The primary malformation apparent with JBS is hypoplasia (underdevelopment) of the nasal alae, or "wing of the nose". Both hypoplasia and aplasia (partial or complete absence) of structural cartilage and tissue in this area of the nose, along with the underlying alae nasi muscle, are prevailing features of the disorder. Together, these malformations give the nose and nostrils an odd shape and appearance.

Mental retardation ranging from mild to severe is present in the majority of JBS patients, and is related to the deleterious nature of the known mutagen responsible for the disorder and its effects on the developing central nervous system. Normal intelligence and age appropriate social development, however, have been reported in a few instances of JBS.

Anterior segment mesenchymal dysgenesis is a failure of the normal development of the tissues of the anterior segment of the eye. It leads to anomalies in the structure of the mature anterior segment, associated with an increased risk of glaucoma and corneal opacity.

Peters' (frequently misspelled Peter's) anomaly is a specific type of mesenchymal anterior segment dysgenesis, in which there is central corneal leukoma, adhesions of the iris and cornea, and abnormalities of the posterior corneal stroma, Descemet's membrane, corneal endothelium, lens, and anterior chamber.

In teratology, proboscis is a blind-ended, tubelike structure, commonly located in the midface.

Proboscis formation are classified in four general types: holoprosencephalic proboscis, lateral nasal proboscis, supernumerary proboscis, and disruptive proboscis.

- Holoprosencephalic proboscis is found in holoprosencephaly. In cyclopia or ethmocephaly, proboscis is an abnormally formed nose. In cyclopia, a single median eye is associated with arrhinia (absence of the nose) and usually with proboscis formation above the eye. In ethmocephaly, two separate hypoteloric eyes are associated with arrhinia and supraocular proboscis formation. In cebocephaly, no proboscis formation occurs, but a single-nostril nose is present.

- Lateral nasal proboscis (proboscis lateralis) is a tubular proboscis-like structure and represents incomplete formation of one side of the nose; it is found instead of a nostril. The olfactory bulb is usually rudimentary on the involved side. The lacrimal duct (tear duct), nasal bone, nasal cavity, vomer, maxillary sinus, cribriform plate, and ethmoid cells are often missing on the involved side. Ocular hypertelorism may be present. The proboscis lateralis is a rare nasal anomaly.

- Supernumerary proboscis (Accessory proboscis) is found when both nostrils are formed and a proboscis occurs additionally. Accessory proboscis arise from a supernumerary olfactory placode.

- Disruptive proboscis occur if an early embryonic hamartoneoplastic lesion arises in the primitive prosencephalon.

Signs of duct ectasia can include nipple retraction, inversion, pain, and sometimes bloody discharge.

Hidrocystoma (also known as cystadenoma, a Moll's gland cyst, and a sudoriferous cyst) is an adenoma of the sweat glands.

Hidrocystomas are cysts of sweat ducts, usually on the eyelids. They are not tumours (a similar-sounding lesion called hidroadenoma is a benign tumour).

There are three types of "sweat" glands: True sweat glands or eccrine glands;

sebaceous glands, which have an oily secretion around hair follicles; and apocrine glands which have more oily product than eccrine glands and are found on the face, armpit, and groin.

Hidrocystomas usually arise from apocrine glands. They are also called Cysts of Moll or sudoriferous cysts. There may be a type of hidroadenoma that arises from eccrine glands, but these are uncommon.

Other related conditions on the eyelids include chalazion ( a granulomatous reaction to sebaceous glands on the eyelid), lacrimal duct cysts (cysts related to tear ducts) and nasolacrimal duct cysts (the nasolacrimal duct drains tears into the nose via a punctum on the lower eyelid).

Benign lymphoepithelial lesion is most likely to occur in adults around 50 years of age. There is a predilection for gender with 60–80% being female. The gland affected has a diffuse swelling. The swelling can be asymptomatic, but mild pain can also be associated. There is a preponderance of this disease in those who suffer from HIV infection.

Most cases of benign lymphoepithelial lesions appear in conjunction with Sjögren's syndrome. When Sjögren's syndrome is present, the swelling is usually bilateral. Otherwise, the affected glands are usually only on one side of the body.

In many cases, a biopsy is needed to distinguish benign lymphoepithelial lesions from sialadenosis (sialosis).

Salivary gland aplasia (also termed salivary gland agenesis) is the congenital absence of salivary glands. Usually the term relates to the absence of some or all of the major salivary glands.

It is a rare condition, and most known cases have been in association with syndromes of the ectodermal tissues, particularly the lacrimal apparatus. Example syndromes which have been reported with salivary gland aplasia include hereditary ectodermal dysplasia, mandibulofacial dysostosis and hemifacial microsomia.

The main significance of the condition is a lack of saliva, causing xerostomia (dry mouth), with accompanying susceptibility to dental caries (tooth decay), infections of the mouth, and upper respiratory tract infections (e.g., candidiasis, ascending sialadenitis, laryngitis and pharyngitis). Patients with salivary gland aplasia typically require regular application of topical fluoride to prevent tooth decay.

