Arakawa's syndrome II is an autosomal dominant metabolic disorder that causes a deficiency of the enzyme tetrahydrofolate-methyltransferase; affected individuals cannot properly metabolize methylcobalamin, a type of Vitamin B.

It is also called Methionine synthase deficiency, Tetrahydrofolate-methyltransferase deficiency syndrome, and N5-methylhomocysteine transferase deficiency.

Arakawa's syndrome II is inherited in an autosomal dominant manner. This means the defective gene responsible for disorder is located on an autosome, and one copy of the defective gene is sufficient to cause the disorder when inherited from a parent who has the disorder.

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.

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.

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.

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.

Hunter syndrome, or mucopolysaccharidosis II (MPS II), is a lysosomal storage disease caused by a deficient (or absent) enzyme, iduronate-2-sulfatase (I2S). The accumulated substrates in Hunter syndrome are heparan sulfate and dermatan sulfate. The syndrome has X-linked recessive inheritance.

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

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.

Alström syndrome, also called Alstrom-Halgren syndrome, is a rare genetic disorder caused by mutations in the gene ALMS1. It is among the rarest genetic disorders in the world, as currently it has only 266 reported cases in medical literature and over 501 known cases in 47 countries. It was first described by Carl-Henry Alström in Sweden in 1959. Alstrom syndrome is sometimes confused with Bardet-Biedl syndrome, which has similar symptoms. Bardet-Biedl syndrome tends to have later onset in its symptoms. The likelihood of two carrier parents both passing the gene and therefore having a child affected by the syndrome is 25% with each pregnancy. The likelihood of having a child who is only a carrier of the gene is 50% with each pregnancy. The likelihood of a child receiving normal genes from both parents and being considered to be "genetically" normal is 25%. The risk for carrying the gene is equivalent for both males and females.

"Alström syndrome (AS) is a rare autosomal recessive disease characterized by multiorgan dysfunction. The key features are childhood obesity, blindness due to congenital retinal dystrophy, and sensorineural hearing loss. Associated endocrinologic features include hyperinsulinemia, early-onset type 2 diabetes, and hypertriglyceridemia."

Thus, AS shares several features with the common metabolic syndrome, namely obesity, hyperinsulinemia, and hypertriglyceridemia. Mutations in the ALMS1 gene have been found to be causative for AS with a total of 79 disease-causing mutations having been described." Prevalence estimates have ranged from 1 in 10,000 to fewer than 1 in 1,000,000 individuals in the general population.

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.

Pearson Syndrome is a very rare mitochondrial disorder that is characterized by health conditions such as sideroblastic anemia, liver disease, and exocrine pancreas deficiency.

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.

Pearson syndrome is a mitochondrial disease characterized by sideroblastic anemia and exocrine pancreas dysfunction. Other clinical features are failure to thrive, pancreatic fibrosis with insulin-dependent diabetes and exocrine pancreatic deficiency, muscle and neurologic impairment, and, frequently, early death. It is usually fatal in infancy. The few patients who survive into adulthood often develop symptoms of Kearns-Sayre syndrome.

It is caused by a deletion in mitochondrial DNA. Pearson syndrome is very rare, less than hundred cases have been reported in medical literature worldwide.

The syndrome was first described by pediatric hematologist and oncologist Howard Pearson in 1979; the deletions causing it were discovered a decade later.

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.

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

Congenital generalized lipodystrophy (also known as Berardinelli–Seip syndrome) is an extremely rare autosomal recessive skin condition, characterized by an extreme scarcity of fat in the subcutaneous tissues. It is a type of lipodystophy disorder where the magnitude of fat loss determines the severity of metabolic complications. Only 250 cases of the condition have been reported, and it is estimated that it occurs in 1 in 10 million people worldwide.

Qazi–Markouizos syndrome is a rare hereditary condition characterized by non-progressive, congenital hypotonia, severe intellectual disability, an increased proportion of type 2 muscle fibers, which additionally exhibited increased size, as well as dysharmonic skeletal maturation. To date, the molecular mechanism of Qazi–Markouizos syndrome, which is also known as Puerto Rican infant hypotonia syndrome, remains unknown.

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).

Juvenile hyaline fibromatosis (also known as "Fibromatosis hyalinica multiplex juvenilis," "Murray–Puretic–Drescher syndrome") is a very rare, autosomal recessive disease due to mutations in capillary morphogenesis protein-2 (CMG-2 gene). It occurs from early childhood to adulthood, and presents as slow-growing, pearly white or skin-colored dermal or subcutaneous papules or nodules on the face, scalp, and back, which may be confused clinically with neurofibromatosis.

Feingold syndrome is caused by mutations in the neuroblastoma-derived V-myc avian myelocytomatosis viral-related oncogene (MYCN) which is located on the short arm of chromosome 2 (2p24.1).

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".

Feingold syndrome (also called oculodigitoesophagoduodenal syndrome) is a rare autosomal dominant hereditary disorder. It is named after Murray Feingold, an American physician who first described the syndrome in 1975. Until 2003, at least 79 patients have been reported worldwide.

Hyper-IgM syndrome type 3 is a form of Hyper IgM syndrome characterized by mutations of the "CD40" gene. In this type, Immature B cells cannot receive signal 2 from helper T cells which is necessary to mature into mature B cells.

Urofacial Syndrome occurs due to either disruption or mutation of a gene on chromosome 10q23q24. The gene is located on a 1 centimorgan interval between D10S1433 and D10S603. Alteration of this gene leads to alteration of facial and urinary developmental fields. This gene is believed to be the HPSE2 gene. The HPSE2 gene is expressed in both the central nervous system as well as the bladder. Heparanase 2 is protein coded by exons 8 and 9 on the HPSE2 gene. This protein is believed to be altered in the case of this syndrome. Studies performed on mice indicate that HPSE2 has no enzymatic activity.

Mutations in the HPSE2 gene on chromosome 10q23q24 have been observed to cause Ochoa Syndrome. This means the defective gene responsible for the disorder is located on an autosome (chromosome 10 is 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 relationship between a defective HPSE2 gene and Ochoa syndrome is unclear. There is postulation that the genetic changes may lead to an abnormality in the brain region, evidence for this postulation is that the areas of the brain that control facial expression and urination are in close proximity of each other. Other hypotheses think that the defective heparanase 2 protein may lead to problems with development of the urinary tract or with muscle function in the face and bladder.