Hemangiomas associated with PHACE Syndrome are usually small or not visible at birth, but are easier to see during the first days to weeks of life. They can grow rapidly. Hemangiomas linked with PHACE Syndrome tend to cover a large area of the face, head or neck, either as one lesion or as many single lesions.

As it grows, the hemangioma can break down skin, distort facial features or get in the way of other vital functions, such as breathing, vision, and hearing. Other complications will depend on what other structures are involved. These could include developmental delay, seizures, headaches, and abnormal muscle tone if the brain is involved.

The key features of this syndrome are an enlargement of the fourth ventricle; complete absence of the cerebellar vermis, the posterior midline area of cerebellar cortex responsible for coordination of the axial musculature; and cyst formation near the internal base of the skull. An increase in the size of the fluid spaces surrounding the brain as well as an increase in pressure may also be present. The syndrome can appear dramatically or develop unnoticed.

Symptoms, which often occur in early infancy, include slower motor development and progressive enlargement of the skull. In older children, symptoms of increased intracranial pressure such as irritability, vomiting, and convulsions and signs of cerebellar dysfunction such as unsteadiness and lack of muscle coordination or jerky movements of the eyes may occur. Other symptoms include increased head circumference, bulging at the back of the skull, problems with the nerves that control the eyes, face and neck, and abnormal breathing patterns.

Dandy–Walker syndrome is frequently associated with disorders of other areas of the central nervous system including absence of the corpus callosum, the bundle of axons connecting the two cerebral hemispheres, and malformations of the heart, face, limbs, fingers and toes.

The Dandy–Walker complex is a genetically sporadic disorder that occurs one in every 30,000 live births. Prenatal diagnosis and prognosis of outcomes associated with Dandy–Walker can be difficult. Prenatal diagnosis is possible with ultrasound. Because the syndrome is associated with an increased risk for fetal karyotype abnormalities, amniocentesis can be offered after prenatal diagnosis. There is a relative contraindication of taking Warfarin during pregnancy, as it is associated with an increased risk of Dandy–Walker syndrome if taken during the first trimester.

The DWS malformation is the most severe presentation of the syndrome. The posterior fossa is enlarged and the tentorium is in high position. There is complete agenesis of the cerebellar vermis. There is also cystic dilation of the fourth ventricle, which fills the posterior fossa. This often involves hydrocephalus and complications due to associated genetic conditions, such as Spina Bifida.

The blockage of cerebrospinal fluid (CSF) flow may also cause a syrinx to form, eventually leading to syringomyelia. Central cord symptoms such as hand weakness, dissociated sensory loss, and, in severe cases, paralysis may occur.

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.

Syringomyelia is a chronic progressive degenerative disorder characterized by a fluid-filled cyst located in the spinal cord. Its symptoms include pain, weakness, numbness, and stiffness in the back, shoulders, arms or legs. Other symptoms include headaches, the inability to feel changes in the temperature, sweating, sexual dysfunction, and loss of bowel and bladder control. It is usually seen in the cervical region but can extend into the medulla oblongata and pons or it can reach downward into the thoracic or lumbar segments. Syringomyelia is often associated with Chiari malformation type I and is commonly seen between the C-4 and C-6 levels. The exact development of syringomyelia is unknown but many theories suggest that the herniated tonsils in Chiari malformation type I form a "plug" which does not allow an outlet of CSF from the brain to the spinal canal. Syringomyelia is present in 25% of patients with Chiari malformation.

Carpenter syndrome presents several features:

- Tower-shaped skull (craniosynostosis)

- Additional or fused digits (fingers and toes)

- Obesity

- Reduced height

Intellectual disability is also common with the disorder, although some patients may have average intellectual capacity.

Carpenter Syndrome belongs to a group of rare genetic disorders known as acrocephalopolysyndactyly, abbreviated ACPS (RN, 2007). There were originally five types of ACPS, but this number has been decreased because they have been found to be closely related to one another or to other disorders (Paul A. Johnson, 2002).

The most common physical manifestation of Carpenter Syndrome is early fusing of the fibrous cranial sutures which results in an abnormally pointed head. The fusion of the skull bones is evident from birth (National Organization for Rare Disorders, Inc., 2008). Babies’ mobile cranial bones form a cone shape as the pass through the birth canal and soon thereafter return to a normal shape; however, a baby affected by carpenter syndrome maintains a cone shaped head.