In 80% of cases, the parotid gland is affected. Lacrimal glands are also affected.

Noninvasive methods to determine duct diameter in live patients are available only recently and it is not clear how the results should be compared with older results from biopsies.

Histologically, dilation of the large duct is prominent. Duct widening with associated periductal fibrosis is frequently included in the wastebasket definition of fibrocystic disease.

In plasma cell rich lesions diagnosed on core biopsies, steroid-responsive IgG4-related mastitis can be identified by IgG/IgG4 immunostaining.

Lachiewicz–Sibley syndrome is a rare autosomal dominant disorder characterized by preauricular pits and renal disease. Persons with this disease may have hypoplasic kidneys or proteinuria. This disease was first described in a Caucasian family of British and Irish descent that emigrated to Ohio in the 19th century before settling in Nebraska. Many of the members of this family still live in Nebraska, although the relatives are now scattered throughout the country.

Unlike branchio-oto-renal (BOR) syndrome, Lachiewicz–Sibley syndrome is characterized by only preauricular pitting and renal disease. Persons with BOR syndrome also present with hearing loss, branchial fistulas or cysts, malformed ears, and lacrimal stenosis. Other anomalies in BOR syndrome may include a long narrow face, a deep overbite, and facial paralysis.

It was characterized in 1985.

Axenfeld syndrome (also known as Axenfeld-Rieger syndrome or Hagedoom syndrome) is a rare autosomal dominant disorder, which affects the development of the teeth, eyes, and abdominal region.

Symptoms, if any, can be mild even in the presence of significant swelling or masses.

Lacrimal gland involvement may cause swelling of the upper eyelid, or proptosis if there is severe swelling. Other orbital masses or inflammation can result in visual disturbance (blurred vision, double vision, visual field impairment), restricted eye movements, pain or discomfort, numbness in the distribution of the supraorbital and/or infraorbital nerves, or proptosis.

IgG4-related ophthalmic disease has been estimated to account for approximately 25% of all cases of proptosis, eyelid swelling and other features of orbital swelling.

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

An imperforate lacrimal punctum is a congenital disorder of dogs involving the lack of an opening to the nasolacrimal duct (tear duct) in the conjunctiva. Dogs normally have two lacrimal puncta, the superior and inferior. This condition can affect either or both. Symptoms include excessive tearing and tear staining of the hair around the eye. Affected breeds include the American Cocker Spaniel, Bedlington Terrier, Golden Retriever, Poodle, and Samoyed. Imperforate lacrimal puncta can be corrected by surgical opening of the punctum.

Granulomatous disease, including sarcoidosis, granulomatosis with polyangiitis, and midline granuloma, may also lead to NLD obstruction.

Neoplasm should be considered in any patient presenting with NLD obstruction.In patients with an atypical presentation, including younger age and male gender, further workup is appropriate. Bloody punctal discharge or lacrimal sac distension above the medial canthal tendon is also highly suggestive of neoplasm.

Microphthalmia (Greek: μικρός "micros" = small; ὀφθαλμός "ophthalmos" = eye), also referred as microphthalmos, is a developmental disorder of the eye in which one (unilateral microphthalmia) or both (bilateral microphthalmia) eyes are abnormally small and have anatomic malformations. It is different from nanophthalmos in which the eye is small in size but has no anatomical alterations.

IgG4-related ophthalmic disease (IgG4-ROD) is the recommended term to describe orbital (eye socket) manifestations of the systemic condition IgG4-related disease, which is characterised by infiltration of lymphocytes and plasma cells and subsequent fibrosis in involved structures. It can involve one or more of the orbital structures.

Frequently involved structures include the lacrimal glands, extraocular muscles, infraorbital nerve, supraorbital nerve and eyelids. It has also been speculated that ligneous conjunctivitis may be a manifestation of IgG4-related disease (IgG4-RD).

As is the case with other manifestations of IgG4-related disease, a prompt response to steroid therapy is a characteristic feature of IgG4-ROD in most cases, unless significant fibrosis has already occurred.

The presence of a small eye within the orbit can be a normal incidental finding but in most cases it is abnormal and results in blindness. The incidence is 14 per 100,000 and the condition affects 3-11% of blind children.

DKC can be characterized by cutaneous pigmentation, premature graying, of the nails, leukoplakia of the oral mucosa, continuous lacrimation due to atresia of the lacrimal ducts, often thrombocytopenia, anemia, testicular atrophy in the male carriers, and predisposition to cancer. Many of these symptoms are characteristic of geriatrics, and those carrying the more serious forms of the disease often have significantly shortened lifespans.

The following are symptoms characteristic with individuals having the disorder. Individuals may display some, most, or all of these symptoms throughout the course of their life, though symptoms may vary with each patient.

