A clinical diagnosis of SCS can be verified by testing the TWIST1 gene (only gene in which mutations are known to cause SCS) for mutations using DNA analysis, such as sequence analysis, deletion/duplication analysis, and cytogenetics/ FISH analysis. Sequence analysis of exon 1 (TWIST1 coding region) provides a good method for detecting the frequency of mutations in the TWIST1 gene. These mutations include nonsense, missense, splice site mutation, and intragenic deletions/insertions. Deletion/duplication analysis identifies mutations in the TWIST1 gene that are not readily detected by sequence analysis. Common methods include PCR, multiplex ligation-dependent probe amplification (MLPA), and chromosomal microarray (CMA). Cytogenetic/FISH analysis attaches fluorescently labels DNA markers to a denatured chromosome and is then examined under fluorescent lighting, which reveals mutations caused by translocations or inversions involving 7p21. Occasionally, individuals with SCS have a chromosome translocation, inversion, or ring chromosome 7 involving 7p21 resulting in atypical findings, such as, increased developmental delay. Individuals with SCS, typically have normal brain functioning and rarely have mental impairments. For this reason, if an individual has both SCS and mental retardation, then they should have their TWIST1 gene screened more carefully because this is not a normal trait of SCS. Cytogenetic testing and direct gene testing can also be used to study gene/chromosome defects. Cytogenetic testing is the study of chromosomes to detect gains or losses of chromosomes or chromosome segments using fluorescent in situ hybridization (FISH) and/or comparative genomic hybridization (CGH). Direct gene testing uses blood, hair, skin, amniotic fluid, or other tissues in order to find genetic disorders. Direct gene testing can determine whether an individual has SCS by testing the individual's blood for mutations in the TWIST1 gene.

Up until recently, experts frequently disagreed on whether a patient had SCS, Crouzon syndrome, isolated craniosynostosis, or some other disease because the symptoms are so closely related, they literally had no way of differentiating between all of them. However, we now have direct gene testing, which allows for a more definitive diagnosis because it allows them to be differentiated from each other based on which gene is mutated in each condition. The following is a list of conditions commonly confused/misdiagnosed for SCS, some of their symptoms, and which mutated gene each contains:

There is no standard treatment for the hand malformations in Apert due to the differences and severity in clinical manifestations in different patients. Every patient should therefore be individually approached and treated, aiming at an adequate balance between hand functionality and aesthetics.

However, some guidelines can be given depending on the severity of the deformities.

In general it is initially recommended to release the first and fourth interdigital spaces, thus releasing the border rays.

This makes it possible for the child to grasp things by hand, a very important function for the child's development. Later the second and third interdigital spaces have to be released.

Because there are three handtypes in Apert, all with their own deformities, they all need a different approach regarding their treatment:

- Type I hand usually needs only the interdigital web space release. First web release is rarely needed but often its deepening is necessary. Thumb clynodactyly correction will be needed.

- In type II hands it is recommended to release the first and fifth rays in the beginning, then the second and the third interdigital web spaces have to be freed. The clynodactyly of the thumb has to be corrected as well. The lengthening of the thumb phalanx may be needed, thus increasing the first web space. In both type I and type II, the recurrent syndactyly of the second web space will occur because of a pseudoepiphysis at the base of the index metacarpal. This should be corrected by later revisions.

- Type III hands are the most challenging to treat because of their complexity. First of all, it is advised to release the first and fourth webspace, thus converting it to type I hand. The treatment of macerations and nail-bed infections should also be done in the beginning. For increasing of the first web space, lengthening of the thumb can be done. It is suggested that in severe cases an amputation of the index finger should be considered. However, before making this decision, it is important to weigh the potential improvement to be achieved against the possible psychological problems of the child later due to the aesthetics of the hand. Later, the second and/or third interdigital web space should be released.

With growing of a child and respectively the hands, secondary revisions are needed to treat the contractures and to improve the aesthetics.

