The cranial malformations are the most apparent effects of acrocephalosyndactyly. Craniosynostosis occurs, in which the cranial sutures close too soon, though the child's brain is still growing and expanding. Brachycephaly is the common pattern of growth, where the coronal sutures close prematurely, preventing the skull from expanding frontward or backward, and causing the brain to expand the skull to the sides and upwards. This results in another common characteristic, a high, prominent forehead with a flat back of the skull. Due to the premature closing of the coronal sutures, increased cranial pressure can develop, leading to mental deficiency. A flat or concave face may develop as a result of deficient growth in the mid-facial bones, leading to a conditir prognathism. Other features of acrocephalosyndactyly may include shallow bony orbits and broadly spaced eyes. Low-set ears are also a typical characteristic of branchial arch syndromes.

Common relevant features of acrocephalosyndactyly are a high-arched palate, pseudomandibular prognathism (appearing as mandibular prognathism), a narrow palate, and crowding of the teeth.

Synostosis (plural: synostoses) is fusion of two bones. It can be normal in puberty, fusion of the epiphysis, or abnormal. When synostosis is abnormal it is a type of dysostosis.

Examples of synostoses include:

- craniosynostosis – an abnormal fusion of two or more cranial bones;

- radioulnar synostosis – the abnormal fusion of the radius and ulna bones of the forearm;

- tarsal coalition – a failure to separately form all seven bones of the tarsus (the hind part of the foot) resulting in an amalgamation of two bones; and

- syndactyly – the abnormal fusion of neighboring digits.

Synostosis within joints can cause ankylosis.

Radioulnar synostosis is one of the more common failures of separation of parts of the upper limb. There are two general types: one is characterized by fusion of the radius and ulna at their proximal borders and the other is fused distal to the proximal radial epiphysis. Most cases are sporadic, congenital (due to a defect in longitudinal segmentation at the 7th week of development) and less often post-traumatic, bilateral in 60%, and more common in males. Familial cases in association with autosomal dominant transmission appear to be concentrated in certain geographic regions, such as Sicily.

The condition frequently is not noted until late childhood, as function may be normal, especially in unilateral cases. Increased wrist motion may compensate for the absent forearm motion. It has been suggested that individuals whose forearms are fixed in greater amounts of pronation (over 60 degrees) face more problems with function than those with around 20 degrees of fixation. Pain is generally not a problem, unless radial head dislocation should occur.

Most examples of radioulnar synostosis are isolated (non-syndromic). Syndromes that may be accompanied by radioulnar synostosis include X chromosome polyploidy (e.g., XXXY) and other chromosome disorders (e.g., 4p- syndrome, Williams syndrome), acrofacial dysostosis, Antley–Bixler syndrome, genitopatellar syndrome, Greig cephalopolysyndactyly syndrome, hereditary multiple osteochondromas (hereditary multiple exostoses), limb-body wall complex, and Nievergelt syndrome.

Craniosynostosis (from cranio, cranium; + syn, together; + ostosis relating to bone) is a condition in which one or more of the fibrous sutures in an infant skull prematurely fuses by turning into bone (ossification). Craniosynostosis has following kinds: scaphocephaly, trigonocephaly, plagiocephaly, anterior plagiocephaly, posterior plagiocephaly, brachycephaly, oxycephaly, pansynostosis.

This is a very rare situation, in which the extra digit is on the ring, middle or index finger. Of these fingers, the index finger is most often affected, whereas the ring finger is rarely affected.

This type of polydactyly can be associated with syndactyly, cleft hand and several syndromes.

Polysyndactyly presents various degrees of syndactyly affecting fingers three and four.

Classification is performed by using x-ray imaging to see the bone structures.

Many of the characteristic facial features (among other) of Jackson–Weiss syndrome result from the premature fusion of the skull bones. The following are some of the more common, such as:

- Preaxial foot polydactyl

- Tarsal synostosis

- Frontal bossing

- Proptosis

Radial aplasia is a congenital defect which affects the formation of the radius bone in the arm. The radius is the lateral bone which connects to the wrist via articulation with the carpal bones. A child born with this condition has either a short or absent radius bone in one or both of his or her arm(s). Radial aplasia also results in the thumb being either partly formed or completely absent from the hand. Radial aplasia is connected with the condition VACTERL association. The cause for radial aplasia in unknown, but it widely believed to occur within the first ten weeks of gestation.