- Abnormal hair (coarse, thick, brittle)

- Calvarial hypomineralization (soft skull)

- Y-shaped cataracts by 1–2 years of age

- Skeletal defects

- Hypertelorism (wide-set eyes)

- Facial dysmorphisms

- Late-closing fontanels

- Abnormal accumulation of proteins in the endoplasmic reticulum

- Scoliosis

- Broad forehead, nose

- Missing, small teeth or abnormal teeth positioning

- Poor skull calcification

- Flat foot

- Motor delay

- Abnormal vertebrae

- Prominent forehead and brow

- High nose bridge

- Capillary hemangioma

- Delayed tooth eruption

- Long upper lip groove

- Large mouth

- High arched palate

- Narrow hips and rib cage

- Thin lips

- Narrow and sloping shoulders

- Hyperpigmentation

- Hyperextensible joints

Onset of the disease is in neonatal development and infancy, and symptoms tend to become evident soon after birth.

Age: The mucocutaneous features of DKC typically develop between ages 5 and 15 years. The median age of onset of the peripheral cytopenia is 10 years.

Sex: The male-to-female ratio is approximately 3:1.

Physical: The triad of reticulated hyperpigmentation of the skin, nail dystrophy, and leukoplakia characterizes DKC. The syndrome is clinically heterogeneous; in addition to the diagnostic mucocutaneous features and bone marrow failure, affected individuals can have a variety of other clinical features.

Cutaneous findings:

The primary finding is abnormal skin pigmentation, with tan-to-gray hyperpigmented or hypopigmented macules and patches in a mottled or reticulated pattern. Reticulated pigmentation occurs in approximately 90% of patients. Poikilodermatous changes with atrophy and telangiectasia are common.

The cutaneous presentation may clinically and histologically resemble graft versus host disease. The typical distribution involves the sun-exposed areas, including the upper trunk, neck, and face. Other cutaneous findings may include alopecia of the scalp, eyebrows, and eyelashes; premature graying of the hair; hyperhidrosis; hyperkeratosis of the palms and soles; and adermatoglyphia (loss of dermal ridges on fingers and toes).

Nail findings:

Nail dystrophy is seen in approximately 90% of patients, with fingernail involvement often preceding toenail involvement.

Progressive nail dystrophy begins with ridging and longitudinal splitting. Progressive atrophy, thinning, pterygium, and distortion eventuate in small, rudimentary, or absent nails.

Mucosal findings:

Mucosal leukoplakia occurs in approximately 80% of patients and typically involves the buccal mucosa, tongue, and oropharynx. The leukoplakia may become verrucous, and ulceration may occur. Patients also may have an increased prevalence and severity of periodontal disease.

Other mucosal sites may be involved (e.g., esophagus, urethral meatus, glans penis, lacrimal duct, conjunctiva, vagina, anus). Constriction and stenosis can occur at these sites, with subsequent development of dysphagia, dysuria, phimosis, and epiphora.

Bone marrow failure:

Approximately 90% have peripheral cytopenia of one or more lineages. In some cases, this is the initial presentation, with a median age of onset of 10 years.

Bone marrow failure is a major cause of death, with approximately 70% of deaths related to bleeding and opportunistic infections as a result of bone marrow failure.

Pulmonary complications:

Approximately 20% of individuals with DKC develop pulmonary complications, including pulmonary fibrosis and abnormalities of pulmonary vasculature.

The recommendation is that DKC patients avoid taking drugs with pulmonary toxicity (e.g., busulfan) and that they have their lungs shielded from radiation during BMT.

Increased risk of malignancy:

Patients have an increased prevalence of malignant mucosal neoplasms, particularly squamous cell carcinoma of the mouth, nasopharynx, esophagus, rectum, vagina, or cervix. These often occur within sites of leukoplakia.

The prevalence of squamous cell carcinoma of the skin is also increased. Other malignancies reported include Hodgkin lymphoma, adenocarcinoma of the gastrointestinal tract, and bronchial and laryngeal carcinoma.

Malignancy tends to develop in the third decade of life.

Neurologic system findings: Patients may have learning difficulties and mental retardation.

Ophthalmic system findings: DKC reportedly is associated with conjunctivitis, blepharitides, and pterygium. Lacrimal duct stenosis resulting in epiphora (i.e., excessive tearing) occurs in approximately 80% of patients.

Skeletal system findings: Patients may have mandibular hypoplasia, osteoporosis, avascular necrosis, and scoliosis.

Gastrointestinal system findings: These may include esophageal webs, hepatosplenomegaly, enteropathy, and cirrhosis.

Genitourinary system findings:: Hypospastic testes, hypospadias, and ureteral stenosis are reported.

Female carriers: Female carriers of DKC may have subtle clinical features. One study showed that 3 of 20 female carriers had clinical features that included a single dystrophic nail, a patch of hypopigmentation, or mild leukoplakia.

ADULT syndrome features include ectrodactyly, syndactyly, excessive freckling, lacrimal duct anomalies, dysplastic nails, hypodontia, hypoplastic breasts and nipples, hypotrichosis, hypohidrosis, broad nasal bridge, midfacial hypoplasia, exfoliative dermatitis, and xerosis. The lack of facial clefting and ankyloblepharon are important because they exist in ectrodactyly–ectodermal dysplasia–cleft syndrome (EEC) but not in ADULT syndrome.

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.