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Adam MP, Bick S, Mirzaa GM, et al., editors. GeneReviews® [Internet]. Seattle (WA): University of Washington, Seattle; 1993-2026.

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Cystinuria

Synonyms: Cystine Nephrolithiasis, Cystine Stone Disease, Cystine Urolithiasis

, MD, , MD, and , MD, MSc, PhD, FERA.

Author Information and Affiliations

Initial Posting: .

Estimated reading time: 39 minutes

Summary

Clinical characteristics.

Cystinuria is characterized by early-onset and recurrent kidney stones composed of cystine. Individuals with cystinuria often present with their first kidney stone in the first two decades of life. Complications of cystinuria include recurrent urinary tract infections, chronic kidney disease (CKD), and hypertension. Some individuals develop end-stage kidney disease.

Diagnosis/testing.

The diagnosis of cystinuria can be established in a proband by identification of cystine urinary stones and elevated 24-hour urinary cystine excretion or identification of biallelic, digenic, or heterozygous pathogenic variants in SLC3A1 or SLC7A9 by molecular genetic testing in an individual with suggestive features.

Management.

Targeted therapies: Potassium citrate or potassium bicarbonate to alkalinize the urine; dietary treatment includes high fluid intake and low-sodium and low-protein diet; cysteine binding medications including tiopronin and D-penicillamine.

Supportive care: Analgesics for renal colic; surgical treatment or percutaneous nephrolithotomy with ultrasonic or laser lithotripsy for kidney stones; antibiotic therapy for recurrent urinary tract infection; management of CKD; antihypertensive therapy.

Surveillance: Thorough physical exam, 24-hour urine for pH, volume, cystine, sodium, calcium, citrate, and creatinine excretion every three to six months until stable on treatment and then every six to 12 months; assessment of urinary-soluble mixed-drug cysteine disulfides and free cystine by liquid chromatography-tandem mass spectrometry as needed to adjust therapy; kidney and urinary tract ultrasound every six to 12 months; abdominal CT as needed for symptomatic kidney stones; blood creatinine, albumin-to-creatinine ratio, or 24-hour urine albumin concentration every three to six months until stable on treatment and then every six to 12 months; daily at home blood pressure assessment; ambulatory blood pressure assessment every three to six months until stable on treatment and then every six to 12 months; 24-hour ambulatory blood pressure monitoring in those with hypertension; serum bone markers and dual-energy x-ray absorptiometry scan in adults with frequency based on bone health and presence of additional risk factors.

Agents/circumstances to avoid: Foods containing methionine such as liver, poultry and horse meat, sardines and tuna in oil, dried cod, and crayfish; dietary and hair supplements with a high methionine concentration.

Evaluation of relatives at risk: It is appropriate to clarify the status of apparently asymptomatic older and younger at-risk relatives of an affected individual by 24-hour urine collection to assess cystine excretion and, in those with elevated cystine excretion, molecular genetic testing for the familial pathogenic variant(s) in order to identify as early as possible those who would benefit from prompt initiation of treatment and preventive measures.

Genetic counseling.

Cystinuria caused by biallelic pathogenic variants in SLC3A1 or SLC7A9 is inherited in an autosomal recessive (AR) manner. Cystinuria caused by pathogenic variants in both SLC3A1 and SLC7A9 is inherited in a digenic manner. Cystinuria caused by a heterozygous pathogenic variant in SLC3A1 or SLC7A9 is inherited in an autosomal dominant (AD) manner.

AR inheritance: If both parents are known to be heterozygous for an SLC3A1 or SLC7A9 pathogenic variant, each sib of an affected individual has at conception a 25% chance of inheriting biallelic pathogenic variants and being affected, a 50% chance of inheriting one pathogenic variant and being heterozygous, and a 25% chance of inheriting neither of the familial pathogenic variants.

Digenic inheritance: If both parents are heterozygous for an SLC3A1 or SLC7A9 pathogenic variant (or if one parent is heterozygous for pathogenic variants in both SLC3A1 and SLC7A9 and the other parent has neither of the pathogenic variants), each sib has at conception a 25% chance of inheriting both pathogenic variants and having digenic cystinuria, a 50% chance of inheriting one pathogenic variant and being heterozygous, and a 25% chance of inheriting neither of the pathogenic variants.