Syndactyly of the border digits (thumb/index finger or ring/small fingers) is treated at early age to prevent the larger digit from curving towards the smaller digit with growth. Typically, syndactyly of these digits is treated at six months of age. The treatment of syndactyly of the other digits is elective and is more commonly performed when the digits have grown, at 18–24 months of age.

There are multiple classifications for the triphalangeal thumb. The reason for these different classifications is the heterogeneity in appearance of the TPT.

The classification according to Wood describes the shape of the extra phalanx: delta (Fig. 4), rectangular or full phalanx (Table 1). With the classification made by Buck-Gramcko a surgical treatment can be chosen (Table 1). Buck-Gramcko differentiates between six different shapes of the extra phalanx and associated malformations.

Table 1: Classifications of Wood and Buck-Gramcko

There are several classifications for cleft hand, but the most used classification is described by Manske and Halikis see table 3. This classification is based on the first web space. The first web space is the space between the thumb and the index.

Table 3: Classification for cleft hand described by Manske and Halikis

Surgical treatment of the cleft hand is based on several indications:

Improving function

- Absent thumb

- Deforming syndactyly (mostly between digits of unequal length like index and thumb)

- Transverse bones (this will progress the deformity; growth of these bones will widen the cleft)

- Narrowed first webspace

- The feet

Aesthetical aspects

- Reducing deformity

The diagnosis of this syndrome can be made on clinical examination and perinatal autopsy.

Koenig and Spranger (1986) noted that eye lesions are apparently nonobligatory components of the syndrome. The diagnosis of Fraser syndrome should be entertained in patients with a combination of acrofacial and urogenital malformations with or without cryptophthalmos. Thomas et al. (1986) also emphasized the occurrence of the cryptophthalmos syndrome without cryptophthalmos and proposed diagnostic criteria for Fraser syndrome. Major criteria consisted of cryptophthalmos, syndactyly, abnormal genitalia, and positive family history. Minor criteria were congenital malformation of the nose, ears, or larynx, cleft lip and/or palate, skeletal defects, umbilical hernia, renal agenesis, and mental retardation. Diagnosis was based on the presence of at least 2 major and 1 minor criteria, or 1 major and 4 minor criteria.

Boyd et al. (1988) suggested that prenatal diagnosis by ultrasound examination of eyes, digits, and kidneys should detect the severe form of the syndrome. Serville et al. (1989) demonstrated the feasibility of ultrasonographic diagnosis of the Fraser syndrome at 18 weeks' gestation. They suggested that the diagnosis could be made if 2 of the following signs are present: obstructive uropathy, microphthalmia, syndactyly, and oligohydramnios. Schauer et al. (1990) made the diagnosis at 18.5 weeks' gestation on the basis of sonography. Both the female fetus and the phenotypically normal father had a chromosome anomaly: inv(9)(p11q21). An earlier born infant had Fraser syndrome and the same chromosome 9 inversion.

Van Haelst et al. (2007) provided a revision of the diagnostic criteria for Fraser syndrome according to Thomas et al. (1986) through the addition of airway tract and urinary tract anomalies to the major criteria and removal of mental retardation and clefting as criteria. Major criteria included syndactyly, cryptophthalmos spectrum, urinary tract abnormalities, ambiguous genitalia, laryngeal and tracheal anomalies, and positive family history. Minor criteria included anorectal defects, dysplastic ears, skull ossification defects, umbilical abnormalities, and nasal anomalies. Cleft lip and/or palate, cardiac malformations, musculoskeletal anomalies, and mental retardation were considered uncommon. Van Haelst et al. (2007) suggested that the diagnosis of Fraser syndrome can be made if either 3 major criteria, or 2 major and 2 minor criteria, or 1 major and 3 minor criteria are present in a patient.

MRI imaging can be used to detect whether the abducens nerve is present.