Many of the characteristic facial features result from the premature fusion of the skull bones (craniosynostosis). The head is unable to grow normally, which leads to a high prominent forehead (turribrachycephaly), and eyes that appear to bulge (proptosis) and are wide-set (hypertelorism). In addition, there is an underdeveloped upper jaw (maxillary hypoplasia). About 50 percent of children with Pfeiffer syndrome have hearing loss, and dental problems are also common.

In people with Pfeiffer syndrome, the thumbs and first (big) toes are wide and bend away from the other digits (pollex varus and hallux varus). Unusually short fingers and toes (brachydactyly) are also common, and there may be some webbing or fusion between the digits (syndactyly).

In general there are five types of thumb hypoplasia, originally described by Muller in 1937 and improved by Blauth, Buck-Gramcko and Manske.

- Type I: the thumb is small, normal components are present but undersized. Two muscles of the thumb, the abductor pollicis brevis and opponens pollicis, are not fully developed

. This type requires no surgical treatment in most cases.

- Type II is characterized by a tight web space between the thumb and index finger which restricts movement, poor thenar muscles and an unstable middle joint of the thumb metacarpophalangeal joint. This unstable thumb is best treated with reconstruction of the mentioned structures.

- Type III thumbs are subclassified into two subtypes by Manske. Both involve a less developed first metacarpal and a nearly absent thenar musculature. Type III-A has a fairly stable carpometacarpal joint and type III-B does not. The function of the thumb is poor. Children with type III are the most difficult patients to treat because there is not one specific treatment for the hypoplastic thumb. The limit between pollicization and reconstruction varies. Some surgeons have said that type IIIA is amenable to reconstruction and not type IIIB. Others say type IIIA is not suitable for reconstruction too. Based on the diagnosis the doctor has to decide what is needed to be done to obtain a more functional thumb, i.e. reconstruction or pollicization. In this group careful attention should be paid to anomalous tendons coming from the forearm (extrinsic muscles, like an aberrant long thumb flexor – flexor pollicis longus).

- Type IV is called a pouce flottant, floating thumb. This thumb has a neurovascular bundle which connects it to the skin of the hand. There’s no evidence of thenar muscles and rarely functioning tendons. It has a few rudimentary bones. Children with type IV are difficult to reconstruct. This type is nearly always treated with an index finger pollicization to improve hand function.

- Type V is no thumb at all and requires pollicization.

Thumb hypoplasia is a spectrum of congenital abnormalities of the thumb varying from small defects to absolute retardation of the thumb. It can be isolated, when only the thumb is affected, and in 60% of the cases it is associated with radial dysplasia (or radial club, radius dysplasia, longitudinal radial deficiency). Radial dysplasia is the condition in which the forearm bone and the soft tissues on the thumb side are underdeveloped or absent.

In an embryo the upper extremities develop from week four of the gestation. During the fifth to eighth week the thumb will further develop. In this period something goes wrong with the growth of the thumb but the exact cause of thumb hypoplasia is unknown.

One out of every 100,000 live births shows thumb hypoplasia. In more than 50% of the cases both hands are affected, otherwise mainly the right hand is affected.

About 86% of the children with hypoplastic thumb have associated abnormalities. Embryological hand development occurs simultaneously with growth and development of the cardiovascular, neurologic and hematopoietic systems. Thumb hypoplasia has been described in 30 syndromes wherein those abnormalities have been seen. A syndrome is a combination of three or more abnormalities. Examples of syndromes with an hypoplastic thumb are Holt-Oram syndrome, VACTERL association and thrombocytopenia absent radius (TAR syndrome).

The triphalangeal thumb has a different appearance than normal thumbs. The appearance can differ widely; the thumb can be a longer thumb, it can be deviated in the radio-ulnar plane (clinodactyly), thumb strength can be diminished. In the case of a five fingered-hand it has a finger-like appearance, with the position in the plane of the four fingers, thenar muscle deficiency, and additional length. There is often a combination with radial polydactyly.

Numerous associated abnormalities of other organ systems may be present. This heterogeneity requires comprehensive evaluation of all patients and treatment regimes that can vary from modification of activities to extensive spinal surgeries. Furthermore, it is unclear whether Klippel–Feil syndrome is a unique disease, or if it is one part of a spectrum of congenital spinal deformities. Klippel–Feil syndrome is usually diagnosed after birth.

The most common sign of the disorder is restricted mobility of the neck and upper spine. A short neck and low hairline at the back of the head may occur in some patients.

