Mutations in the SLC3A1 and SLC7A9 genes cause cystinuria. The SLC3A1 and SLC7A9 genes provide instructions for making the two parts (subunits) of a transporter protein complex that is made primarily 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 transporter protein complex to reabsorb amino acids, which causes them 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 transporter protein complex do not create crystals when they accumulate in the urine.
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