Neonatal ichthyosis–sclerosing cholangitis syndrome (also known as "NISCH syndrome" and "ichthyosis–sclerosing cholangitis syndrome") is a cutaneous condition caused by mutations in the Claudin 1 gene.

Eosinophilic gastroenteritis (EG) is a rare and heterogeneous condition characterized by patchy or diffuse eosinophilic infiltration of gastrointestinal (GI) tissue, first described by Kaijser in 1937. Presentation may vary depending on location as well as depth and extent of bowel wall involvement and usually runs a chronic relapsing course. It can be classified into mucosal, muscular and serosal types based on the depth of involvement. Any part of the GI tract can be affected, and isolated biliary tract involvement has also been reported.

The stomach is the organ most commonly affected, followed by the small intestine and the colon.

EG typically presents with a combination of chronic nonspecific GI symptoms which include abdominal pain, diarrhea, occasional nausea and vomiting, weight loss and abdominal distension. Approximately 80% have symptoms for several years; a high degree of clinical suspicion is often required to establish the diagnosis, as the disease is extremely rare. It doesn't come all of a sudden but takes about 3–4 years to develop depending upon the age of the patient. Occasionally, the disease may manifest itself as an acute abdomen or bowel obstruction.

- Mucosal EG (25–100%) is the most common variety, which presents with features of malabsorption and protein losing enteropathy. Failure to thrive and anaemia may also be present. Lower gastrointestinal bleeding may imply colonic involvement.

- Muscular EG (13–70%) present with obstruction of gastric outlet or small intestine; sometimes as an obstructing caecal mass or intussusception.

- Subserosal EG (4.5% to 9% in Japan and 13% in the US) presents with ascites which is usually exudative in nature, abundant peripheral eosinophilia, and has favourable responses to corticosteroids.

- Other documented features are cholangitis, pancreatitis, eosinophilic splenitis, acute appendicitis and giant refractory duodenal ulcer.

The most common symptoms of CAEBV include:

- Fever

- Hepatitis

- Pancytopenia

- Spleen enlargement

- Hypersensitivity to mosquito bites

Complications include:

- Interstitial pneumonia

- Lymphoma, including B-cell, T-cell and NK-cell lymphomas

- Haemophagocytic syndrome

- Coronary artery aneurysms

- Liver failure

- Nasopharyngeal carcinoma

- Gastric adenocarcinoma

- CNS

- Intestinal perforation

- Myocarditis

- Peripheral neuropathy

Autoimmune pancreatitis (AIP) is an increasingly recognized type of chronic pancreatitis that can be difficult to distinguish from pancreatic carcinoma but which responds to treatment with corticosteroids, particularly prednisone. There are two categories of AIP: Type 1 and Type 2, each with distinct clinical profiles.

Type 1 AIP is now regarded as a manifestation of IgG4-related disease, and those affected have tended to be older and to have a high relapse rate. Type 1 is associated with pancreatitis, Sjogren syndrome, Primary sclerosing cholangitis and Inflammatory bowel disease. Patients with Type 2 AIP do not experience relapse, tend to be younger and not associated with systemic disease. AIP occurring in association with an autoimmune disorder has been referred to as "secondary" or "syndromic" AIP. AIP does not affect long-term survival.

Chronic active EBV infection (CAEBV) or in its expanded form, chronic active Epstein-Barr virus infection is a very rare and often fatal complication of Epstein-Barr virus (EBV) infection that most often occurs in children or adolescents of Asian or South American lineage, although cases in Hispanics, Europeans and Africans have been reported.

AIP is relatively uncommon and is characterized by the following features:

1. Scleral Icterus (yellow eyes), jaundice (yellow skin) which is usually painless, usually without acute attacks of pancreatitis.

2. Relatively mild symptoms, such as minimal weight loss or nausea.

3. Increased serum levels of gamma globulins, immunoglobulin G (IgG) or IgG4.

4. The presence of serum autoantibodies such as anti-nuclear antibody (ANA), anti-lactoferrin antibody, anti-carbonic anhydrase II antibody, and rheumatoid factor (RF).

5. Contrast-enhanced CT demonstrates a diffusely enlarged (sausage-shaped) pancreas.

6. Diffuse irregular narrowing of the main pancreatic duct, and stenosis of the intrapancreatic bile duct on endoscopic retrograde cholangiopancreatography (ERCP).