AD inheritance: Each child of an individual with autosomal dominant cystinuria has a 50% chance of inheriting an SLC3A1 or SLC7A9 pathogenic variant. Penetrance in heterozygotes is reduced.

Individuals who are heterozygous for an SLC7A9 pathogenic variant or heterozygous for a specific tandem duplication of SLC3A1 may have higher levels of urinary cystine excretion and are therefore at risk of forming cystine stones over a lifetime. If the SLC3A1 and/or SLC7A9 pathogenic variant(s) have been identified in an affected family member, prenatal and preimplantation genetic testing are possible. Identification of hyperechoic colon on prenatal ultrasound before 36 weeks' gestation has a high positive predictive value of cystinuria.

Diagnosis

Clinical diagnostic criteria were published after a consensus conference in January 2019 involving experts in cystinuria and the Metabolic Nephropathy Joint Working Group of the European Reference Network for Rare Kidney Diseases (ERKNet) and eUROGEN members [Servais et al 2021] and are consistent with a United States consensus statement [Eisner et al 2020].

Suggestive Findings

Cystinuria should be suspected in probands with the following clinical, laboratory, and imaging findings.

Clinical findings

  • Early-onset nephrolithiasis
  • Large or recurrent kidney stones; cystine stones are yellowish brown with a granular surface
  • Recurrent urinary tract infections
  • Kidney failure (some individuals)

Laboratory findings

  • Cystine urinary stones
    Note: (1) Stone composition analysis should be performed every time a stone is available through infrared spectroscopy (FT-IR) or x-ray diffraction [Primiano et al 2014, Primiano et al 2019], avoiding semi-quantitative chemical assays, which can be frequently misleading [Siener et al 2016]. Urinary spectra analysis via attenuated total reflection FT-IR can detect affected individuals easily and cost effectively [Primiano et al 2021]. (2) Calculi made of calcium, oxalate, phosphate, and struvite is found in approximately 10% of affected individuals [Bostroem & Hambraeus 1964, Spasiano et al 2023].
  • Pathognomonic radial structure with hexagonal cystine crystals on first morning or random urine sample [Servais et al 2021, D'Ambrosio et al 2022] (found in about 70% of individuals [Wong et al 2016])
  • Abnormal cystine excretion on 24-hour urine collection
  • Elevated cystine and other dibasic amino acids (lysine, ornithine, arginine) in urine amino acids

Imaging findings on prenatal ultrasound. Identification of hyperechoic colon on prenatal ultrasound before 36 weeks' gestation has a high positive predictive value of cystinuria [Tostivint et al 2017, Servais et al 2021].

Establishing the Diagnosis

Clinical Diagnosis

The clinical diagnosis of cystinuria can be established in a proband by identification of cystine urinary stones and elevated 24-hour urinary cystine excretion.

Molecular Diagnosis

Molecular genetic testing is not mandatory for diagnosis but is useful in those with atypical presentations and/or an uncertain pattern of inheritance [Servais et al 2021]. The diagnosis of cystinuria is established in a proband with suggestive findings who has one of the following on molecular genetic testing (see Table 1):

  • Biallelic pathogenic (or likely pathogenic) variants in SLC3A1 (type AA) or SLC7A9 (type BB)
  • Digenic pathogenic (or likely pathogenic) variants in SLC3A1 and SLC7A9 (type AB)
    Note: Digenic inheritance has been reported in some individuals with cystinuria. Evidence of digenic inheritance in cystinuria is limited; most supporting data come from murine models [Gucev et al 2011, Espino et al 2015]. It is possible that some individuals previously classified as type AB actually represent more complex allelic combinations (type AAB or ABB), which may better explain the phenotypic variability observed [Font-Llitjós et al 2005].
  • Heterozygous pathogenic (or likely pathogenic) variants in SLC3A1 (type A0) or SLC7A9 (type B0)
    Note: To date, the only SLC3A1 pathogenic variant reported to cause autosomal dominant cystinuria is a specific tandem duplication of SLC3A1 including exons 5 to 9 [Schmidt et al 2003].

Note: (1) Per American College of Medical Genetics and Genomics / Association for Molecular Pathology variant interpretation guidelines, the terms "pathogenic variant" and "likely pathogenic variant" are synonymous in a clinical setting, meaning that both are considered diagnostic and can be used for clinical decision making [Richards et al 2015]. Reference to "pathogenic variants" in this GeneReview is understood to include likely pathogenic variants. (2) Identification of variant(s) of uncertain significance cannot be used to confirm or rule out the diagnosis.

