Rare Gastroenterology News

Disease Profile


Prevalence estimates on Rare Medical Network websites are calculated based on data available from numerous sources, including US and European government statistics, the NIH, Orphanet, and published epidemiologic studies. Rare disease population data is recognized to be highly variable, and based on a wide variety of source data and methodologies, so the prevalence data on this site should be assumed to be estimated and cannot be considered to be absolutely correct.

1-5 / 10 000

US Estimated

Europe Estimated

Age of onset

All ages





Autosomal dominant A pathogenic variant in only one gene copy in each cell is sufficient to cause an autosomal dominant disease.


Autosomal recessive Pathogenic variants in both copies of each gene of the chromosome are needed to cause an autosomal recessive disease and observe the mutant phenotype.


dominant X-linked dominant inheritance, sometimes referred to as X-linked dominance, is a mode of genetic inheritance by which a dominant gene is carried on the X chromosome.


recessive Pathogenic variants in both copies of a gene on the X chromosome cause an X-linked recessive disorder.


Mitochondrial or multigenic Mitochondrial genetic disorders can be caused by changes (mutations) in either the mitochondrial DNA or nuclear DNA that lead to dysfunction of the mitochondria and inadequate production of energy.


Multigenic or multifactor Inheritance involving many factors, of which at least one is genetic but none is of overwhelming importance, as in the causation of a disease by multiple genetic and environmental factors.


Not applicable


Other names (AKA)

CSNU; Cystinuria-lysinuria


Kidney and Urinary Diseases; RDCRN


Cystinuria is an inherited condition characterized by a buildup of the amino acid, cystine, in the kidneys and bladder. This leads to the formation of cystine crystals and/or stones which may block the urinary tract. Signs and symptoms of the condition are related to the presence of stones and may include nausea, hematuria, flank pain, and/or frequent urinary tract infections. Cystinuria is caused by changes (mutations) in the SLC3A1 and SLC7A9 genes and is inherited in an autosomal recessive manner. The goal of treatment is to relieve symptoms and prevent the formation of stones.[1][2][3]


Cystinuria is primarily characterized by a buildup of the amino acid, cystine, in the kidneys and bladder. This leads to the formation of cystine crystals and/or stones which may block the urinary tract. Signs and symptoms of cystinuria are a consequence of stone formation and may include:[1][2][3]

This table lists symptoms that people with this disease may have. For most diseases, symptoms will vary from person to person. People with the same disease may not have all the symptoms listed. This information comes from a database called the Human Phenotype Ontology (HPO) . The HPO collects information on symptoms that have been described in medical resources. The HPO is updated regularly. Use the HPO ID to access more in-depth information about a symptom.

Medical Terms Other Names
Learn More:
80%-99% of people have these symptoms
Abnormality of amino acid metabolism
Blood in urine
Kidney stones
30%-79% of people have these symptoms
High blood uric acid level
Renal insufficiency
Renal failure
Renal failure in adulthood

[ more ]

Percent of people who have these symptoms is not available through HPO
Abnormality of the nervous system
Neurologic abnormalities
Neurological abnormality

[ more ]

High urine arginine levels
Autosomal dominant inheritance
Autosomal recessive inheritance
High urine cystine levels
High urine lysine levels
Recurrent urinary tract infections
Frequent urinary tract infections
Repeated bladder infections
Repeated urinary tract infections
Urinary tract infections
Urinary tract infections, recurrent

[ more ]

Variable expressivity


Cystinuria is caused by changes (mutations) in the SLC3A1 and SLC7A9 genes. These genes encode a protein complex that helps control the reabsorption of amino acids (such as cystine) in the kidneys. Mutations in these genes disrupt the function of the protein complex, causing cystine to become more concentrated in the urine. As the concentration of cystine increases, cystine crystals and/or stones begin to form in the urinary tract leading to the many signs and symptoms associated with cystinuria.[4]


Screening for cystinuria should be considered in people with recurrent or bilateral (i.e. affecting both kidneys) stones; those who develop stones at an early age (before age 30); and people who have a family history of cystinuria. A diagnosis is typically made after an episode of kidney stones when testing reveals that the stones are made of cystine.[1][2][3]

The following tests may be recommended to detect kidney stones and diagnose cystinuria:[1][2][3]

Testing Resources

  • The Genetic Testing Registry (GTR) provides information about the genetic tests for this condition. The intended audience for the GTR is health care providers and researchers. Patients and consumers with specific questions about a genetic test should contact a health care provider or a genetics professional.