Associated abnormalities may include:

- scoliosis (side-to-side curvature of the spine), which is abnormal curving of the spine. The spine sometimes appears as a "C" or an "S"

- spina bifida, when the spinal canal and the back bone do not close completely during birth

- anomalies of the kidneys and the ribs

- cleft palate (hole in the roof of the mouth)

- dental problems (late dentition, high-risk of caries, oligo- and hypodontia)

- respiratory problems

- heart malformations

- short stature

- Duane syndrome

- Approximately 35% of patients with Klippel–Feil syndrome will also have a congenital elevation of the scapula known as Sprengel's deformity

The disorder also may be associated with abnormalities of the head and face, skeleton, sex organs, muscles, brain and spinal cord, arms, legs, fingers and heart defects. These heart defects often lead to a shortened life expectancy, the average being 35–45 years of age among males and 40–50 among females. This condition is similar to the heart failure seen in gigantism.

In 2011, a study identifying the occurrence of symptoms of 100 patients was published.

Generally, triphalangeal thumbs are non-opposable. In contrast to most people with opposable thumbs, a person suffering from TPT cannot easily place his or her thumb opposite the other four digits of the same hand. The opposable thumb's ability to effortlessly utilize fingers in a "pinch" formation is critical in precision gripping. For the thumb to adequately grip, certain thumb criteria must be met (e.g. suitable position and length, stable joints and good thenar muscle strength). Because triphalangeal thumbs cannot easily oppose and do not possess many of the optimal qualities found in most opposable thumbs, they tend to cause the hand to be less effective in use and, therefore, prove to be more problematic in daily life.

Radioulnar synostosis is a rare condition where there is an abnormal connection between the radius and ulna bones of the forearm. This can be present at birth (congenital), when it is a result of a failure of the bones to form separately, or following an injury (post-traumatic).

It typically causes restricted movement of the forearm, in particular rotation (pronation and supination), though is not usually painful unless it causes subluxation of the radial head. It can be associated with dislocation of the radial head which leads to limited elbow extension.

Jackson–Weiss syndrome (JWS) is a genetic disorder characterized by foot abnormalities and the premature fusion of certain bones of the skull (craniosynostosis), which prevents further growth of the skull and affects the shape of the head and face. This genetic disorder can also sometimes cause intellectual disability and crossed eyes as well, it was characterized in 1976.

Pfeiffer syndrome is a very rare genetic disorder characterized by the premature fusion of certain bones of the skull which affects the shape of the head and face. In addition, the syndrome includes abnormalities of the hands (such as wide and deviated thumbs) and feet (such as wide and deviated big toes). Pfeiffer syndrome affects about 1 in 100,000 births.

The most common and defining features of BGS are craniosynostosis and radial ray deficiency. The observations of these features allow for a diagnosis of BGS to be made, as these symptoms characterize the syndrome. Craniosynostosis involves the pre-mature fusion of bones in the skull. The coronal craniosynostosis that is commonly seen in patients with BGS results in the fusion of the skull along the coronal suture. Because of the changes in how the bones of the skull are connected together, people with BGS will have an abnormally shaped head, known as brachycephaly. Features commonly seen in those with coronal craniosynostosis are bulging eyes, shallow eye pockets, and a prominent forehead. Radial ray deficiency is another clinical characteristic of those with BGS, and results in the under-development (hypoplasia) or the absence (aplasia) of the bones in the arms and the hands. These bones include the radius, the carpal bones associated with the radius and the thumb. Oligodactyly can also result from radial ray deficiency, meaning that someone with BGS may have fewer than five fingers. Radial ray deficiency that is associated with syndromes (such as BGS) occurs bi-laterally, affecting both arms.

Some of the other clinical characteristics sometimes associated with this disorder are growth retardation and poikiloderma. Although the presentation of BGS may differ between individuals, these characteristics are often observed. People with BGS may have stunted growth, short stature and misshapen kneecaps. Poikiloderma may also be present in people with this syndrome, meaning that their skin may have regions of hyperpigmentation and hypopigmentation, or regions where the skin is missing (atrophy).

Congenital radioulnar synostosis is rare, with approximately 350 cases reported in journals, and it typically affects both sides (bilateral) and can be associated with other skeletal problems such as hip and knee abnormalities, finger abnormalities (syndactyly or clinodactyly), or Madelung's deformity. It is sometimes part of known genetic syndromes such as triple X-Y (XXXY), Apert's, William's, or Holt-Oram. It has been reported to run in families typically following an autosomal dominant inheritance pattern which means children of an affected parent have a 50% chance of having the condition. When associated wth amegakaryocytic thrombocytopenia this inheritance has been found to be caused by mutations to the "HOXA11" gene.