Molecular genetic testing approaches can include a combination of gene-targeted testing (concurrent single-gene testing, multigene panel) and comprehensive genomic testing (exome sequencing, genome sequencing). Gene-targeted testing requires that the clinician determine which gene(s) are likely involved (see Option 1), whereas comprehensive genomic testing does not (see Option 2).

Option 1

Concurrent single-gene testing may be considered in those with suggestive findings including stone composition analysis that shows 100% cystine stone(s). Testing should include sequence analysis and deletion/duplication analysis of SLC3A1 and SLC7A9 to detect missense, nonsense, and splice site variants and intragenic deletions/insertions. Large deletions/duplications of SLC3A1 or SLC7A9 are common in individuals with cystinuria; methods to detect large genetic rearrangements (e.g., multiplex ligation-dependent probe amplification [MLPA]) should be used.

A nephrolithiasis multigene panel that includes SLC3A1, SLC7A9, and other genes of interest (see Differential Diagnosis) is recommended when there is incomplete clinical data (e.g., missing stone composition analysis) to identify the genetic cause of the condition while limiting identification of pathogenic variants and variants of uncertain significance in genes that do not explain the underlying phenotype. Note: (1) The genes included in the panel and the diagnostic sensitivity of the testing used for each gene vary by laboratory and are likely to change over time. (2) Some multigene panels may include genes not associated with the condition discussed in this GeneReview. (3) In some laboratories, panel options may include a custom laboratory-designed panel and/or custom phenotype-focused exome analysis that includes genes specified by the clinician. (4) Methods used in a panel may include sequence analysis, deletion/duplication analysis, and/or other non-sequencing-based tests. (5) Large deletions/duplications of SLC3A1 or SLC7A9 are common in individuals with cystinuria; methods to detect large genetic rearrangements (e.g., MLPA) should be included in the multigene panel analysis.

For an introduction to multigene panels click here. More detailed information for clinicians ordering genetic tests can be found here.

Option 2

In those with recurrent kidney stones and additional extrarenal manifestations or atypical features, broader genetic testing may be beneficial [Spasiano et al 2024]. Comprehensive genomic testing does not require the clinician to determine which gene(s) are likely involved. Exome sequencing is most commonly used; genome sequencing is also possible. To date, the majority of SLC3A1 or SLC7A9 pathogenic variants reported (e.g., missense, nonsense) are within the coding region and are likely to be identified on exome sequencing.

For an introduction to comprehensive genomic testing click here. More detailed information for clinicians ordering genomic testing can be found here.

Table 1.

Cystinuria: Molecular Genetic Testing

Gene 1, 2Proportion of Cystinuria Attributed to Pathogenic Variants in GeneProportion of Pathogenic Variants 3 Identified by Method
Sequence analysis 4Gene-targeted deletion/duplication analysis 5
SLC3A1 50%-70% 680%-85% 615%-20% 6
SLC7A9 25%-45% 680%-85% 615%-20% 6
Unknown5%-7% 7NA
1.

Genes are listed in alphabetic order.

2.
3.

See Molecular Genetics for information on variants detected in these genes.

4.

Sequence analysis detects variants that are benign, likely benign, of uncertain significance, likely pathogenic, or pathogenic. Variants may include missense, nonsense, and splice site variants and small intragenic deletions/insertions; typically, exon or whole-gene deletions/duplications are not detected. For issues to consider in interpretation of sequence analysis results, click here.

5.

Gene-targeted deletion/duplication analysis detects intragenic deletions or duplications. Methods used may include a range of techniques such as quantitative PCR, long-range PCR, multiplex ligation-dependent probe amplification (MLPA), and a gene-targeted microarray designed to detect single-exon deletions or duplications. Exome and genome sequencing may be able to detect deletions/duplications using breakpoint detection or read depth; however, sensitivity can be lower than gene-targeted deletion/duplication analysis.

6.
7.

Clinical Characteristics

Clinical Description

Cystinuria is characterized by early-onset and recurrent kidney stones composed of cystine. Complications include recurrent urinary tract infections, chronic kidney disease (CKD), and hypertension. Some individuals develop end-stage kidney disease (ESKD).