7. Rare pancreatic calcification or cyst formation.

8. Marked responsiveness to treatment with corticosteroids.

Two-thirds of patients present with either obstructive painless jaundice or a "mass" in the head of the pancreas mimicking carcinoma. It is mandatory to rule out carcinoma prior to making a diagnosis of AIP.

The diagnosis of SSC requires the exclusion of secondary causes of sclerosing cholangitis and recognition of associated conditions that may potentially imitate its classic cholangiographic features. It is morphologically similar to primary sclerosing cholangitis (PSC) but originates from a known pathological process. Its clinical and cholangiographic features may mimic PSC, yet its natural history may be more favorable if recognition is prompt and appropriate therapy is introduced. Sclerosing cholangitis in critically ill patients, however, is associated with rapid disease progression and poor outcome. Serologic testing, radiological imaging and histological analysis can help diagnose SSC.

Secondary sclerosing cholangitis (SSC) is a chronic cholestatic liver disease. It is an aggressive and rare disease with complex and multiple causes. It is characterized by inflammation, fibrosis, destruction of the biliary tree and biliary cirrhosis. It can be treated with minor interventions, antibiotics, and monitoring, or with more serious cases, surgery, endoscopic intervention, and liver transplantation.

In addition to the extent of involvement, people may also be characterized by the severity of their disease.

- "Mild disease" correlates with fewer than four stools daily, with or without blood, no systemic signs of toxicity, and a normal erythrocyte sedimentation rate (ESR) or C-reactive protein (CRP). Mild abdominal pain or cramping may occur. Patients may believe they are constipated when in fact they are experiencing tenesmus, which is a constant feeling of the need to empty the bowel accompanied by involuntary straining efforts, pain, and cramping with little or no fecal output. Rectal pain is uncommon.

- "Moderate disease" correlates with more than four stools daily, but with minimal signs of toxicity. Patients may display anemia (not requiring transfusions), moderate abdominal pain, and low grade fever, .

- "Severe disease", correlates with more than six bloody stools a day or observable massive and significant bloody bowel movement, and evidence of toxicity as demonstrated by fever, tachycardia, anemia or an elevated ESR or CRP.

- "Fulminant disease" correlates with more than ten bowel movements daily, continuous bleeding, toxicity, abdominal tenderness and distension, blood transfusion requirement and colonic dilation (expansion). Patients in this category may have inflammation extending beyond just the mucosal layer, causing impaired colonic motility and leading to toxic megacolon. If the serous membrane is involved, a colonic perforation may ensue. Unless treated, the fulminant disease will soon lead to death.

These are pleomorphic and include

- dolichocephaly (with or without sagittal suture synostosis)

- microcephaly

- pre- and postnatal growth retardation

- brachydactyly

- narrow thorax

- rhizomelic dwarfism

- epicanthal folds

- hypodontia and/or microdontia

- sparse, slow-growing, hyperpigmented, fine hair

- nail dysplasia

- hypohydrosis

- chronic renal failure

- heart defects

- liver fibrosis

- visual deficits

- photophobia

- hypoplasia of the posterior corpus callosum

- aberrant calcium homeostasis

Electroretinography shows gross abnormalities.

Two fetuses of 19 and 23 weeks gestation have also been reported. They showed acromesomelic shortening, craniofacial characteristics with absence of craniosynostosis, small kidneys with tubular and glomerular microscopic cysts, persistent ductal plate with portal fibrosis in the liver, small adrenals, an enlarged cisterna magna and a posterior fossa cyst.

As ulcerative colitis is believed to have a systemic (i.e., autoimmune) origin, patients may present with comorbidities leading to symptoms and complications outside the colon. The frequency of such extraintestinal manifestations has been reported as anywhere between 6 and 47 percent, and include the following:

- Aphthous ulcer of the mouth

- Ophthalmic

- Iritis or uveitis, which is inflammation of the eye's iris

- Episcleritis

- Musculoskeletal:

- Seronegative arthritis, which can be a large-joint oligoarthritis (affecting one or two joints), or may affect many small joints of the hands and feet

- Ankylosing spondylitis, arthritis of the spine

- Sacroiliitis, arthritis of the lower spine

- Cutaneous (related to the skin):

- Erythema nodosum, which is a panniculitis, or inflammation of subcutaneous tissue involving the lower extremities

- Pyoderma gangrenosum, which is a painful ulcerating lesion involving the skin

- Deep venous thrombosis and pulmonary embolism

- Autoimmune hemolytic anemia

- Clubbing, a deformity of the ends of the fingers.

