Cystinuria is a condition characterized by the buildup of the amino acid cystine, a building block of most proteins, in the kidneys and bladder. As the kidneys filter blood to create urine, cystine is normally absorbed back into the bloodstream. People with cystinuria cannot properly reabsorb cystine into their bloodstream, so the amino acid accumulates in their urine.

As urine becomes more concentrated in the kidneys, the excess cystine forms crystals. Larger crystals become stones that may lodge in the kidneys or in the bladder. Sometimes cystine crystals combine with calcium molecules in the kidneys to form large stones. These crystals and stones can create blockages in the urinary tract and reduce the ability of the kidneys to eliminate waste through urine. The stones also provide sites where bacteria may cause infections.

Mutations in the SLC3A1 or SLC7A9 gene cause cystinuria. The SLC3A1 and SLC7A9 genes provide instructions for making the two parts (subunits) of a protein complex that is primarily found in the kidneys. Normally this protein complex controls the reabsorption of certain amino acids, including cystine, into the blood from the filtered fluid that will become urine. Mutations in either the SLC3A1 gene or SLC7A9 gene disrupt the ability of the protein complex to reabsorb amino acids, which causes the amino acids to become concentrated in the urine. As the levels of cystine in the urine increase, the crystals typical of cystinuria form. The other amino acids that are reabsorbed by the protein complex do not create crystals when they accumulate in the urine.

Normal Function

The SLC3A1 gene provides instructions for producing one part (subunit) of a protein made primarily in the kidneys. This subunit joins with another protein subunit, produced from the SLC7A9 gene, to form a transporter protein complex. During the process of urine formation in the kidneys, this protein complex absorbs particular protein building blocks (amino acids) back into the blood. In particular, the amino acids cystine, ornithine, arginine, and lysine are absorbed back into the blood through this mechanism.

Health Conditions Related to Genetic Changes

Cystinuria

More than 120 mutations in the SLC3A1 gene have been found to cause cystinuria. Many of these mutations alter a single DNA building block (nucleotide) or insert or delete a small number of nucleotides in the SLC3A1 gene. These changes lead to an abnormally functioning transporter protein complex, which causes certain amino acids to become concentrated in the urine. Cystine is the only amino acid that forms crystals and stones in the bladder or kidneys, leading to the signs and symptoms of cystinuria.

Other disorders

Some people with cystinuria have large DNA deletions that remove not only the SLC3A1 gene but one or more neighboring genes. Individuals with these large DNA deletions have the signs and symptoms of cystinuria, but they can also have other features.

Deletions of the SLC3A1 gene and the neighboring PREPL gene cause hypotonia-cystinuria syndrome. In addition to cystinuria, people with this condition have low muscle tone (hypotonia) and poor feeding, which usually improves by early childhood. They may also have droopy eyelids (ptosis), an elongated head (dolichocephaly), and mild intellectual disability. Most people with this condition have short stature.

Deletions of the SLC3A1 gene, the PREPL gene, and the C2orf34 gene cause atypical hypotonia-cystinuria syndrome. In addition to the symptoms of hypotonia-cystinuria syndrome, individuals with the atypical form have mild to moderate delay in the development of mental and motor skills (psychomotor delay).

Deletions of the SLC3A1 gene, the PREPL gene, the C2orf34 gene, and the PPM1B gene cause 2p21 deletion syndrome. In addition to all the symptoms of the previous syndromes, individuals with 2p21 deletion syndrome have seizures soon after birth, moderate to severe psychomotor delay, and impairments in the process from which cells derive much of their energy (oxidative phosphorylation). People with this condition typically have a characteristic facial appearance with a prominent forehead, long eyelashes, a flat nasal bridge, and abnormally turned ears.

Other Names for This Gene

• amino acid transporter 1
• ATR1
• CSNU1
• D2H
• NBAT
• RBAT
• SLC31_HUMAN
• solute carrier family 3 (amino acid transporter heavy chain), member 1
• solute carrier family 3 (cystine, dibasic and neutral amino acid transporters), member 1
• solute carrier family 3 (cystine, dibasic and neutral amino acid transporters, activator of cystine, dibasic and neutral amino acid transport), member 1
• solute carrier family 3, member 1

Genomic Location

Normal Function

The SLC7A9 gene provides instructions for producing one part (subunit) of a protein made primarily in the kidneys. This subunit joins with another protein subunit, produced from the SLC3A1 gene, to form a transporter protein complex. During the process of urine formation in the kidneys, this protein complex absorbs particular protein building blocks (amino acids) back into the blood. In particular, the amino acids cystine, ornithine, arginine, and lysine are absorbed back into the blood through this mechanism.

Health Conditions Related to Genetic Changes

Cystinuria

At least 95 mutations in the SLC7A9 gene have been found to cause cystinuria. Many of these mutations alter a single DNA building block (nucleotide) or insert or delete a small number of nucleotides in the SLC7A9 gene. These changes lead to an abnormally functioning transporter protein complex, which causes certain amino acids to become concentrated in the urine. Cystine is the only amino acid that forms crystals and stones in the bladder or kidneys, leading to the signs and symptoms of cystinuria.

Other Names for This Gene

• b0,+AT
• BAT1_HUMAN
• CSNU3
• solute carrier family 7 (amino acid transporter light chain, bo,+ system), member 9
• solute carrier family 7 (glycoprotein-associated amino acid transporter light chain, bo,+ system), member 9
• solute carrier family 7, member 9

Genomic Location

• Nausea
• Blood in the urine (hematuria)
• Flank pain
• Frequent urinary tract infections
• Chronic or acute renal failure (rare)

• 24-hour urine collection
• Abdominal imaging (CT scan, MRI, or ultrasound)
• Intravenous pyelogram (IVP)
• Urinalysis
• Genetic testing

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.

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

• Extracorporeal shock wave lithotripsy (ESWL)
• Ureteroscopy
• Percutaneous nephrolithotomy
• Open surgery (in rare cases)