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 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

The timing of surgical interventions is debatable. Parents have to decide about their child in a very vulnerable time of their parenthood. Indications for early treatment are progressive deformities, such as syndactyly between index and thumb or transverse bones between the digital rays. Other surgical interventions are less urgent and can wait for 1 or 2 years.

When surgery is indicated, the choice of treatment is based on the classification. Table 4 shows the treatment of cleft hand divided into the classification of Manske and Halikis.

Techniques described by Ueba, Miura and Komada and the procedure of Snow-Littler are guidelines; since clinical and anatomical presentation within the types differ, the actual treatment is based on the individual abnormality.

Table 4: Treatment based on the classification of Manske and Halikis

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.

Suspicion of a chromosome abnormality is typically raised due to the presence of developmental delays or birth defects. Diagnosis of ring 18 is usually made via a blood sample. A routine chromosome analysis, or karyotype, is usually used to make the initial diagnosis, although it may also be made by microarray analysis. Increasingly, microarray analysis is also being used to clarify breakpoints. Prenatal diagnosis is possible via amniocentesis or chorionic villus sampling.

Type II should be managed conservatively whereas type I and Ia requires to be treated surgically. Surgery involves four major steps:

- Development of the calcaneal part of the foot

- Repositioning of the navicular bone

- New adjustment of the ankle, and

- Various stabilization measures including the Grice operation and transposition of various tendons.

At present, treatment for ring 18 is symptomatic, meaning that the focus is on treating the signs and symptoms of the conditions as they arise. To ensure early diagnosis and treatment, it is suggested that people with ring 18 undergo routine screenings for thyroid, hearing, and vision problems.

As the causes of local gigantism are varied, treatment depends on the particular condition. Treatment may range from antibiotics and other medical therapy, to surgery in order to correct the anatomical anomaly.

The cause of fibular hemimelia is unclear. Purportedly, there have been some incidents of genetic distribution in a family; however, this does not account for all cases. Maternal viral infections, embryonic trauma, teratogenic environmental exposures or vascular dysgenesis (failure of the embryo to form a satisfactory blood supply) between four and seven weeks gestation are considered possible causes.

In an experimental mouse model, change in the expression of a homeobox gene led to similar, but bilateral, fibular defects.

Oligodactyly (from the Ancient Greek "oligos" meaning "few" and δάκτυλος "daktylos" meaning "finger") is the presence of fewer than five fingers or toes on a hand or foot.

It is quite often incorrectly called "hypodactyly", but the Greek prefixes and are used for scales (e.g. in hypoglycaemia and hypercholesterolemia). This as opposed to or scales, where and should be used (e.g. in oligarchy and polygamy). Oligodactyly is therefore the opposite of polydactyly. Very rare, this medical condition usually has a genetic or familial cause.

Oligodactyly is sometimes a sign or symptom of several syndromes including Poland syndrome and Weyer Ulnar Ray Syndrome. It is a type of Dysmelia.

Ectrodactyly is an extreme instance of oligodactyly, involving the absence of one or more central digits of the hand or foot and is also known as split hand/split foot malformation (SHFM). The hands and feet of people with ectrodactyly are often described as "claw-like" and may include only the thumb and one finger (usually either the little finger, ring finger, or a syndactyly of the two) with similar abnormalities of the feet.

People with oligodactyly often have full use of the remaining digits and adapt well to their condition. They are not greatly hindered in their daily activities, if at all. Even those with the most extreme forms are known to engage in tasks that require fine control, such as writing and bootmaking as well as working as a cab driver.

Vadoma people of Zimbabwe have a high frequency of oligodactyly.

Diagnosis of clubfoot deformity is by physical examination. Typically, a newborn is examined shortly after delivery with a head to toe assessment. Examination of the lower extremity and foot reveals the deformity, which may affect one or both feet. Examination of the foot shows four components of deformity.

- First, there is a higher arch on the inside of the foot. This component of the deformity can occur without the other aspects of clubfoot deformity. In isolation, this aspect of the deformity is called cavus deformity.

- Second, the forefoot is curved inward or medially (toward the big toe). This component of the deformity can occur without the other aspects of clubfoot deformity. In isolation, this aspect of the deformity is called metatarsus adductus.

- Third, the heel is turned inward. This is a natural motion of the heel and subtalar joint, typically referred to as inversion. In clubfoot deformity, the turning in (inversion) of the heel is fixed (not passively correctable) and considered a varus deformity.

- Fourth, and finally, the ankle is pointed downward. This is a natural motion of the ankle referred to as plantar flexion. In clubfoot deformity, this position is fixed (not correctable) and is referred to as equinus deformity.

A foot that shows all four components are diagnosed as having clubfoot deformity. These four components of a clubfoot deformity can be remembered with the acronym CAVE (cavus, forefoot adductus, varus, and equinus).

The severity of the deformity can also be assessed on physical exam, but is subjective to quantify. One way to assess severity is based on the stiffness of the deformity or how much it can be corrected with manual manipulation of the foot to bring it into a corrected position. Other factors used to assess severity include the presence of skin creases in the arch and at the heel and poor muscle consistency.

In some cases, it may be possible to detect the disease prior to birth during a prenatal ultrasound. Prenatal diagnosis by ultrasound can allow parents the opportunity to get information about this condition and make plans for treatment after their baby is born.

Other testing and imaging is typically not needed. Further testing may be needed if there are concerns for other associated conditions.

