As its name indicates, a person with the syndrome has one Y chromosome and four X chromosomes on the 23rd pair, thus having 49 chromosomes rather than the normal 46. As with most categories of aneuploidy disorders, 49,XXXXY syndrome is often accompanied by intellectual disability. It can be considered a form of 47, XXY Klinefelter syndrome, or a variant of it.

It is genetic but not hereditary. This means that while the genes of the parents cause the syndrome, there is a small chance of more than one child having the syndrome. The probability of inheriting the disease is about 1%.

The individuals with this syndrome are males, but 49, XXXXX also exists with similar characteristics.

The aneuploidy is thought to be caused by problems occurring during meiosis, either in the mother or in both the mother and father. Successive nondisjunctions have been observed in the mother of at least one patient.

The features of the syndrome likely arise due to failure of X-inactivation and the presence of multiple X chromosomes from the same parent causing problems with parental imprinting. In theory, X-inactivation should occur and leave only one X chromosome active in each cell. However, failure of this process has been observed in one individual studied. The reason for this is thought to be the presence of an unusually large, and imbalanced, number of X chromosomes interfering with the process.

This disorder is present at birth, however, it may not be understood until several years after birth. Acrodysostosis affects males and females in almost similar numbers. It is difficult to determine the frequency of acrodysostosis in the population as many cases of this disorder cannot be diagnosed properly.

The cause of this condition is unknown but evidence of familial inheritance and sporadic genetic mutation has been linked to cases of FHS. Two possibly familial cases have been reported—one in a mother and son, and the other in a mother and daughter. This suggests an autosomal dominant inheritance but additional cases need to be investigated to establish this. Another report has suggested that the inheritance may be autosomal recessive. In all of these cases, however, the mothers and children were not similarly affected, suggesting a variable clinical expression of the syndrome.

In a study published by the "American Journal of Human Genetics" in 2012, exome sequencing was used to investigate a group of unrelated individuals with classic features of FHS and identified heterozygous mutations in SRCAP as causative of this disorder. Each reported mutation was truncating (nonsense or frameshift) and occurred between codons 2,407 and 2,517 in exon 34, resulting in the loss of three C-terminal AT-hook motifs. SRCAP encodes a SNF2-related chromatin-remodeling ATPase that is a coactivator for CREB-binding protein (or CBP), which is the major cause of Rubinstein–Taybi syndrome. This disrupted interaction between the proteins most likely explains the clinical overlap between FHS and RTS.

- SRCAP has been shown to transduce signals of nuclear (steroid) hormone receptors and Notch pathways, showing that it plays diverse roles in gene expression.

- SRCAP contains several functional domains (SNF2 like ATPase, an N-terminal HSA domain, and three C-terminal AT-hook DNA-binding motifs).

- The CBP interaction domain of SRCAP is located centrally.

Thus, the mechanism of disease in FHS is suspected to be dominant-negative (or antimorphic) due to the mutation in the final exon that results in the loss of the major transactivation function of SRCAP (or loss of one or more critical domains). All of the patients that carried the mutation also had obvious physical symptoms (i.e., prominent nose, delayed bone age, and short stature). Those who tested negative for the mutation often had dysmorphic facial features distinct from classical FHS, as well as a formal diagnosis of autism.

This disorder affects all demographics equally. The two families that were studied are of European ancestry. Wilson–Turner syndrome is considered to be a rare disease because it affects one individual out of one million.

Screening methods are mostly done for females to determine if they are carriers. Males do not have to be tested because those with the disorder will show symptoms close to the time they are born because the disorder is inherited from the X chromosome. Female can be tested if they are carriers by performing a X chromosome inactivation analysis on DNA isolated from the peripheral lymphocytes. The CAG repeat in this section must be amplified and methylated DNA must be sorted from unmethylated DNA with PCR. Carrier females will show skewed X-inactivation pattern (skewing close to 100%) with the mutated allele inactivated. This indicates a selection against cells with an active X chromosome with the mutated HDAC8 gene.

Floating–Harbor syndrome, also known as Pelletier–Leisti syndrome, is a rare disease with fewer than 50 cases described in the literature. It is usually diagnosed in early childhood and is characterized by the triad of proportionate short stature with delayed bone age, characteristic facial appearance, and delayed speech development. Although its cause is unknown, it is thought to result from genetic mutation, and diagnosis is established by the presence of a heterozygous SRCAP mutation in those with clinical findings of FHS.

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.

Nicolaides–Baraitser syndrome (NCBRS) is a rare genetic condition caused by de novo missense mutations in the SMARCA2 gene and has only been reported in less than 100 cases worldwide. NCBRS is a distinct condition and well recognizable once the symptoms have been identified.

PWS affects approximately 1 in 10,000 to 1 in 25,000 newborns. There are more than 400,000 people who live with PWS around the world.

One case of Cohen Syndrome, in a Palestinian boy from Tul-Karem, was reported in the Israeli monthly Kol Israel BeAsakim (in Hebrew) in the December 2007 issue. Over the past several years there have been approximately 50 new cases worldwide. There are population groups with this condition in Australia, the UK and the US. It still seems to go undiagnosed leaving the number of cases less than 500.

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.

Acrodysostosis also known as Arkless-Graham syndrome or Maroteaux-Malamut syndrome is a rare congenital malformation syndrome which involves shortening of the interphalangeal joints of the hands and feet, intellectual disability in approximately 90% of affected children, and peculiar facies. Other common abnormalities include short head (as measured front to back), small broad upturned nose with flat nasal bridge, protruding jaw, increased bone age, intrauterine growth retardation, juvenile arthritis and short stature. Further abnormalities of the skin, genitals, teeth, and skeleton may occur.

