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.

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.

The presenting characteristics of DDS include loss of playfulness, decreased appetite, weight loss, growth delay, abnormal skeletal development, insomnia, abdominal pain, constipation, and anuria.

Clinically, Denys–Drash is characterized by the triad of pseudohermaphroditism, mesangial renal sclerosis, and Wilms' tumor. The condition first manifests as early nephrotic syndrome and progresses to mesangial renal sclerosis, and ultimately renal failure—usually within the first three years of life.

Acorea or fibrous occlusion of the pupil, microphthalmia and cataracts are present in both eyes. Microcornea and iridocorneal dysgenesis also occur. The retina and optic disc are normal.

Acorea, microphthalmia and cataract syndrome is a rare genetically inherited condition.

Facial femoral syndrome is a rare congenital disorder. It is also known as femoral dysgenesis, bilateral femoral dysgenesis, bilateral-Robin anomaly and femoral hypoplasia-unusual facies syndrome. The main features of this disorder are underdeveloped thigh bones (femurs) and unusual facial features.

Symptoms begin in infancy and include:

- hypotonia

- areflexia

- amyotrophy

- variable degrees of dysgenesis of the corpus callosum

- mild to severe intellectual and developmental delay

- psychiatric problems including paranoid delusions, depression, hallucinations and autistic-like behavior

Cerebral dysgenesis–neuropathy–ichthyosis–keratoderma syndrome (also known as "CEDNIK syndrome") is a cutaneous condition caused by mutation in the SNAP29 gene.

The diagnosis is based on the combination of unusual facial features and the dysplastic or absent femurs.

Diagnosis may be made antenatally.

Bamforth–Lazarus syndrome is a genetic condition that results in thyroid dysgenesis. It is due to recessive mutations in forkhead/winged-helix domain transcription factor ("FKLH15" or "TTF2").

It is associated with "FOXE1".

Denys–Drash syndrome (DDS) or Drash syndrome is a rare disorder or syndrome characterized by gonadal dysgenesis, nephropathy, and Wilms' tumor.

Microcephaly is a characteristic in which the circumference of the head is smaller than normal due to improper development of the brain. It is caused by genetic disorders, infections, radiation, medications or alcohol abuse during pregnancy. Defects in the growth of the cerebral cortex lead to many of the features associated with microcephaly. There is currently no known method of correcting microcephaly. However, there are a variety of symptomatic treatments that help to counter some of its adverse effects, such as speech and occupational therapies, as well as medication to control seizures and hyperactivity. Microcephaly has a vast range of prognoses: some patients experience little to very mental retardation and can reach regular age-appropriate milestones. Others may experience severe mental retardation and neuromuscular side effects.

Aphalangy, hemivertebrae and urogenital-intestinal dysgenesis is an extremely rare syndrome, described only in three siblings. It associates hypoplasia or aplasia of phalanges of hands and feet, hemivertebrae and various urogenital and/or intestinal abnormalities. Intrafamilial variability is important as one sister had lethal abnormalities (Potter sequence and pulmonary hypoplasia), while her affected brother was in good health with normal psychomotor development at 6 months of age. Prognosis seems to depend mainly on the severity of visceral malformations. Etiology and inheritance remain unknown.

Dubowitz syndrome is a rare genetic disorder characterized by microcephaly, stunted growth, and a receding chin. Symptoms vary among patients, but other characteristics include a soft, high-pitched voice; partial webbing of the fingers and toes; palate deformations; genital abnormalities; language difficulties; and an aversion to crowds. The pathogenesis of the disease is yet to be identified, and no medical tests can definitively diagnose the disease. The primary method of diagnosis is to identify facial phenotypes. Since it was first described in 1965 by English physician Victor Dubowitz, over 140 cases have been reported worldwide. Although the majority of cases have been reported from the United States, Germany, and Russia, the disorder appears to affect both genders and all ethnicities equally.

Malouf syndrome (also known as "congestive cardiomyopathy-hypergonadotropic hypogonadism syndrome") is a congenital disorder that causes one or more of the following symptoms: mental retardation, ovarian dysgenesis, congestive cardiomyopathy, broad nasal base, blepharoptosis, and bone abnormalities, and occasionally marfanoid habitus (tall stature with long and thin limbs, little subcutaneous fat, arachnodactyly, joint hyperextension, narrow face, small chin, large testes, and hypotonia).

This disease is named after J. Malouf, who performed a case study on a family suffering from this disease in 1985.

Andermann syndrome also known as agenesis of corpus callosum with neuronopathy (ACCPN), Charlevoix disease among others is a very rare neurodegenerative genetic disorder that damages the nerves used to control muscles and related to sensation, and is often associated with agenesis of the corpus collosum.

It was first described by Eva Andermann et al. in 1972.

The prognosis for children with NMDs varies depending on the specific disorder and the degree of brain abnormality and subsequent neurological signs and symptoms.

Renal-hepatic-pancreatic dysplasia is an autosomal recessive congenital disorder characterized by pancreatic fibrosis, renal dysplasia and hepatic dysgenesis. It is usually fatal soon after birth.

An association with NPHP3 has been described.

It was characterized in 1959.

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.

More than 25 syndromes resulting from abnormal neuronal migration have been described. Among them are syndromes with several different patterns of inheritance; genetic counseling thus differs greatly between syndromes.

- Lissencephaly

- Microlissencephaly

- Schizencephaly

- Porencephaly

- Pachygyria

- Polymicrogyria

- Agyria

- Macrogyria

- Microgyria

- Micropolygyria

- Neuronal heterotopias

- Agenesis of the corpus callosum

- Agenesis of the cranial nerves

- Band heterotopias

Focal cortical dysplasia. Miller-Dieker syndrome, , Fukuyama congenital muscular dystrophy and Walker Warburg syndrome are genetic disorders associated with lissencephaly.

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).

Tooth and nail syndrome (also known as "Hypodontia with nail dysgenesis," and "Witkop syndrome") is a rare disorder, first described in 1965, characterized by nails that are thin, small, and friable, and which may show koilonychia at birth.

It is associated with "MSX1".

A wide variety of symptoms are potential clinical features of ciliopathy.

- Chemosensation abnormalities, typically via ciliated epithelial cellular dysfunction.

- Defective thermosensation or mechanosensation, often via ciliated epithelial cellular dysfunction.

- Cellular motility dysfunction

- Issues with displacement of extracellular fluid

- Paracrine signal transduction abnormalities

In organisms of normal health, cilia are critical for:

- development

- homeostasis

- reproduction

Some syndromes that frequently include ACC are Aicardi syndrome, Andermann syndrome, Shapiro syndrome, acrocallosal syndrome, septo-optic dysplasia (optic nerve hypoplasia), Mowat–Wilson syndrome, John Sayden syndrome, Menkes syndrome, and L1CAM Syndrome. Some conditions that are sometimes associated with ACC include maternal nutritional deficiencies or infections, metabolic disorders, fetal alcohol syndrome, craniofacial abnormalities, and other oral and maxillofacial pathologies.

Anterior segment mesenchymal dysgenesis is a failure of the normal development of the tissues of the anterior segment of the eye. It leads to anomalies in the structure of the mature anterior segment, associated with an increased risk of glaucoma and corneal opacity.

Peters' (frequently misspelled Peter's) anomaly is a specific type of mesenchymal anterior segment dysgenesis, in which there is central corneal leukoma, adhesions of the iris and cornea, and abnormalities of the posterior corneal stroma, Descemet's membrane, corneal endothelium, lens, and anterior chamber.