The true prevalence of PMS has not been determined. More than 1200 people have been identified worldwide according the Phelan-McDermid Syndrome Foundation. However, it is believed to be underdiagnosed due to inadequate genetic testing and lack of specific clinical features. It is known to occur with equal frequency in males and females. Studies using chromosomal microarray for diagnosis indicate that at least 0.5% of cases of ASD can be explained by mutations or deletions in the "SHANK3" gene. In addition when ASD is associated with ID, "SHANK3" mutations or deletions have been found in up to 2% of individuals.

Recent findings in genetic research have suggested that a large number of genetic disorders, both genetic syndromes and genetic diseases, that were not previously identified in the medical literature as related, may be, in fact, highly related in the genetypical root cause of the widely varying, phenotypically-observed disorders. Thus, Alstrom syndrome is a ciliopathy. Other known ciliopathies include primary ciliary dyskinesia, Bardet-Biedl syndrome, polycystic kidney and liver disease, nephronophthisis, Meckel-Gruber syndrome and some forms of retinal degeneration.

A prognosis for Alström syndrome is complicated because it widely varies. Any person that has the syndrome have different set of disorders. Permanent blindness, deafness, and Type 2 diabetes may occur. Liver and kidney failure can progressively get worse. The life expectancy is usually reduced and the patients rarely live past 50 years old.

Griscelli syndrome type 2 (also known as "partial albinism with immunodeficiency") is a rare autosomal recessive syndrome characterized by variable pigmentary dilution, hair with silvery metallic sheen, frequent pyogenic infections, neutropenia, and thrombocytopenia.

Galloway Mowat syndrome is a very rare autosomal recessive genetic disorder, consisting of a variety of features including hiatal hernia, microcephaly and nephrotic syndrome.

22q13 deletion syndrome (spoken as "twenty-two q one three", see Locus (genetics)) is a genetic disorder caused by deletions or rearrangements on the q terminal end (long arm) of chromosome 22. Any abnormal genetic variation in the q13 region that presents with significant manifestations (phenotype) typical of a terminal deletion may be diagnosed as 22q13 deletion syndrome. 22q13 deletion syndrome is often called Phelan-McDermid syndrome (abbreviated PMS). There is disagreement among researchers as to the exact definition of 22q13 deletion syndrome. The Developmental Synaptopathies Consortium defines PMS as being caused by "SHANK3" mutations, a definition that appears to exclude terminal deletions. The requirement to include "SHANK3" in the definition is supported by many, but not by those who first described 22q13 deletion syndrome.

A prototypical terminal deletion of 22q13 can be uncovered by karyotype analysis, but many terminal and interstitial deletions are too small. The availability of DNA microarray technology for revealing multiple genetic problems simultaneously has been the diagnostic tool of choice. The falling cost for whole exome sequencing and, eventually, whole genome sequencing, may replace DNA microarray technology for candidate evaluation. However, fluorescence in situ hybridization (FISH) tests remain valuable for diagnosing cases of mosaicism (mosaic genetics) and chromosomal rearrangements (e.g., ring chromosome, unbalanced chromosomal translocation). Although early researchers sought a monogenic (single gene genetic disorder) explanation, recent studies have not supported that hypothesis (see Etiology, below).

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.

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.

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

The disorder is expressed in an autosomal dominant fashion and may result from a loss of function mutation or total deletion of the ZEB2 gene located on chromosome 2q22.

Galloway Mowat syndrome is an autosomal recessive disorder, which means the defective gene responsible for the disorder is located on an autosome, and two copies of the defective gene (one inherited from each parent) are required in order to be born with the disorder. The parents of an individual with an autosomal recessive disorder both carry one copy of the defective gene, but usually do not experience any signs or symptoms of the disorder.

The fifth type of hyper-IgM syndrome has been characterized in three patients from France and Japan. The symptoms are similar to hyper IgM syndrome type 2, but the AICDA gene is intact. These three patients instead had mutations in the catalytic domain of uracil-DNA glycosylase, an enzyme that removes uracil from DNA. In both type 2 and type 5 hyper-IgM syndromes, the patients are profoundly deficient in IgG and IgA because the B cells can't carry out the recombination steps necessary to class-switch.

GAPO syndrome is caused by a deletion in both copies of the ANTXR1 gene, which encodes Anthrax Toxin Receptor 1. This gene is critical for the creation of actin, and its disruption inhibits proper function of the actin network. As a result, individuals with GAPO syndrome have a buildup of extracellular matrix, and degraded cell adhesions. The alteration can occur in the form of nonsense mutations or mutations which alter the splice sites, and result in alternative RNA splicing, leading to synthesis of a different or modified protein. In humans, the ANTXR1 gene is located on Chromosome 2 and has 22 exons.

GAPO syndrome is inherited in an autosomal recessive fashion, and requires both parents to pass on the mutant genotype. Since this mutation is so rare, most confirmed cases have a history of ancestral inbreeding.

