-associated cerebellar hypoplasia (VLDLRCH; alternative names: dysequilibrium syndrome, DES; nonprogressive cerebellar disorder with mental retardation) is a rare autosomal recessive condition caused by a disruption of the VLDLR gene. First described as a form of cerebral palsy in the 1970s, it is associated with parental consanguinity and is found in secluded communities, with a number of cases described in Hutterite families.

Cohen syndrome (also known as Pepper syndrome or Cervenka syndrome, named after Michael Cohen, William Pepper and Jaroslav Cervenka, who researched the illness) is a genetic disorder.

One of the principle symptoms of GAPO syndrome is growth retardation, caused by slow skeletal formation and results in individuals being below average height. Alopecia, or hair loss, is another key indication of GAPO syndrome. Their hair is typically thinly dispersed, and fragile, which often leads to baldness later in life. Similarly, tooth growth is stunted, with teeth failing to emerge form the gums or otherwise develop normally. Atrophy of the optic nerve occurs in approximately one third of individuals. This degradation leads to inhibited peripheral vision, and increased difficulty distinguishing colours.

While not a defining feature, most sufferers of GAPO syndrome have coarse facial features, and abnormal structure of the middle portion of their faces, typically coupled with a large forehead. Individuals with the disease tend to have depressed nose bridges, protruding ears, and abnormally thick lips, though these symptoms are not unique to this disorder.

No direct correlation has been found between GAPO syndrome and mental retardation, though cases of individuals having both have been reported.

Due to the severity of the phenotype, GAPO syndrome can be diagnosed very early on. Most cases can be diagnosed by 6 months of age, and most symptoms will be apparent by age 2.

Theoretically, a mutation in any of the may cause disease, but below are some notable ones, with short description of symptoms:

- Adrenoleukodystrophy; leads to progressive brain damage, failure of the adrenal glands and eventually death.

- Alport syndrome; glomerulonephritis, endstage kidney disease, and hearing loss.

- Androgen insensitivity syndrome; variable degrees of undervirilization and/or infertility in XY persons of either gender

- Barth syndrome; metabolism distortion, delayed motor skills, stamina deficiency, hypotonia, chronic fatigue, delayed growth, cardiomyopathy, and compromised immune system.

- Blue cone monochromacy; low vision acuity, color blindness, photophobia, infantile nystagmus.

- Centronuclear myopathy; where cell nuclei are abnormally located in skeletal muscle cells. In CNM the nuclei are located at a position in the center of the cell, instead of their normal location at the periphery.

- Charcot–Marie–Tooth disease (CMTX2-3); disorder of nerves (neuropathy) that is characterized by loss of muscle tissue and touch sensation, predominantly in the feet and legs but also in the hands and arms in the advanced stages of disease.

- Coffin–Lowry syndrome; severe mental retardation sometimes associated with abnormalities of growth, cardiac abnormalities, kyphoscoliosis as well as auditory and visual abnormalities.

- Fabry disease; A lysosomal storage disease causing anhidrosis, fatigue, angiokeratomas, burning extremity pain and ocular involvement.

- Hunter's Syndrome; potentially causing hearing loss, thickening of the heart valves leading to a decline in cardiac function, obstructive airway disease, sleep apnea, and enlargement of the liver and spleen.

- Hypohidrotic ectodermal dysplasia, presenting with hypohidrosis, hypotrichosis, hypodontia

- Kabuki syndrome; multiple congenital anomalies and mental retardation.

- Spinal and bulbar muscular atrophy; muscle cramps and progressive weakness

- Lesch-Nyhan syndrome; neurologic dysfunction, cognitive and behavioral disturbances including self-mutilation, and uric acid overproduction (hyperuricemia)

- Lowe Syndrome; hydrophthalmia, cataracts, intellectual disabilities, aminoaciduria, reduced renal ammonia production and vitamin D-resistant rickets

- Menkes disease; sparse and coarse hair, growth failure, and deterioration of the nervous system

- Nasodigitoacoustic syndrome; mishaped nose, brachydactyly of the distal phalanges, sensorineural deafness

- Nonsyndromic deafness; hearing loss

- Norrie disease; cataracts, leukocoria along with other developmental issues in the eye

- Occipital horn syndrome; deformations in the skeleton

- Ocular albinism; lack of pigmentation in the eye

- Ornithine transcarbamylase deficiency; developmental delay and mental retardation. Progressive liver damage, skin lesions, and brittle hair may also be seen

- Siderius X-linked mental retardation syndrome; cleft lip and palate with mental retardation and facial dysmorphism, caused by mutations in the histone demethylase PHF8

- Simpson-Golabi-Behmel syndrome; coarse faces with protruding jaw and tongue, widened nasal bridge, and upturned nasal tip

- Spinal muscular atrophy caused by UBE1 gene mutation; weakness due to loss of the motor neurons of the spinal cord and brainstem

- Wiskott-Aldrich syndrome; eczema, thrombocytopenia, immune deficiency, and bloody diarrhea

- X-linked Severe Combined Immunodeficiency (SCID); infections, usually causing death in the first years of life

- X-linked sideroblastic anemia; skin paleness, fatigue, dizziness and enlarged spleen and liver.

Arts syndrome is a rare metabolic disorder that causes serious neurological problems in males due to a malfunction of the PRPP synthetase 1 enzyme. Arts Syndrome is part of a spectrum of PRPS-1 related disorders with reduced activity of the enzyme that includes Charcot–Marie–Tooth disease and X-linked non-syndromic sensorineural deafness.