Classification of radial dysplasia is practised through different models. Some only include the different deformities or absences of the radius, where others also include anomalies of the thumb and carpal bones. The Bayne and Klug classification discriminates four different types of radial dysplasia. A fifth type was added by Goldfarb et al. describing a radial dysplasia with participation of the humerus. In this classification only anomalies of the radius and the humerus are taken in consideration. James and colleagues expanded this classification by including deficiencies of the carpal bones with a normal distal radius length as type 0 and isolated thumb anomalies as type N.

Type N: Isolated thumb anomaly

Type 0: Deficiency of the carpal bones

Type I: Short distal radius

Type II: Hypoplastic radius in miniature

Type III: Absent distal radius

Type IV: Complete absent radius

Type V: Complete absent radius and manifestations in the proximal humerus

The term absent radius can refer to the last 3 types.

Klippel–Feil syndrome is a rare disease, initially reported in 1884 by Maurice Klippel and André Feil from France, characterized by the congenital fusion of any two of the seven cervical vertebrae.

The syndrome occurs in a heterogeneous group of patients unified only by the presence of a congenital defect in the formation or segmentation of the cervical spine. Klippel-Feil results in limited movement of the neck. Klippel–Feil syndrome is sometimes identified by shortness of the neck, but not all people with this disorder have a visibly shortened neck. Some people with the syndrome have a very low hairline.

In 1919, in his PhD thesis, André Feil suggested another classification of the syndrome encompassing not only deformation of the cervical spine but also deformation of the lumbar and thoracic spine.

People who are affected by Liebenberg Syndrome suffer from three main symptoms:

1. Dysplasia (improper formation) of the bony components of the elbow

2. Abnormal shape of carpal bones

3. Brachydactyly, a symptom where the fingers and toes are shorter than normal.

It is a congenital subluxation or dislocation of the ulna's distal end, due to malformation of the bones. Sometimes, minor abnormalities of other bone structures, often caused by disease or injury, such as a fracture of the distal end of the radius with upward displacement of the distal fragment. The deformity varies in degree from a slight protrusion of the lower end of the ulna, to complete dislocation of the inferior radio-ulnar joint with marked radial deviation of the hand. Severe deformities are associated with congenital absence or hypoplasia of the radius.

The male:female rate of this disorder is 1:4. The incidence is unknown, and there is no described racial predominance. Even though Madelung's Deformity is considered a congenital disorder, symptoms sometimes aren't seen until adulthood. In most cases, symptoms find their onset during midchildhood. At this age, the relatively slower growth of the ulnar and palmar part of the radius, leads to an increasingly progressive deformity. Pain and deformity are the main symptoms patients present with. Typical clinical presentation consists of a short forearm, anterior-ulnar bow of the radius and a forward subluxation of the hand on the forearm. As mentioned before, the severity of the disorder varies greatly, which also leads to a spectrum of presentation.

Radial dysplasia, also known as radial club hand or radial longitudinal deficiency, is a congenital difference occurring in a longitudinal direction resulting in radial deviation of the wrist and shortening of the forearm. It can occur in different ways, from a minor anomaly to complete absence of the radius, radial side of the carpal bones and thumb. Hypoplasia of the distal humerus may be present as well and can lead to stiffnes of the elbow. Radial deviation of the wrist is caused by lack of support to the carpus, radial deviation may be reinforced if forearm muscles are functioning poorly or have abnormal insertions. Although radial longitudinal deficiency is often bilateral, the extent of involvement is most often asymmetric.

The incidence is between 1:30,000 and 1:100,000 and it is more often a sporadic mutation rather than an inherited condition. In case of an inherited condition, several syndromes are known for an association with radial dysplasia, such as the cardiovascular Holt-Oram syndrome, the gastrointestinal VATER syndrome and the hematologic Fanconi anemia and TAR syndrome. Other possible causes are an injury to the apical ectodermal ridge during upper limb development, intrauterine compression, or maternal drug use (thalidomide).

This is characterized by hand and arm abnormalities. The following are specific characteristics:

- Malformed or absent (aplasia) thumb

- A thumb that looks more like a finger

- Partial or complete absence of a radius

- Shortening and radial deviation of the forearms

- Triphalangeal thumb

- Duplication of the thumb (preaxial polydactyly)