2q37 monosomy is a rare genetic disorder caused by a deletion of a segment at the end of chromosome 2.

There are estimated to be approximately 2,000 people afflicted with Hunter syndrome worldwide, 500 of whom live in the United States. There are 2 Hunter syndrome patients in New Zealand, 6 Hunter syndrome patients in Ireland, at least 1 case in Iran, 1 case in Saudi Arabia, 1 case in Chile, 1 case in Pakistan, 20 cases in the Philippines, 1 case in the West Bank (Palestine) and 70 Hunter syndrome patients reported in Korea. There is one case in the city of Kolkata and, as broadcast on local media channel CCN Siliguri on 1 April 2015, a boy in the city of Siliguri, West Bengal, India. In Gangtok, the 8-year-old son of the editor of 'Voice of Sikkim' also suffers from the disease.

A study in the United Kingdom indicated an incidence among males of approximately 1 in 130,000 male live births.

There is no cure for this syndrome. Treatment is supportive and symptomatic. All children with Mowat–Wilson syndrome required early intervention with speech therapy, occupational therapy and physical therapy.

The condition was first described in 1978 by Pitt and Hopkins in two unrelated patients.

The genetic cause of this disorder was described in 2007. This disorder is due to a haploinsufficiency of the transcription factor 4 (TCF4) gene which is located on the long arm of chromosome 18 (18q21.2) The mutational spectrum appears to be 40% point mutations, 30% small deletions/insertions and 30% deletions. All appear to be "de novo" mutations and to date no risk factors have been identified.

A Pitt–Hopkins like phenotype has been assigned to autosomal recessive mutations of the contactin associated protein like 2 (CNTNAP2) gene on the long arm of chromosome 7 (7q33-q36) and the neurexin 1 alpha (NRXN1) gene on the short arm of chromosome 2 (2p16.3).

This includes Chediak-Higashi syndrome and Elejalde syndrome (neuroectodermal melanolysosomal disease).

The minimal deletion causing this syndrome has been defined as a 3 megabase region that contains the genes GPR35, GPC1 and STK25.

Almost all deletions are found to be terminal deletions at the end of chromosome 2. There is a high frequency of "de novo" deletions, but multiple cases within a single family are also observed. Equal proportions of maternally and paternally derived rearrangements were seen in Aldred's series. No common breakpoints for the deletion were identified indicating that the 2q37 rearrangement is unlikely to be mediated by non-homologous recombination and low-copy repeats. In a study of 20 patients, no clear relationship was found between clinical features and the size or position of the monosomic region.

The incidence of Fraser syndrome is 0.043 per 10,000 live born infants and 1.1 in 10,000 stillbirths, making it a rare syndrome.

Acrocallosal syndrome (also known as ACLS) is a rare autosomal recessive syndrome characterized by corpus callosum agenesis, polydactyly, multiple dysmorphic features, motor and mental retardation, and other symptoms. The syndrome was first described by Albert Schinzel in 1979.

It is associated with "GLI3".

For a long time, the most efficient approach had been to use bone marrow graft, or hematopoietic stem cell transplantation. They each have the advantage of providing a new source of the missing I2S. However, the results have been considered imperfect at best.

While this treatment alternative is able to improve or stop the progression of some of the so-called "physical" symptoms, it does not prevent the eventual cognitive regression that occurs in Hunter syndrome patients who are cognitively affected, although it may slow such regression early on. Therefore, for attenuated patients, this may still serve as a viable treatment option because of its more permanent nature, possibly even equivalent to weekly enzyme replacement therapy, resulting in much improved life expectancy.

However, even for attenuated patients, it is a major intervention with significant mortality risks and potential for life-threatening or altering complications such as graft-versus-host disease. For cognitively affected patients, without solving the challenge of cognitive regression, at best it is limited as a permanent treatment alternative. Because of all these reasons, bone marrow grafts or hematopoietic stem cell transplantation have seen a decrease in their application as Hunter syndrome treatment.

Currently there is no specific treatment for this condition. Management is supportive.

There is no known cure for Winchester syndrome; however, there are many therapies that can aid in the treatment of symptoms. Such treatments can include medications: anti-inflammatories, muscle relaxants, and antibiotics. Many individuals will require physical therapy to promote movement and use of the limbs affected by the syndrome. Genetic counseling is typically prescribed for families to help aid in the understanding of the disease. There are a few clinical trials available to participate in. The prognosis for patients diagnosed with Winchester syndrome is positive. It has been reported that several affected individuals have lived to middle age; however,the disease is progressive and mobility will become limited towards the end of life. Eventually, the contractures will remain even with medical intervention, such as surgery.

With appropriate treatment and management, patients with Weaver syndrome appear to do well, both physically and intellectually, throughout their life and have a normal lifespan. Their adult height is normal as well.