Table 2.

Cystinuria: Frequency of Select Features

Feature% of Persons w/Feature
SLC3A1- & SLC7A9-related AR cystinuria 1SLC7A9 heterozygotes 2
Cystinuria100%86%-90% 3
↑ urinary lysine, arginine, & ornithine100%86%-90% 3
Nephrolithiasis94%2%-18%
CKD20%-25%

AR = autosomal recessive; CKD = chronic kidney disease

1.

Cystinuria caused by biallelic pathogenic variants in SLC3A1 or SLC7A9 may be referred to as type AA or type BB, respectively.

2.

Cystinuria caused by a heterozygous SLC7A9 pathogenic variant may be referred to as type B0.

3.

In SLC7A9 heterozygotes, urinary excretion of cystine and dibasic amino acids is mostly elevated, though ~14% of individuals show a normal profile [Fjellstedt et al 2003].

Nephrolithiasis. Individuals with cystinuria often present with their first kidney stone in the first two decades of life (median age: 13 years) [Dello Strologo et al 2002]. The age range of first stone development can be from childhood to late adulthood [Dello Strologo et al 2002, Lambert et al 2010]. Clinical manifestations include acute flank pain, commonly radiating toward testicles and groin, nausea, and vomiting. Signs or symptoms of stone passage can be present, such as micro- or macrohematuria and recurrent urinary tract infections.

Males are usually more severely affected than females [Dello Strologo et al 2002], although more recent reports indicate that disease severity may not differ significantly between males and females [Prot-Bertoye et al 2015, Rhodes et al 2015]. In addition, not all individuals with cystinuria form stones [Piñero-Fernández et al 2023]. The phenotype can vary even in affected individuals from the same family [D'Ambrosio et al 2022].

CKD. Individuals with cystinuria are reported to have a higher incidence of CKD and a greater risk of ESKD compared to the general population and compared to individuals with other causes of nephrolithiasis [Assimos et al 2002, Prot-Bertoye et al 2015]. Approximately 20%-25% of individuals have an estimated glomerular filtration rate (eGFR) <60 mL/min/1.73 m2 [Prot-Bertoye et al 2015, Rhodes et al 2015, Kum et al 2019], probably related to staghorn calculi, recurrent urologic procedures since infancy, and intratubular obstruction by cystine crystals [Gambaro et al 2017].

Hypertension occurs in 29%-51% of adults with cystinuria and is frequently associated with CKD [Prot-Bertoye et al 2015, Kum et al 2019]; development of CKD then can further exacerbate hypertension.

Low bone mineral density (BMD). A strong correlation was found between low BMD and cystinuria. Individuals with cystinuria were found to have lower BMD, with z scores below the mean for BMD across most sites when compared to healthy individuals of the same sex and age. These findings were independent of the presence of CKD [D'Ambrosio et al 2025].

Heterozygotes

Individuals heterozygous for an SLC7A9 pathogenic variant or heterozygous for a specific tandem duplication of SLC3A1 including exons 5 to 9 [Schmidt et al 2003] may have higher levels of urinary cystine excretion and are therefore at risk of forming cystine stones over a lifetime. Penetrance in heterozygotes is reduced, clinical severity is reduced, and the risk of developing kidney stones may depend on the presence of an additional risk factor (e.g., dehydration) [Dello Strologo et al 2002].

Note: Newborn screening studies have reported infants with transiently elevated urine cystine concentration who subsequently "grew out of the phenotype" [Boutros et al 2005]. This phenomenon may be due to maturation of SLC3A1 expression between mid-gestation and approximately age 4.5 years. However, it remains uncertain whether these reports represented heterozygous individuals or if other factors contributed to the transient biochemical phenotype.

Phenotype Correlations by Gene

Individuals with autosomal dominant cystinuria are more likely to have a heterozygous pathogenic variant in SLC7A9; only one SLC3A1 pathogenic variant has been reported in individuals with autosomal dominant inheritance to date (see Genotype-Phenotype Correlations).

Genotype-Phenotype Correlations

SLC3A1. To date, autosomal dominant inheritance with reduced penetrance of SLC3A1-related cystinuria has only been reported in individuals with a specific tandem duplication in SLC3A1 including exons 5 to 9 [Schmidt et al 2003].

SLC7A9. No clinically relevant genotype-phenotype correlations have been identified.