The key problem is the early fusion of the skull, which can be corrected by a series of surgical procedures, often within the first three months after birth. Later surgeries are necessary to correct respiratory and facial deformities.

Evaluations by certain specialists should be performed following the initial diagnosis of Duane-radial ray syndrome. These evaluations will be used to determine the extent of the disease as well as the needs of the individual.

- Eyes - Complete eye exam by an ophthalmologist especially focusing on the extraocular movements of the eye and the structural eye defects

- Heart - evaluation by a cardiologist along with an echocardiogram and ECG

- Kidneys - Laboratory tests to check kidney function and a renal ultrasound

- Hearing

- Endocrine - evaluation for growth hormone deficit if growth retardation present

- Blood - CBC to check for thrombocytopenia and leukocytosis

- Clinical genetics consultation

The Wassel classification is the most widely used classification of radial polydactyly, based upon the most proximal level of skeletal duplication. The most common type is Wassel 4 (about 50% of such duplications) followed by Wassel 2 (20%) and Wassel 6 (12%).

The complete or partial absence of the pectoralis muscle is the malformation that defines Poland Syndrome. It can be treated by inserting a custom implant designed by CAD (computer aided design). A 3D reconstruction of the patient's chest is performed from a medical scanner to design a virtual implant perfectly adapted to the anatomy of each one. The implant is made of medical silicone unbreakable rubber. This treatment is purely cosmetic and does not make up for the patient's imbalanced upper body strength.

The Poland syndrome malformations being morphological, correction by custom implant is a first-line treatment. This technique allows a wide variety of patients to be treated with good outcomes. Poland Syndrome can be associated with bones, subcutaneous and mammary atrophy: if the first, as for pectus excavatum, is successfully corrected by a custom implant, the others can require surgical intervention such as lipofilling or silicone breast implant, in a second operation.

The goals of surgical treatment are: reducing length of the thumb, creating a good functioning, a stable and non deviated joint and improving the position of the thumb if necessary. Hereby improving function of the hand and thumb.

In general the surgical treatment is done for improvement of the thumb function. However, an extra advantage of the surgery is the improvement in appearance of the thumb. In the past, surgical treatment of the triphalangeal thumb was not indicated, but now it is generally agreed that operative treatment improves function and appearance. Because an operation was not indicated in the past, there’s still a population with an untreated triphalangeal thumb. The majority of this population doesn’t want surgery, because the daily functioning of the hand is good. The main obstacle for the untreated patients might not be the diminished function, but the appearance of the triphalangeal thumb.

The timing of surgery differs between Wood and Buck-Gramcko. Wood advises operation between the age of six months and two years, while Buck-Gramcko advises to operate for all indications before the age of six years.

- For TPT types I and II of the Buck-Gramcko classification, the surgical treatment typically consists of removing the extra phalanx and reconstructing the ulnar collateral ligament and the radial collateral ligament if necessary.

- For type III of Buck-Gramcko classification proposable surgical treatments:

- For type IV of Buck-Gramcko classification the surgical treatment typically consists of an osteotomy which reduces the middle phalanx and arthrodesis of the DIP. This gives a shortening of 1 to 1.5 cm. In most cases, this technique is combined with a shortening, rotation and palmar abduction osteotomy at metacarpal level to correct for position and length of the thumb. The extensor tendons and the intrinsic muscles are shortened as well.

- For type V of the Buck-Gramcko classification the surgical treatment proposably consists of a "pollicization". With a pollicization the malpositioned thumb is repositioned, rotated and shortened, the above-described rotation reduction osteotomy of the first metacarpal can be performed as well.

- For type VI of the Buck-Gramcko classification, the surgical treatment typically consists of removing the additional mostly hypoplastic thumb(s). Further procedures of reconstruction of the triphalangeal thumb are performed according to the shape of the extra phalanx as described above.