A baby affected by Carpenter Syndrome will also display malformations of the face. An individual affected by the syndrome may have broad cheeks, a flat nasal bridge, and a wide upturned nose with abnormally large nasal openings. Their ears will most commonly be low, unevenly set, and malformed in structure. In addition to these facial abnormalities, individuals also have an underdeveloped maxilla and/ or mandible with a highly arched and narrow palate which makes speech a very difficult skill to master. Teeth are usually very late to come in and will be undersized and spaced far apart (Carpenter Syndrome-description).

Other physical abnormalities often associated with Carpenter Syndrome include extra digits. Extra toes are more commonly seen than fingers. Often both the toes and fingers are webbed, a process that occurs before the sixth week gestational period. Often their digits will be abnormally short, and the fingers are commonly missing an interphalangeal joint. Roughly half of the babies born with Carpenter Syndrome have some type of heart defect, and seventy five percent of individuals with this disease will experience some degree of development delay due to mild mental retardation (Carpenter Syndrome-description).

Macrocephaly-capillary malformation (M-CM) is a multiple malformation syndrome causing abnormal body and head overgrowth and cutaneous, vascular, neurologic, and limb abnormalities. Though not every patient has all features, commonly found signs include macrocephaly, congenital macrosomia, extensive cutaneous capillary malformation (naevus flammeus or port-wine stain type birthmark over much of the body; a capillary malformation of the upper lip or philtrum is seen in many patients with this condition), body asymmetry (also called hemihyperplasia or hemihypertrophy), polydactyly or syndactyly of the hands and feet, lax joints, doughy skin, variable developmental delay and other neurologic problems such as seizures and low muscle tone.

Additional symptoms include:

- anencephaly (failure of major sections of the brain to form)

- encephalocele (cranial contents protrudes from the skull)

- cyclopia (the two eye cavities fuse into one)

- agnathia

- cleft palate

- arthrogryposis

- clubfeet

- holoprosencephaly

- spina bifida

- low-set ears

- pulmonary hypoplasia

- omphalocele

- gastroschisis

- cardiovascular disorders

- diaphragmatic hernias

- gastrointestinal atresia

- single umbilical artery

- renal abnormalities

- genu recurvatum

- hydramnios

Preauricular sinuses and cysts result from developmental defects of the first and second pharyngeal arches. This and other congenital ear malformations are sometimes associated with renal anomalies. They may be present in Beckwith–Wiedemann syndrome, and in rare cases, they may be associated with branchio-oto-renal syndrome.

The classical triad of symptoms that defines 3C syndrome includes certain heart defects, hypoplasia (underdevelopment) of the cerebellum, and cranial dysmorphisms, which can take various forms. The heart defects and cranial dysmorphisms are heterogeneous in individuals who are all classed as having Ritscher-Schinzel syndrome.

Heart defects commonly seen with Ritscher-Schinzel syndrome are associated with the endocardial cushion and are the most important factor in determining a diagnosis. The mitral valve and tricuspid valve of the heart can be malformed, the atrioventricular canal can be complete instead of developing into the interatrial septum and interventricular septum, and conotruncal heart defects, which include tetralogy of Fallot, double outlet right ventricle, transposition of the great vessels, and hypoplastic left heart syndrome. Aortic stenosis and pulmonary stenosis have also been associated with 3C syndrome.

The cranial dysmorphisms associated with 3C syndrome are heterogeneous and include a degree of macrocephaly, a large anterior fontanel, a particularly prominent occiput and forehead, ocular hypertelorism (wide-set eyes), slanted palpebral fissures, cleft palate, a depressed nasal bridge, cleft palate with associated bifid uvula, low-set ears, micrognathia (an abnormally small jaw), brachycephaly (flattened head), and ocular coloboma. Low-set ears are the most common cranial dysmorphism seen in 3C syndrome, and ocular coloboma is the least common of the non-concurrent symptoms (cleft lip co-occurring with cleft palate is the least common).

Cranial dysplasias associated with 3C syndrome are also reflected in the brain. Besides the cerebellar hypoplasia, cysts are commonly found in the posterior cranial fossa, the ventricles and the cisterna magna are dilated/enlarged, and Dandy-Walker malformation is present. These are reflected in the developmental delays typical of the disease. 75% of children with 3C syndrome have Dandy-Walker malformation and hydrocephalus.

