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.

This disorder is caused by an abnormality of the TBCE gene, the locus for which is on Chromosome 1q42.3. The locus is a 230 kb region of gene with identified deletions and mutations in affected individuals. There are rare cases of the disorder not being due to a TBCE gene abnormality.

Other features include:

- Stunting

- Small hands and feet with long, tapering fingers and clinodactyly

- Dental anomalies in the form of malalignment and malocclusion

In another study of six patients, the patients were investigated further. They were found to have low levels of IGF-1 and markedly retarded bone age.

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:

Branchio-oculo-facial syndrome is difficult to diagnose because it has incomplete penetrance. It is often misdiagnosed as branchio-oto-renal syndrome because of their similarities in symptoms.

It was estimated that only about 50 cases of BOFS have been documented in the medical literature as of 2004.

Research on the risk for developing schizophrenia in Ashkenazi Jews and other populations showed that 3q29 microdeletion syndrome leads to a significant higher rate of schizophrenia.

Because this genetic anomaly is genetically linked, genetic counseling may be the only way to decrease occurrences of Cherubism. The lack of severe symptoms in the parents may be the cause of failure in recognizing the disorder. The optimal time to be tested for mutations is prior to having children. The disorder results from a genetic mutation, and this gene has been found to spontaneously mutate. Therefore, there may be no prevention techniques available.

Kosaki overgrowth syndrome (KOGS) is a rare (27 cases reported by 2017) syndrome caused by mutations in the PDGFRB gene.

Beare–Stevenson cutis gyrata syndrome is so rare that a reliable incidence cannot be established as of yet; fewer than 20 patients with the condition have been reported.

LINES was first described in a 54-year-old male with history of hypothyroidism who presented to an urgent care facility with bilateral axillary adenopathy and severe malaise. Incision and drainage of the nodes was performed and he was discharged home with sulfamethoxazole/trimethoprim for presumed Methicillin-resistant Staphylococcus aureus (MRSA) infection.

The patient subsequently developed a temperature of 37.5°C, expressed rigors, and night sweats. He returned to the ED the next day and on further history admitted to 3 weeks of “snorting 6-8 lines of coke a day” and smoking marijuana every evening to “come down.” He was hospitalized and treated with cefepime, doxycycline, and fluconazole empirically. The next day erythematous painful papules appeared on his trunk, arms, face, and ears. Blood cultures were negative. There was prominent necrosis of the malar region, nose, and lips with complete sparing of the back. Skin biopsy revealed extensive small vessel thrombosis throughout the superficial and deep dermal plexuses with perivascular mononuclear inflammatory infiltrate and a few neutrophils surrounding the vessels. ESR was elevated at 35 mm/hour; cardiolipin IgM was weakly positive at 16.3;C4 was decreased at 10 mg/dl; antinuclear antibodies were negative and p-ANCA was reactive. Coagulation studies were within normal limits. There was an elevated d-dimer of 17.54 mg/mL and platelets were slightly decreased. The patient’s urine drug screen was positive for cannabis but not cocaine.

Methylprednisolone was started and wound care was initiated. Epidermal necrosis then evolved to myonecrosis extending from midthigh to the foot which necessitated below knee amputation of the right extremity.The patient also required allografts to his chest and abdomen and autografts to his face and left lower extremity.

Diagnosis can be made solely on the basis of history and physical examination in people who present with only facial asymmetry. For those who report neurological symptoms such as migraine or seizures, MRI scan of the brain is the imaging modality of choice. A diagnostic lumbar puncture and serum test for autoantibodies may also be indicated in people who present with a seizure disorder of recent onset.

3q29 microdeletion syndrome is a rare genetic disorder resulting from the deletion of a segment of chromosome 3. This syndrome was first described in 2005.

Several mutations in the FGFR2 gene (a gene coding for a protein called fibroblast growth factor receptor 2, which is involved in important signaling pathways) are known to cause Beare–Stevenson cutis gyrata syndrome; however, not all patients with the condition have a mutation in their FGFR2 gene. Any alternative underlying causes are currently unidentified. The syndrome follows an autosomal dominant pattern, meaning that if one of the two available genes carries a mutation the syndrome will result. Currently, no familial histories are known (in other words, there are no reports of cases in which a parent carrying a mutation in their FGFR2 gene then propagated said mutation to his or her child).

The chemical imbalance is usually diagnosed when dental abnormalities are found. These abnormalities include premature deciduous teeth and abnormal growth of permanent teeth due to displacement by cysts and lesions. The only definite way to correctly diagnose the condition is by sequence analysis of the SH3BP2 gene. The gene has been found to have missense mutation in exon 9. Initial study of the patient is usually conducted using x-ray and CT scans. Neurofibromatosis may resemble Cherubism and may accompany the condition. Genetic testing is the final diagnosis tool.