Because neither of the two thumb components is normal, a decision should be taken on combining which elements to create the best possible composite digit. Instead of amputating the most hypoplastic thumb, preservation of skin, nail, collateral ligaments and tendons is needed to augment the residual thumb. Surgery is recommended in the first year of life, generally between 9 and 15 months of age.

Surgical options depend on type of polydactyly.

Omphalocele has been described in two patients with Apert syndrome by Herman T.E. et al. (USA, 2010) and by Ercoli G. et al. (Argentina, 2014). An omphalocele is a birth defect in which an intestine or other abdominal organs are outside of the body of an infant because of a hole in the bellybutton area. However, the association between omphalocele and Apert syndrome is not confirmed yet, so additional studies are necessary.

Because the circumference of the conjoined fingers is smaller than the circumference of the two separated fingers, there is not enough skin to cover both digits once they are separated at the time of surgery. Therefore, the surgeon must bring new skin into the area at the time of surgery. This is most commonly done with a skin graft (from groin or anterior elbow). Skin can also be used from the back of the hand by mobilizing it (called a "graftless" syndactyly correction), which requires planning over a period of months prior to surgery.

Early intervention is considered important. For infants, breathing and feeding difficulties, are monitored. Therapies used are "symptomatic and supportive."

The surgery takes place under general anaesthesia and lasts less than 1 hour. The surgeon prepares the locus to the size of the implant after performing a 8-cm axillary incision and inserts the implant beneath the skin. The closure is made in 2 planes.

The implant will replace the pectoralis major muscle, thus enabling the thorax to be symmetrical and, in women, the breast as well. If necessary, especially in the case of women, a second operation will complement the result by the implantation of a breast implant and / or lipofilling.

Lipomodelling is progressively used in the correction of breast and chest wall deformities. In Poland syndrome, this technique appears to be a major advance that will probably revolutionize the treatment of severe cases. This is mainly due to its ability to achieve previously unachievable quality of reconstruction with minimal scaring.

Webbed toes can be separated through surgery. Surgical separation of webbed toes is an example of body modification.

As with any form of surgery, there are risks of complications.

The end results depend on the extent of the webbing and underlying bone structure. There is usually some degree of scarring, and skin grafts may be required. In rare instances, nerve damage may lead to loss of feeling in the toes and a tingling sensation. There are also reports of partial web grow-back. The skin grafts needed to fill in the space between the toes can lead to additional scars in the places where the skin is removed.

Three main support groups of this syndrome are the ASGA in Australia, The Association for Children with Genetic Disorders in Poland, and the Association of People of Genetic Disorders in Greece.

Children with Pfeiffer syndrome types 2 and 3 "have a higher risk for neurodevelopmental disorders and a reduced life expectancy" than children with Pfeiffer syndrome type 1, but if treated, favorable outcomes are possible. In severe cases, respiratory and neurological complications often lead to early death.

Synpolydactyly is a joint presentation of syndactyly (fusion of digits) and polydactyly (production of supernumerary digits). This is often a result of a mutation in the HOX D13 gene.

Types include:

YVS has been described relatively recently in the 1980s and since then less than 15 cases have been reported around the world. Many of the infants did not survive beyond one year of age.

It has several different types:

- type 1 - Apert syndrome

- type 2 - Crouzon syndrome

- type 3 - Saethre-Chotzen syndrome

- type 5 - Pfeiffer syndrome

A related term, "acrocephalopolysyndactyly" (ACPS), refers to the inclusion of polydactyly to the presentation. It also has multiple types:

- type 1 - Noack syndrome; now classified with Pfeiffer syndrome

- type 2 - Carpenter syndrome

- type 3 - Sakati-Nyhan-Tisdale syndrome

- type 4 - Goodman syndrome; now classified with Carpenter syndrome

- type 5 - Pfeiffer syndrome

It has been suggested that the distinction between "acrocephalosyndactyly" versus "acrocephalopolysyndactyly" should be abandoned.