Signs and symptoms in other body systems are also associated with 3C syndrome. In the skeletal system, ribs may be absent, and hemivertebrae, syndactyly (fusion of fingers together), and clinodactyly (curvature of the fifth finger) may be present. In the GI and genitourinary systems, anal atresia, hypospadia (misplaced urethra), and hydronephrosis may exist. Adrenal hypoplasia and growth hormone deficiency are associated endocrine consequences of Ritscher-Schinzel syndrome. Some immunodeficiency has also been reported in connection with 3C syndrome.

Many children with the disorder die as infants due to severe congenital heart disease. The proband of Ritscher and Schinzel's original study was still alive at the age of 21.

A fetus with 3C syndrome may have an umbilical cord with one umbilical artery instead of two.

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.

Imperforate anus is associated with an increased incidence of some other specific anomalies as well, together being called the VACTERL association:

- V – Vertebral anomalies

- A – "Anal atresia"

- C – Cardiovascular anomalies

- T – Tracheoesophageal fistula

- E – Esophageal atresia

- R – Renal (kidney) and/or radial anomalies

- L – Limb defects

Other entities associated with an imperforate anus are trisomies 18 and 21, the cat-eye syndrome (partial trisomy or tetrasomy of a maternally derived number 22 chromosome), Baller-Gerold syndrome, Currarino syndrome, caudal regression syndrome, FG syndrome, Johanson-Blizzard syndrome, McKusick-Kaufman syndrome, Pallister-Hall syndrome, short rib-polydactyly syndrome type 1, Townes-Brocks syndrome, 13q deletion syndrome, urorectal septum malformation sequence, and the OEIS complex (omphalocele, exstrophy of the cloaca, imperforate anus, spinal defects).

a combination of various vascular malformations. They are 'complex' because they involve a combination of two different types of vessels.

- CVM: capillary venous malformation

- CLM: capillary lymphatic malformation

- LVM: lymphatic venous malformation

- CLVM: capillary lymphatic venous malformation. CLVM is associated with Klippel-Trenaunay syndrome

- AVM-LM: Arteriovenous malformation- lymphatic malformation

- CM-AVM: capillary malformation- arteriovenous malformation

All fast-flow malformations are malformations involving arteries. They constitute about 14% of all vascular malformations.

- Arterial malformation

- Arteriovenous fistula (AVF) : a lesion with a direct communication via fistulae between an artery and a vein.

- Arteriovenous malformation : a lesion with a direct connection between an artery and a vein, without an intervening capillary bed, but with an interposed nidus of dysplastic vascular channels in between.

As a result of the changes to the developing embryo, the symptoms are very pronounced features, especially in the face. Low-set ears are a typical characteristic, as in all of the disorders which are called branchial arch syndromes. The reason for this abnormality is that ears on a foetus are much lower than those on an adult. During normal development, the ears "travel" upward on the head; however, in Crouzon patients, this pattern of development is disrupted. Ear canal malformations are extremely common, generally resulting in some hearing loss. In particularly severe cases, Ménière's disease may occur.

The most notable characteristic of Crouzon syndrome is craniosynostosis, as described above; however it usually presents as brachycephaly resulting in the appearance of a short and broad head. Exophthalmos (bulging eyes due to shallow eye sockets after early fusion of surrounding bones), hypertelorism (greater than normal distance between the eyes), and psittichorhina (beak-like nose) are also symptoms. Additionally, external strabismus is a common occurrence, which can be thought of as opposite from the eye position found in Down syndrome. Lastly, hypoplastic maxilla (insufficient growth of the midface) results in relative mandibular prognathism (chin appears to protrude despite normal growth of mandible) and gives the effect of the patient having a concave face. Crouzon syndrome is also associated with patent ductus arteriosus (PDA) and aortic coarctation.

For reasons that are not entirely clear, most Crouzon patients also have noticeably shorter humerus and femur bones relative to the rest of their bodies than members of the general population. A small percentage of Crouzon patients also have what is called "Type II" Crouzon syndrome, distinguished by partial syndactyly.

There are several forms of imperforate anus and anorectal malformations. The new classification is in relation of the type of associated fistula.

The classical Wingspread classification was in low and high anomalies:

- A low lesion, in which the colon remains close to the skin. In this case, there may be a stenosis (narrowing) of the anus, or the anus may be missing altogether, with the rectum ending in a blind pouch.

- A high lesion, in which the colon is higher up in the pelvis and there is a fistula connecting the rectum and the bladder, urethra or the vagina.