Most reported cases have been sporadic, but it has been suggested that the condition might be genetically related i.e. in an autosomal dominant mode of transmission. Both males and females are affected. The disorder has been associated with the older age of parents at the time of conception.

A PRKAR1A mutation has been identified in acrodysostosis with hormone resistance.

49,XXXXX, also known as pentasomy X, penta X, or XXXXX syndrome, is a chromosomal aneuploidy where females have five X chromosomes rather than the normal two. It is unclear exactly how rare it is, but it appears to affect fewer than 1 in 100,000 women.

Some characteristics of Abruzzo–Erickson syndrome include deafness, protruding ears, coloboma, a cleft palate or palatal rugosity, and short stature.

It was characterized in 1977.

Renpenning's syndrome is a neurodevelopmental disorder recognised in males that causes intellectual disability, mild growth retardation with examples in the testes and head, and a somewhat short stature. The condition only affects males, starting at birth, and was first characterized in 1962. but first described by Hans Renpenning in 1963 after he documented these traits on many children in one family alone.

It can be associated with "PQBP1".

Some people may have some mental slowness, but children with this condition often have good social skills. Some males may have problems with fertility.

SHORT syndrome is a medical condition in which affected individuals have multiple birth defects in different organ systems.

It was characterized in 1975.

SFMS is an X-linked disease by chromosome Xq13. X-linked diseases map to the human X chromosome because this syndrome is an X chromosome linked females who have two chromosomes are not affected but because males only have one X chromosome, they are more likely to be affected and show the full clinical symptoms. This disease only requires one copy of the abnormal X-linked gene to display the syndrome. Since females have two X chromosomes, the effect of one X chromosome is recessive and the second chromosome masks the affected chromosome.

Affected fathers can never pass this X-linked disease to their sons but affected fathers can pass the X-linked gene to their daughters who has a 50% chance to pass this disease-causing gene to each of her children. Since females who inherit this gene do not show symptoms, they are called carriers. Each of the female's carrier's son has a 50% chance to display the symptoms but none of the female carrier's daughters would display any symptoms.

Some patients with SFMS have been founded to have a mutation of the gene in the ATRX on the X chromosome, also known as the Xq13 location. ATRX is a gene disease that is associated with other forms of X-linked mental retardation like Alpha-thalassemia/mental retardation syndrome, Carpenter syndrome, Juberg-Marsidi syndrome, and soastic paraplegia. It is possible that patients with SFMS have Alpha-thalassemia/mental retardation syndrome without the affected hemoglobin H that leads to Alphathalassemia/ mental retardation syndrome in the traditionally recognized disease.

RAPADILINO syndrome is an autosomal recessive disorder characterized by:

- RA: radial ray defect

- PA: patellar aplasia, arched or cleft palate

- DI: diarrhea, dislocated joints

- LI: little size (short stature), limb malformation

- NO: nose slender and normal intelligence.

It is more prevalent in Finland than elsewhere in the world.

It has been associated with the gene RECQL4. This is also associated with Rothmund-Thomson syndrome and Baller-Gerold syndrome.

49,XXXXY syndrome is an extremely rare aneuploidic sex chromosomal abnormality. It occurs in approximately 1 out of 85,000 to 100,000 males.

Most cases are X-linked recessive but there may be as many as three types. As well as a classical X-linked form, there is another type where females are partially affected and another where females have full IFAP symptoms. The gene or genes causing this disease are not known.

Rud syndrome is a poorly characterized disorder, probably of X-linked recessive inheritance, named after Einar Rud who described 2 patients with the case in 1927 and 1929. It was argued that all reported cases of Rud syndrome are genetically heterogeneous and significantly differ from the original case reports of Rud and that the designation Rud syndrome should be eliminated and that the patients with such diagnosis should be reassigned to other syndromes, such as Refsum disease and Sjögren-Larsson syndrome.Some consider Rud syndrome and Sjögren-Larsson syndrome the same entity and that Rud syndrome doesn't exist.

Berk–Tabatznik syndrome is a medical condition with an unknown cause that shows symptoms of short stature, congenital optic atrophy and brachytelephalangy. This condition is extremely rare with only two cases being found.

Wiedemann–Rautenstrauch (WR) syndrome , also known as neonatal progeroid syndrome, is an autosomal recessive progeroid syndrome.

WR was first reported by Rautenstrauch and Snigula in 1977; and the earliest reports made subsequently have been by Wiedemann in 1979, by Devos in 1981, and Rudin in 1988. There have been over 30 cases of WR.

WR is associated with abnormalities in bone maturation, and lipids and hormone metabolism. Affected individuals exhibit intrauterine and postnatal growth retardation, leading to short stature and an aged appearance from birth. They have physical abnormalities including a large head (macrocephaly), sparse hair, prominent scalp veins, inward-folded eyelid (entropion), widened anterior fontanelles, hollow cheeks (malar hypoplasia), general loss of fat tissues under the skin (lipoatrophy), delayed tooth eruption, abnormal hair pattern (hypotrichosis), beaked nose, mild to severe mental retardation and dysmorphism.

Marfan lipodystrophy syndrome (MFLS) has sometimes been confused with Wiedemann–Rautenstrauch syndrome, since the Marfanoid features are progressive and sometimes incomplete. MFLS is caused by mutations near the 3'-terminus of "FBN1" that cause a deficiency of the protein hormone asprosin and progeroid-like symptoms with reduced subcutaneous white adipose tissue.