- Primary sclerosing cholangitis, a distinct disease that causes inflammation of the bile ducts

Mirizzi's syndrome has no consistent or unique clinical features that distinguish it from other more common forms of obstructive jaundice. Symptoms of recurrent cholangitis, jaundice, right upper quadrant pain, and elevated bilirubin and alkaline phosphatase may or may not be present. Acute presentations of the syndrome include symptoms consistent with cholecystitis.

Surgery is extremely difficult as Calot's triangle is often completely obliterated and the risks of causing injury to the CBD are high.

Sensenbrenner syndrome (OMIM #218330) is a rare (less than 20 cases reported by 2010) multisystem disease first described in 1975. It is inherited in an autosomal recessive fashion, and a number of genes appear to be responsible. Three genes responsible have been identified: intraflagellar transport (IFT)122 (WDR10), IFT43 — a subunit of the IFT complex A machinery of primary cilia, and WDR35 (IFT121: TULP4)

It is also known as Sensenbrenner–Dorst–Owens syndrome, Levin Syndrome I and cranioectodermal dysplasia (CED)

People with PBC experience fatigue (80%) that leads to sleepiness during the daytime; more than half of those have severe fatigue. Itching (pruritus) occurs in 20–70%. People with more severe PBC may have jaundice (yellowing of the eyes and skin). PBC impairs bone density and there is an increased risk of fracture. Xanthelasma (skin lesions around the eyes) or other xanthoma may be present as a result of increased cholesterol levels.

PBC can eventually progress to cirrhosis of the liver. This in turn may lead to a number of symptoms or complications:

- Fluid retention in the abdomen (ascites) in more advanced disease

- Enlarged spleen in more advanced disease

- Oesophageal varices in more advanced disease

- Hepatic encephalopathy, including coma in extreme cases in more advanced disease.

People with PBC may also sometimes have the findings of an associated extrahepatic autoimmune disorder such as rheumatoid arthritis or Sjögren's syndrome (in up to 80% of cases).

The symptoms of Felty's syndrome are similar to those of rheumatoid arthritis. Patients suffer from painful, stiff, and swollen joints, most commonly in the joints of the hands, feet, and arms. In some affected individuals, Felty's syndrome may develop during a period when the symptoms and physical findings associated with rheumatoid arthritis have subsided or are not present; in this case, Felty's syndrome may remain undiagnosed. In more rare instances, the development of Felty's syndrome may precede the development of the symptoms and physical findings associated with rheumatoid arthritis.

Felty's syndrome is also characterized by an abnormally enlarged spleen (splenomegaly) and abnormally low levels of certain white blood cells (neutropenia). As a result of neutropenia, affected individuals are increasingly susceptible to certain infections. Keratoconjunctivitis sicca may occur due to secondary Sjorgen's syndrome. Individuals with Felty's syndrome may also experience fever, weight loss, and/or fatigue. In some cases, affected individuals may have discoloration (abnormal brown pigmentation) of the skin, particularly of the leg, sores (ulcers) on the lower leg, and/or an abnormally large liver (hepatomegaly). In addition, affected individuals may have abnormally low levels of circulating red blood cells (anemia), a decrease in circulating blood platelets that assist in blood clotting functions (thrombocytopenia), abnormal liver function tests and/or inflammation of the blood vessels (vasculitis).

Chilaiditi syndrome is a rare condition when pain occurs due to transposition of a loop of large intestine (usually transverse colon) in between the diaphragm and the liver, visible on plain abdominal X-ray or chest X-ray.

Normally this causes no symptoms, and this is called Chilaiditi's sign. The sign can be permanently present, or sporadically. This anatomical variant is sometimes mistaken for the more serious condition of having air under the diaphragm (pneumoperitoneum) which is usually an indication of bowel perforation, possibly leading to surgical interventions.

Chilaiditi syndrome refers only to complications in the presence of Chilaiditi's sign. These include abdominal pain, torsion of the bowel (transverse colon volvulus) or shortness of breath.

Suppurative cholangitis, liver abscess, empyema of the gallbladder, acute pancreatitis, thrombophlebitis of hepatic or portal veins, and septicemia are acute complications of the disease, to which patients may succumb during the acute attacks.

Chronically, complications include cholangiocarcinoma and intraductal papillary neoplasm.