The presentation of "LINES" is unique and there may be differences in the temporal presentation. Other diagnostic considerations with a similar progression include disseminated intravascular coagulation (DIC), catastrophic antiphospholipid syndrome (CAPS) and purpura fulminans (PF).

Clinicians should consider the diagnosis of "LINES" in patients with skin necrosis, neutropenia and fever associated with cocaine abuse.

Genetic studies have linked the autosomal recessive form of the disorder to the "ROR2" gene on position 9 of the long arm of chromosome 9. The gene is responsible for aspects of bone and cartilage growth. This same gene is involved in causing autosomal dominant brachydactyly B.

The autosomal dominant form has been linked to three genes - WNT5A, Segment polarity protein dishevelled homolog DVL-1 (DVL1) and Segment polarity protein dishevelled homolog DVL-3 (DVL3). This form is often caused by new mutations and is generally less severe then the recessive form. Two further genes have been linked to this disorder - Frizzled-2 (FZD2) and Nucleoredoxin (NXN gene). All of these genes belong to the same metabolic pathway - the WNT system. This system is involved in secretion for various compounds both in the fetus and in the adult.

A fetal ultrasound can offer prenatal diagnosis 19 weeks into pregnancy. However, the characteristics of a fetus suffering from the milder dominant form may not always be easy to differentiate from a more serious recessive case. Genetic counseling is an option given the availability of a family history.

Medical conditions include frequent ear infection, hearing loss, hypotonia, developmental problems, respiratory problems, eating difficulties, light sensitivity, and esophageal reflux.

Data on fertility and the development of secondary sex characteristics is relatively sparse. It has been reported that both male and female patients have had children. Males who have reproduced have all had the autosomal dominant form of the disorder; the fertility of those with the recessive variant is unknown.

Researchers have also reported abnormalities in the renal tract of affected patients. Hydronephrosis is a relatively common condition, and researchers have theorized that this may lead to urinary tract infections. In addition, a number of patients have suffered from cystic dysplasia of the kidney.

A number of other conditions are often associated with Robinow syndrome. About 15% of reported patients suffer from congenital heart defects. Though there is no clear pattern, the most common conditions include pulmonary stenosis and atresia. In addition, though intelligence is generally normal, around 15% of patients show developmental delays.

Figueroa and Pruzanksky classified HFM patients into three different types:

- Type I : Mild hypoplasia of the ramus , and the body of the mandible is slightly affected.

- Type II : The condyle and ramus are small, the head of the condyle is flattened , the glenoid fossa is absent , the condyle is hinged on a flat, often convex, infratemporal surface , the coronoid may be absent.

- Type III: The ramus is reduced to a thin lamina of bone or is completely absent. There is no evidence of a TMJ.

The features of this syndrome affect the face, skin, brain and the body.

Face:

- downslanting palpebral fissures

- pointed chin

- prominent forehead

- proptosis

- thin upper lip

- wide nasal bridge

Skin:

- fragile

- hyperelastic

Brain:

- Low IQ

- Periventricular white matter lesions

Body:

The height, lower-segment, hand, and foot length are all greater than usual.

Depending upon the treatment required, it is sometimes most appropriate to wait until later in life for a surgical remedy – the childhood growth of the face may highlight or increase the symptoms. When surgery is required, particularly when there is a severe disfiguration of the jaw, it is common to use a rib graft to help correct the shape.

According to literature, HFM patients can be treated with various treatment options such functional therapy with an appliance, distraction osteogenesis, or costochondral graft. The treatment is based on the type of severity for these patients. According to Pruzanksky's classification, if the patient has moderate to severe symptoms, then surgery is preferred. If patient has mild symptoms, then a functional appliance is generally used.

Patients can also benefit from a Bone Anchored Hearing Aid (BAHA).

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.

Diagnosis of Harlequin syndrome is made when the individual has consistent signs and symptoms of the condition, therefore, it is made by clinical observation. In addition, a neurologist or primary care physician may require an MRI test to rule out similar disorders such as Horner's syndrome, Adie's syndrome, and Ross' syndrome. In an MRI, a radiologist may observe areas near brain or spinal cord for lesions, or any damage to the nerve endings. It is also important that the clinician rules out traumatic causes by performing autonomic function tests. Such tests includes the following: tilt table test, orthostatic blood pressure measurement, head-up test, valsalva maneuver, thermoregulatory sweat test, tendon reflex test, and electrocardiography (ECG). CT scan of the heart and lungs may also be performed to rule out a structural underlying lesion. The medical history of the individual should be carefully noted.

Medical management may involve immunosuppressive drugs such as methotrexate, corticosteroids, cyclophosphamide, and azathioprine. No randomized controlled trials have yet been conducted to evaluate such treatments, so the benefits have not been clearly established.

Membranous aplasia cutis is a cutaneous condition, a type of aplasia cutis congenita, which can be seen along the embryonic fusion lines of the face.