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.

The main diagnostic tools for evaluating FND are X-rays and CT-scans of the skull. These tools could display any possible intracranial pathology in FND. For example, CT can be used to reveal widening of nasal bones. Diagnostics are mainly used before reconstructive surgery, for proper planning and preparation.

Prenatally, various features of FND (such as hypertelorism) can be recognized using ultrasound techniques. However, only three cases of FND have been diagnosed based on a prenatal ultrasound.

Other conditions may also show symptoms of FND. For example, there are other syndromes that also represent with hypertelorism. Furthermore, disorders like an intracranial cyst can affect the frontonasal region, which can lead to symptoms similar to FND. Therefore, other options should always be considered in the differential diagnosis.

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:

No surgical outcomes studies exist for evaluating the function of the thumbs after an on-top plasty reconstruction.

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.

Most children with symbrachydactyly have excellent function in daily activities. Due to the length of their arm, they do not qualify for most artificial limbs. However, some adaptive prosthetics and equipment for sports and leisure activities may be helpful when the child is older. Children who demonstrate some functional movement in their remaining fingers and within the palm are evaluated for possible surgery such as toe transfers.

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.

The diagnosis of Muenke syndrome is suspected bases on abnormal skull shape and a diagnosis of coronal craniosynostosis. In 2006, Agochukwu and her colleagues concluded that “A distinct Muenke syndrome phenotype includes: uni or bilateral coronal synostosis, midface hypoplasia, broad toes, and brachydactyly.” Due to phenotypic overlap and/or mild phenotypes, clinical differentiation of this syndrome may be difficult. The suspected diagnosis is confirmed by a blood test to check for gene mutation. To establish the extent of disease in an individual diagnosed with Muenke syndrome, various evaluations are recommended.

The diagnosis of this condition can be done via x-rays (with lack of normal distance L1 to L5), and additionally genetic testing is available to ascertain hypochondroplasia However, the physical characteristics(physical finding) is one of the most important in determining the condition.

Surgery is an option to correct some of the morphological changes made by Liebenberg Syndrome. Cases exist where surgery is performed to correct radial deviations and flexion deformities in the wrist. A surgery called a carpectomy has been performed on a patient whereby a surgeon removes the proximal row of the carpal bones. This procedure removes some of the carpal bones to create a more regular wrist function than is observed in people with this condition.

The exact cause of the condition is unknown. In some cases, close family members may share this condition. In other cases, no other related persons have this condition. The scientific name for the condition is syndactyly, although this term covers both webbed fingers and webbed toes. Syndactyly occurs when apoptosis or programmed cell death during gestation is absent or incomplete. Webbed toes occur most commonly in the following circumstances:

- Syndactyly or Familial Syndactyly

- Down syndrome

It is also associated with a number of rare conditions, notably:

- Aarskog–Scott syndrome

- Acrocallosal syndrome

- Apert's syndrome

- Bardet-Biedl syndrome

- Carpenter syndrome

- Cornelia de Lange syndrome

- Edwards syndrome

- Jackson–Weiss syndrome

- Fetal hydantoin syndrome

- Miller syndrome

- Pfeiffer syndrome

- Smith-Lemli-Opitz syndrome

- Timothy syndrome

- Ectodermal Dysplasia

- Klippel-Feil Syndrome

In the above brachydactyly syndromes, short digits are the most prominent of the anomalies, but in many other syndromes (Down syndrome, Rubinstein-Taybi syndrome, etc.), brachydactyly is a minor feature compared to the other anomalies or problems comprising the syndrome.

Genetic counseling for VWS involves discussion of disease transmission in the autosomal dominant manner and possibilities for penetrance and expression in offspring. Autosomal dominance means affected parents have a 50% chance of passing on their mutated "IRF6" allele to a their child. Furthermore, if a cleft patient has lip pits, he or she has a ten times greater risk of having a child with cleft lip with or without cleft palate than a cleft patient who does not have lip pits. Types of clefting between parents and affected children are significantly associated; however, different types of clefts may occur horizontally and vertically within the same pedigree. In cases where clefting is the only symptom, a complete family history must be taken to ensure the patient does not have non-syndromic clefting.

Research on prenatal diagnosis has shown that a diagnosis can be made prenatally in approximately 50% of fetuses presenting arthrogryposis. It could be found during routine ultrasound scanning showing a lack of mobility and abnormal position of the foetus. Nowadays there are more options for visualization of details and structures can be seen well, like the use of 4D ultrasound. In clinic a child can be diagnosed with arthrogryposis with physical examination, confirmed by ultrasound, , or muscle biopsy.

Via a photo shown on a Facebook page, the mother of a child previously diagnosed with this condition recognised the symptoms and reported them to the family involved, resulting in an immediate diagnosis that medical professionals had overlooked in all earlier consultations.

Symbrachydactyly is a congenital abnormality, characterized by limb anomalies consisting of brachydactyly, cutaneous syndactyly and global hypoplasia of the hand or foot. In many cases, bones will be missing from the fingers and some fingers or toes may be missing altogether. The ends of the hand may have "nubbins"—small stumps where the finger would have developed, which may have tiny residual nails.