    Treatment of cystinuria is focused on relieving symptoms and preventing the formation of additional stones. A more conservative approach is typically tried first. This may include increasing fluid intake, regular monitoring of urinary pH, dietary restrictions (i.e. eating less salt) and increasing the pH of urine with potassium citrate supplements. If these strategies do not prevent the formation of stones, medications may be added to help dissolve the cystine crystals.[1][2][3]

    Treatment for cystinuria-related stones varies depending on the size and location of the stone, but may include:[1][2][3]

    Medscape Reference's Web site offers more specific information regarding the treatment and management of cystinuria. Please click on the link to access this resource.

    FDA-Approved Treatments

    The medication(s) listed below have been approved by the Food and Drug Administration (FDA) as orphan products for treatment of this condition. Learn more orphan products.


    Support and advocacy groups can help you connect with other patients and families, and they can provide valuable services. Many develop patient-centered information and are the driving force behind research for better treatments and possible cures. They can direct you to research, resources, and services. Many organizations also have experts who serve as medical advisors or provide lists of doctors/clinics. Visit the group’s website or contact them to learn about the services they offer. Inclusion on this list is not an endorsement by GARD.

    Organizations Supporting this Disease

      Social Networking Websites

        Organizations Providing General Support

          Learn more

          These resources provide more information about this condition or associated symptoms. The in-depth resources contain medical and scientific language that may be hard to understand. You may want to review these resources with a medical professional.

          Where to Start

          • MedlinePlus was designed by the National Library of Medicine to help you research your health questions, and it provides more information about this topic.
          • Genetics Home Reference (GHR) contains information on Cystinuria. This website is maintained by the National Library of Medicine.
          • The National Organization for Rare Disorders (NORD) has a report for patients and families about this condition. NORD is a patient advocacy organization for individuals with rare diseases and the organizations that serve them.

            In-Depth Information

            • Medscape Reference provides information on this topic. You may need to register to view the medical textbook, but registration is free.
            • The Monarch Initiative brings together data about this condition from humans and other species to help physicians and biomedical researchers. Monarch’s tools are designed to make it easier to compare the signs and symptoms (phenotypes) of different diseases and discover common features. This initiative is a collaboration between several academic institutions across the world and is funded by the National Institutes of Health. Visit the website to explore the biology of this condition.
            • Online Mendelian Inheritance in Man (OMIM) is a catalog of human genes and genetic disorders. Each entry has a summary of related medical articles. It is meant for health care professionals and researchers. OMIM is maintained by Johns Hopkins University School of Medicine. 
            • Orphanet is a European reference portal for information on rare diseases and orphan drugs. Access to this database is free of charge.
            • PubMed is a searchable database of medical literature and lists journal articles that discuss Cystinuria. Click on the link to view a sample search on this topic.


              1. Cystinuria. MedlinePlus. October 2013; https://www.nlm.nih.gov/medlineplus/ency/article/000346.htm.
              2. Chandra Shekhar Biyani, MBBS, MS, DUrol, FRCS(Urol), FEBU. Cystinuria. Medscape Reference. April 2015; https://emedicine.medscape.com/article/435678-overview.
              3. Saravakos P, Kokkinou V, Giannatos E. Cystinuria: current diagnosis and management. Urology. April 2014; 83(4):693-699.
              4. Cystinuria. Genetics Home Reference. June 2014; https://www.ghr.nlm.nih.gov/condition/cystinuria.

              Rare Gastroenterology News