Presentation can be atypical with no pain or fever especially in the elderly population. Hepatolithiasis may present with biliary colic, acute pancreatitis, obstructive jaundice and less commonly, hepatomegaly and abnormal liver chemistry. Chronic biliary obstruction may cause jaundice, pruritus, liver abscess, and liver atrophy, mostly affecting the left lobe and the left lateral segment of the liver, and eventually secondary biliary cirrhosis and cholangiocarcinoma.

The exact cause is not always known, but it may occur in patients with a long and mobile colon (dolichocolon), chronic lung disease such as emphysema, or liver problems such as cirrhosis and ascites. Chilaiditi's sign is generally not associated with symptoms, and is most commonly an incidental finding in normal individuals.

Absence or laxity of the ligament suspending the transverse colon or of the falciform ligament are also thought to contribute to the condition. It can also be associated with relative atrophy of the medial segment of the left lobe of the liver. In this case, the gallbladder position is often anomalous as well – it is often located anterior to the liver, rather than posterior.

Primary sclerosing cholangitis is typically classified into three subgroups based on whether the small and/or large bile ducts are affected. The subgroups of PSC include the following:

- Classic PSC

- Small-duct PSC

- PSC associated with autoimmune hepatitis

The small intestine consists of the duodenum, jejunum and ileum. Inflammation of the small intestine is called enteritis, which if localised to just part is called duodenitis, jejunitis and ileitis, respectively. Peptic ulcers are also common in the duodenum.

Chronic diseases of malabsorption may affect the small intestine, including the autoimmune coeliac disease, infective Tropical sprue, and congenital or surgical short bowel syndrome. Other rarer diseases affecting the small intestine include Curling's ulcer, blind loop syndrome, Milroy disease and Whipple's disease. Tumours of the small intestine include gastrointestinal stromal tumours, lipomas, hamartomas and carcinoid syndromes.

Diseases of the small intestine may present with symptoms such as diarrhoea, malnutrition, fatigue and weight loss. Investigations pursued may include blood tests to monitor nutrition, such as iron levels, folate and calcium, endoscopy and biopsy of the duodenum, and barium swallow. Treatments may include renutrition, and antibiotics for infections.

Diseases that affect the large intestine may affect it in whole or in part. Appendicitis is one such disease, caused by inflammation of the appendix. Generalised inflammation of the large intestine is referred to as colitis, which when caused be the bacteria "Clostridium difficile" is referred to as pseudomembranous colitis. Diverticulitis is a common cause of abdominal pain resulting from outpouchings that particularly affects the colon. Functional colonic diseases refer to disorders without a known cause, and include irritable bowel syndrome and intestinal pseudoobstruction. Constipation may result from lifestyle factors, impaction of a rigid stool in the rectum, or in neonates, Hirschprung's disease.

Diseases affecting the large intestine may cause blood to be passed with stool, may cause constipation, or may result in abdominal pain or a fever. Tests that specifically examine the function of the large intestine include barium swallows, abdominal x-rays, and colonoscopy.

According to recent studies, calcifications of channels seen in dementia can also occur in specific brain areas such as the visual complex in the occipital lobe. Such calcium channel blockages can cause visual problems or partial field hallucinations (Paroxysmal visual manifestations). Other papers show a link between migraine, visual aura and cerebral calcifications. Disturbances may be followed by

convulsions and associated with gastrointestinal phenomena.

Nearly half of people with PSC do not have symptoms and are often incidentally discovered to have PSC due to abnormal liver function tests, but a substantial proportion will have debilitating signs and symptoms of the disease. Signs and symptoms of PSC may include severe itching and non-specific fatigue. Yellowing of the skin and white portion of the eyes may also be seen. Enlargement of the liver and spleen are seen in approximately 40% of affected individuals. Abdominal pain affects about 20% of people with PSC.

Multiple episodes of life-threatening acute cholangitis (infection within the bile ducts) can be seen due to impaired drainage of the bile ducts, which increases the risk of infection.

- Dark urine due to excess conjugated bilirubin, which is water-soluble and excreted by the kidneys (i.e. choluria)

- Malabsorption, especially of fat, and steatorrhea (fatty stool), due to an inadequate amount of bile reaching the small intestine, leading to decreased levels of the fat-soluble vitamins, A, D, E and K.

- Portal hypertension, a complication of cirrhosis, which can manifest with esophageal and parastomal varices as well as hepatic encephalopathy (mental status alteration/disturbance caused by liver dysfunction and shunting of blood away from the scarred liver; such that ammonia detoxification is reduced with concomitant encephalopathy).