Symbrachydactyly has been reported to appear without other combined limb anomalies and usually in one arm in 1 in 30,000 births to 1 in 40,000 births.

The cause of symbrachydactyly is unknown. One possible cause might be an interruption of the blood supply to the developing arm at four to six weeks of pregnancy. There is no link to anything the mother did or did not do during pregnancy. There is also no increased risk of having another child with the same condition or that the child will pass the condition on to his or her children.

In most cases, children born with symbrachydactyly are able to adapt to their physical limitations and experience a fully functional life with no treatment. Most children with this condition can use their hands well enough to do all the usual things children do. Possible treatment includes surgery or a routine of regularly stretching the fingers.

Because newborns can breathe only through their nose, the main goal of postnatal treatment is to establish a proper airway. Primary surgical treatment of FND can already be performed at the age of 6 months, but most surgeons wait for the children to reach the age of 6 to 8 years. This decision is made because then the neurocranium and orbits have developed to 90% of their eventual form. Furthermore, the dental placement in the jaw has been finalized around this age.

Diagnosis can be characterized by typical facial and cranial deformities.

Observatory signs of trigonocephaly are:

- a triangular shaped forehead seen from top view leading to a smaller anterior cranial fossa

- a visible and palpable midline ridge

- hypotelorism inducing ethmoidal hypoplasia

Imaging techniques (3D-CT, Röntgenography, MRI) show:

- epicanthal folds in limited cases

- teardrop shaped orbits angulated towards the midline of the forehead ('surprised coon' sign) in severe cases

- a contrast difference between a röntgenograph of a normal and a trigonocephalic skull

- anterior curving of the metopic suture seen from lateral view of the cranium on a röntgenograph

- a normal cephalic index (maximum cranium width / maximum cranium length) however, there is bitemporal shortening and biparietal broadening

The neuropsychological development is not always affected. These effects are only visible in a small percentage of children with trigonocephaly or other suture synostoses. Neuropsychological signs are:

- problems in behaviour, speech and language

- mental retardation

- neurodevelopmental delays such as ADHD (Attention Deficit Hyperactivity Disorder), ODD (Oppositional Defiant Disorder), ASD (Autism Spectrum Disorder) and CD (Conduct Disorder). Many of these delays become evident at school age.

Brachydactyly (Greek βραχύς = "short" plus δάκτυλος = "finger"), is a medical term which literally means "shortness of the fingers and toes" (digits). The shortness is relative to the length of other long bones and other parts of the body. Brachydactyly is an inherited, usually dominant trait. It most often occurs as an isolated dysmelia, but can also occur with other anomalies as part of many congenital syndromes.

Nomograms for normal values of finger length as a ratio to other body measurements have been published. In clinical genetics the most commonly used index of digit length is the dimensionless ratio of the length of the 3rd (middle) finger to the hand length. Both are expressed in the same units (centimeters, for example) and are measured in an open hand from the fingertip to the principal creases where the finger joins the palm and where the palm joins the wrist.

The constellation of anomalies seen with Nasodigitoacoustic syndrome result in a distinct diagnosis. The diagnostic criteria for the disorder are broad distal phalanges of the thumbs and big toes, accompanied by a broad and shortened nose, sensorineural hearing loss and developmental delay, with predominant occurrence in males.

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.

Many other surgeries are also able to improve function in joints of arthrogryposis patients. These surgeries usually exist out of tendon transfers and skin flap movements, adjusted to the individual.

Nasodigitoacoustic syndrome is similar to several syndromes that share its features. Brachydactyly of the distal phalanges, sensorineural deafness and pulmonary stenosis are common with Keutel syndrome. In Muenke syndrome, developmental delay, distal brachydactyly and sensorineural hearing loss are reported; features of Teunissen-Cremers syndrome include nasal aberrations and broadness of the thumbs and big toes, also with brachydactyly. Broad thumbs and big toes are primary characteristics of Rubinstein syndrome.

Craniometaphyseal dysplasia is diagnosed based on clinical and radiographic findings that include hyperostosis. Some things such as cranial base sclerosis and nasal sinuses obstruction can be seen during the beginning of the child's life. In radiographic findings the most common thing that will be found is the narrowing of foramen magnum and the widening of long bones. Once spotted treatment is soon suggested to prevent further compression of the foramen magnum and disabling conditions.

Lip pits may be surgically removed either for aesthetic reasons or discomfort due to inflammation caused by bacterial infections or chronic saliva excretion, though spontaneous shrinkage of the lip pits has occurred in some rare cases. Chronic inflammation has also been reported to cause squamous-cell carcinoma. It is essential to completely remove the entire lip pit canal, as mucoid cysts can develop if mucous glands are not removed. A possible side effect of removing the lip pits is a loose lip muscle. Other conditions associated with VWS, including CL, CP, congenital heart defects, etc. are surgically corrected or otherwise treated as they would be if they were non-syndromic.