The gene for Darwin's tubercle was once thought to be inherited in an autosomal dominant pattern with incomplete penetrance, meaning that those who possess the allele (version of a gene) will not necessarily present with the phenotype. However, genetic and family studies have demonstrated that the presence of Darwin's Tubercle may be more likely to be influenced by one's environment or developmental accidents than it is by genetics alone. There is no clear argument for whether the trait has significance in sexual dimorphism studies or age related studies. In some studies, there is clear data that Darwin's tubercle is not associated with sex. In contrast, others indicate that there is a correlation with sexual dimorphism between men and women, where men tend to have the tubercle more than women in some populations. Two studies indicate that older men tend to have greater expression of Darwin's tubercle than do older women.

Fibular hemimelia or longitudinal fibular deficiency is "the congenital absence of the fibula and it is the most common congenital absence of long bone of the extremities." It is the shortening of the fibula at birth, or the complete lack thereof. In humans, the disorder can be noted by ultrasound in utero to prepare for amputation after birth or complex bone lengthening surgery. The amputation usually takes place at six months with removal of portions of the legs to prepare them for prosthetic use. The other treatments which include repeated corrective osteotomies and leg-lengthening surgery (Ilizarov apparatus) are costly and associated with residual deformity.

Rocker bottom foot, also known as congenital vertical talus, is an anomaly of the foot. It is characterized by a prominent calcaneus (heel bone) and a convex rounded bottom of the foot. It gets its name from the foot's resemblance to the bottom of a rocking chair.

It can be associated with Edwards' syndrome (trisomy 18), Patau syndrome (trisomy 13), Trisomy 9 and mutation in the gene HOXD10.

It can also be associated with Charcots foot.

Diagnosis is made on the basis of history and a high index of suspicion. On examination there is tenderness to palpation on navicular head. Radiographs reveal typical changes of increased density and narrowing of the navicular bone

Asymmetric crying facies (ACF), also called Cayler cardiofacial syndrome, partial unilateral facial paresis and hypoplasia of depressor angula oris muscle, is a minor congenital anomaly caused by agenesis or hypoplasia of the depressor anguli oris muscle, one of the muscles that control the movements of the lower lip. This unilateral facial weakness is first noticed when the infant cries or smiles, affecting only one corner of the mouth and occurs on the left side in nearly 80% of cases. It is associated with other birth defects in more than 50% of cases.

When the hypoplasia of the depressor anguli oris muscle is associated with congenital cardiac defects, the term 'Cayler cardiofacial syndrome' is used.

Cayler syndrome is part of 22q11.2 deletion syndrome.

It was characterized by Cayler in 1969.

Hemifacial hypertrophy (also termed facial hemihypertrophy, facial hemihyperplasia, or Friedreich's disease) abbreviated as (HFH) is rare congenital disease characterized by unilateral enlargement of the head and teeth. It is classified as true HFH (THFH) with unilateral enlargement of the viscerocranium, and partial HFH (PHFH) in which not all structures are enlarged. Hemifacial hypertrophy can cause a wide spectrum of defects or may involve only muscle or bone. it is usually treated surgically. It is believed to be a minor form of hemihypertrophy.

Congenital causes include:

- Klippel Trenaunay Weber syndrome

- Maffucci syndrome

- macrodystrophia lipomatosa

- neurofibromatosis,

- lipoatrophic diabetes.

- Proteus syndrome, which by one theory accounts for the deformities of the Elephant Man

Diplopodia is a congenital anomaly in tetrapods that involves duplication of elements of the foot on the hind limb. It comes from the Greek roots diplo = "double" and pod = "foot". Diplopodia is often found in conjunction with other structural abnormalities and can be lethal. It is more extreme than polydactyly, the presence of extra digits.

The feature is present in approximately 10.4% of the Spanish adult population, 40% of Indian adults, and 58% of Swedish school children. This acuminate nodule represents the point of the mammalian ear. The trait can potentially be bilateral, meaning present on both ears, or unilateral, where it is only present on one ear. There is mixed evidence in regard to whether the bilateral or unilateral expression is related to population, or other factors. Some populations express full bilaterality, while others may express either unilateral or bilaterality. However, bilaterality appears to be more common than unilateral as it pertains to the expression of the trait.

Treatment is usually with some combination of the Ponseti or French methods. The Ponseti method includes the following: casting together with manipulation, cutting the Achilles tendon, and bracing. The Ponseti method has been found to be effective in correcting the problem in those under the age of two. The French method involves realignment and tapping of the foot is often effective but requires a lot of effort by caregivers. Another technique known as Kite does not appear as good. In about 20% of cases further surgery is required.

Encephalocraniocutaneous lipomatosis (ECCL), otherwise known as Haberland syndrome, is a rare condition primarily affecting the brain, eyes, and skin of the head and face. It is characterized by unilateral subcutaneous and intracranial lipomas, alopecia, unilateral porencephalic cysts, epibulbar choristoma and other ophtalmic abnormalities.

It was named after Haberland and Perou who first described it.

Generally, no treatment is required for idiopathic presentation as it is a normal anatomical variant in young children. Treatment is indicated when it persists beyond 3 and a half years old. In the case of unilateral presentation or progressive worsening of the curvature, when caused by rickets, the most important thing is to treat the constitutional disease, at the same time instructing the care-giver never to place the child on its feet. In many cases this is quite sufficient in itself to effect a cure, but matters can be hastened somewhat by applying splints. When the deformity arises in older patients, either from trauma or occupation, the only permanent treatment is surgery, but orthopaedic bracing can provide relief.