Pontocerebellar hypoplasia is classified as follows:

Pontine and cerebellar hypoplasia is also observed in certain phenotypes of X-linked mental retardation – so called MICPCH.

Complete trisomy 8 causes severe effects on the developing fetus and can be a cause of miscarriage.

Complete trisomy 8 is usually an early lethal condition, whereas trisomy 8 mosaicism is less severe and individuals with a low proportion of affected cells may exhibit a comparatively mild range of physical abnormalities and developmental delay. Individuals with trisomy 8 mosaicism are more likely to survive into childhood and adulthood, and exhibit a characteristic and recognizable pattern of developmental abnormalities. Common findings include retarded psychomotor development, moderate to severe mental retardation, variable growth patterns which can result in either abnormally short or tall stature, an expressionless face, and many musculoskeletal, visceral, and eye abnormalities, as well as other anomalies. A deep plantar furrow is considered to be pathognomonic of this condition, especially when seen in combination with other associated features. The type and severity of symptoms are dependent upon the location and proportion of trisomy 8 cells compared to normal cells.

There is substantial variability in the severity of features of A-T among affected individuals, and at different ages. The following symptoms or problems are either common or important features of A-T:

- Ataxia (difficulty with control of movement) that is apparent early but worsens in school to pre-teen years

- Oculomotor apraxia (difficulty with coordination of head and eye movement when shifting gaze from one place to the next)

- Involuntary movements

- Telangiectasia (dilated blood vessels) over the white (sclera) of the eyes, making them appear bloodshot. These are not apparent in infancy and may first appear at age 5–8 years. Telangiectasia may also appear on sun-exposed areas of skin.

- Problems with infections, especially of the ears, sinuses and lungs

- Increased incidence of cancer (primarily, but not exclusively, lymphomas and leukemias)

- Delayed onset or incomplete pubertal development, and very early menopause

- Slowed rate of growth (weight and/or height)

- Drooling particularly in young children when they are tired or concentrating on activities

- Dysarthria (slurred, slow, or distorted speech sounds)

- Diabetes in adolescence or later

- Premature changes in hair and skin

Many children are initially misdiagnosed as having ataxic cerebral palsy. The diagnosis of A-T may not be made until the preschool years when the neurologic symptoms of impaired gait, hand coordination, speech and eye movement appear or worsen, and the telangiectasia first appear. Because A-T is so rare, doctors may not be familiar with the symptoms, or methods of making a diagnosis. The late appearance of telangiectasia may be a barrier to the diagnosis. It may take some time before doctors consider A-T as a possibility because of the early stability of symptoms and signs.

GAPO syndrome is a rare, autosomal recessive disorder that causes severe growth retardation, and has been observed fewer than 30 times before 2011. GAPO is an acronym that encompasses the predominant traits of the disorder: growth retardation, alopecia, pseudoanodontia (teeth failing to emerge from the gums), and worsening optic atrophy in some subjects. Other common symptoms include premature aging, large, prominent foreheads, and delayed bone aging. GAPO syndrome typically results in premature death around age 30-40, due to interstitial fibrosis and atherosclerosis.

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.

The first indications of A-T usually occur during the toddler years. Children start walking at a normal age, but may not improve much from their initial wobbly gait. Sometimes they have problems standing or sitting still and tend to sway backward or from side to side. In primary school years, walking becomes more difficult, and children will use doorways and walls for support. Children with A-T often appear better when running or walking quickly in comparison to when they are walking slowly or standing in one place. Around the beginning of their second decade, children with typical forms of A-T start using a wheelchair for long distances. During school years, children may have increasing difficulty with reading because of impaired coordination of eye movement. At the same time, other problems with fine-motor functions (writing, coloring, and using utensils to eat), and with slurring of speech (dysarthria) may arise. Most of these neurologic problems stop progressing after the age of about 12 – 15 years, though involuntary movements may start at any age and may worsen over time. These extra movements can take many forms, including small jerks of the hands and feet that look like fidgeting (chorea), slower twisting movements of the upper body (athetosis), adoption of stiff and twisted postures (dystonia), occasional uncontrolled jerks (myoclonic jerks), and various rhythmic and non-rhythmic movements with attempts at coordinated action (tremors).

In at least some case, the gene lesion involves a mutation in the "CSB" gene.

It can be associated with "ERCC6".

Mental retardation and microcephaly with pontine and cerebellar hypoplasia (MICPCH), also known as Mental retardation, X-linked, syndromic, Najm type (MRXSNA), is a rare genetic disorder of infants characterised by intellectual disability and pontocerebellar hypoplasia.

The disorder is associated with a mutation in the "CASK" gene which is transmitted in an X-linked manner. As with the vast majority of genetic disorders, there is no known cure to MICPCH.

The following values seem to be aberrant in children with CASK gene defects: lactate, pyruvate, 2-ketoglutarate, adipic acid and suberic acid, which seems to backup the proposal that CASK affects mitochondrial function. It is also speculated that phosphoinositide 3-kinase in the inositol metabolism is impacted in the disease, causing folic acid metabolization problems.

The severity of different forms of PCH varies, but many children inheriting the mutated gene responsible do not survive infancy or childhood; nevertheless, some individuals born with PCH have reached adulthood.