- A persistent cloaca (from the term cloaca, an analogous orifice in reptiles and amphibians), in which the rectum, vagina and urinary tract are joined into a single channel.

Imperforate anus is usually present along with other birth defects—spinal problems, heart problems, tracheoesophageal fistula, esophageal atresia, renal anomalies, and limb anomalies are among the possibilities.

The affected infant tends to be short, with a disproportionately large head. The fetal head of Infants born with iniencephaly are hyperextended while the foramen magnum is enlarged and opens through the widened pedicles. The defective neural arches directly into the upper cervical reach of the spinal canal, causing the formation of a common cavity between most of the spinal cord and the brain. The skin of the anterior chest is connected directly to the face, bypassing the formation of a neck, while the scalp is directly connected to the skin of the back. Because of this, those born with this anomaly either have a highly shortened neck or no neck at all. This causes extreme retroflexion, or backward bending, of the head in a "star-gazing" fashion. The spine is severely distorted as well along with significant shortening due to marked lordosis. The vertebrae, especially cervical, are fused together in abnormal shapes and their numbers are reduced. The spinal cord is almost always defective while the ventricular system is often dilated and the cortex is thinned. Sometimes, in the case of iniencephaly apertus, an encephalocele (sac-like protrusions of the brain through an opening in the cranium) forms.

Cystic hygromas are increasingly diagnosed by prenatal ultrasonography. A common symptom is a neck growth. It may be found at birth, or discovered later in an infant after an upper respiratory tract infection. Cystic hygromas can grow very large and may affect breathing and swallowing. Some symptoms may include a mass or lump in the mouth, neck, cheek, or tongue. It feels like a large fluid-filled sac. In addition, cystic hygromas can be found in other body parts such as the arm, chest, legs, groin, and buttocks. Cystic hygromas are also often seen in Turner's syndrome, although a patient who does not have Turner's syndrome can present with this condition.

The diagnosis of constriction ring syndrome can be confirmed with an ultrasonography. The clinical manifestations can be extremely variable. It could be a single or multiple manifestation. This can be confirmed at the end of the first trimester or at the beginning of the second trimester. But not every patient will be diagnosed at that moment, most will get this diagnosis at birth.

Amelia may be present as an isolated defect, but it is often associated with major malformations in other organ systems. These frequently include cleft lip and/or palate, body wall defects, malformed head, and defects of the neural tube, kidneys, and diaphragm. Facial clefts may be accompanied by other facial anomalies such as abnormally small jaw, and missing ears or nose. The body wall defects allow internal organs to protrude through the abdomen. Head malformations may be minor to severe with a near absence of the brain. The diaphragm may be herniated or absent and one or both kidneys may be small or absent.

Constriction ring syndrome (CRS) is a congenital disorder with unknown cause. Because of the unknown cause there are many different, and sometimes wrong names. It is a malformation due to intrauterine bands or rings that give deep grooves in, most commonly, distal extremities like fingers and toes. In rare cases the constriction ring can form around other parts of the fetus and cause amputation or even intrauterine death (see Types and Classification). The anatomy proximal to the site of constriction (or amputation) is developmentally normal.

CRS can be associated with other malformations with club foot being most common.

(see also Types and Classification).

The precise configuration of the bands, lymphedema, and character of the amputations are not predictable and vary with each individual patient. Also more than one extremity is usually affected, and it is rare for only one ring to present as an isolated malformation with no other manifestation of this syndrome.

The birth defect is diagnosed by the presence of a combination of these symptoms (often on approximately ¼ of the body, though some cases may present more or less affected tissue):

- One or more distinctive port-wine stains with sharp borders

- Varicose veins

- Hypertrophy of bony and soft tissues, that may lead to local gigantism or shrinking, most typically in the lower body/legs.

- An improperly developed lymph system

In some cases, port-wine stains (capillary port wine type) may be absent. Such cases are very rare and may be classified as "atypical Klippel–Trenaunay syndrome".

KTS can either affect blood vessels, lymph vessels, or both. The condition most commonly presents with a mixture of the two. Those with venous involvement experience increased pain and complications, such as venous ulceration in the lower extremities.

Those with large AVMs are at risk of formation of blood clots in the vascular lesion, which may migrate to the lungs (pulmonary embolism). If there is large-volume blood flow through the lesion, "high-output heart failure" may develop due to the inability of the heart to generate sufficient cardiac output.