Prevalence

The estimated worldwide prevalence of cystinuria is one in 7,000 births, with high geographic variability [Eggermann et al 2012a]. It represents the most common monogenic cause of kidney stones, accounting for 1%-2% of all kidney stones in adults and 6%-8% in children [Chillarón et al 2010].

Founder variants in SLC3A1 have been reported in the Ashkenazi Jewish and Mennonite populations (see Table 9).

Founder variants in SLC7A9 have been reported in the Libyan Jewish and Mennonite populations (see Table 9).

Differential Diagnosis

Biallelic contiguous gene deletions in the 2p21 region involving SLC3A1 and adjacent genes are associated with kidney stones with or without increased cystinuria excretion and should be considered in the differential diagnosis of cystinuria (see Table 3).

Table 3.

Cystinuria: Differential Diagnosis – Contiguous Gene Deletions in the 2p21 Region Involving SLC3A1

Genes Involved in the 2p21 DeletionDisorder 1MOIFeatures of Disorder
Overlapping w/CystinuriaDistinguishing from Cystinuria
PREPL &
SLC3A1
Hypotonia-cystinuria syndrome (OMIM 606407)AR
  • ↑ cystinuria excretion
  • Recurrent kidney stones
  • Infantile hypotonia
  • Xerostomia
  • Poor feeding
  • Developmental delay
  • Deficit of growth hormone
  • ↑ serum lactate levels
CAMKMT,
PREPL, &
SLC3A1
Atypical hypotonia-cystinuria syndromeARMild-to-moderate intellectual disability in addition to typical manifestations of hypotonia-cystinuria syndrome
CAMKMT,
PPM1B,
PREPL, &
SLC3A1
2p21 deletion syndromeAR
  • ↑ cystinuria excretion
  • Early-onset kidney stones
Frontal bossing, long eyelashes, almond-shaped eyes, depressed nasal bridge, & large, posteriorly rotated ears in addition to typical manifestations of hypotonia-cystinuria syndrome

Management

Clinical practice guidelines for cystinuria were developed after a consensus conference in January 2019 involving experts in cystinuria and the Metabolic Nephropathy Joint Working Group of the European Reference Network for Rare Kidney Diseases (ERKNet) and eUROGEN members [Servais et al 2021] and are consistent with a United States consensus statement [Eisner et al 2020].

Evaluations Following Initial Diagnosis

To establish the extent of disease and needs in an individual diagnosed with cystinuria, the evaluations summarized in Table 4 (if not performed as part of the evaluation that led to the diagnosis) are recommended.

Treatment of Manifestations

The main goal of treatment is to reduce urinary cystine concentration below its solubility level by adjusting urinary pH (solubility increases in an alkaline environment) and urine volume and reduce intake of sodium and animal proteins [Servais et al 2021]. The limit of solubility can be experimentally fixed at 1 mmol/L cystine at urinary pH ≥7; therefore, physicians should aim for a cystine concentration <1 mmol/L (250 mg/L) and a urinary pH 7.5-8, allowing the potential dissolution of cystine crystals.

To prevent new stone formation and dissolve previous calculi, individuals should reach a supersaturation level <0.6 mmol/L cystine in a 24-hour urine collection, leaving an adequate allowance for overnight supersaturation increase [Coe et al 1992, Nakagawa et al 2000, Rogers et al 2007].

Targeted Therapies

In GeneReviews, a targeted therapy is one that addresses the specific underlying mechanism of disease causation (regardless of whether the therapy is significantly efficacious for one or more manifestation of the genetic condition); would otherwise not be considered without knowledge of the underlying genetic cause of the condition; or could lead to a cure. —ED

Table 5.

Cystinuria: Targeted Therapies

TypeTreatmentDosage 1Consideration
Urine alkalinization Potassium citrate or potassium bicarbonate
  • 20 mEq 3x/day in adults
  • 10 mEq 3x/day in children
Starting dose should be carefully adjusted until urinary pH is 7.5-8.0.
Dietary High fluid intake
  • 3 L/day in adults
  • >2 L/day in children
Avoid drinks w/high sugar & sodium content.
Low-sodium diet<6 g/day of sodium chloride6 g = 1 tsp of sodium chloride
Low-protein diet0.8-1 g/kg/day
  • Vegetable proteins are recommended; avoid animal proteins & food/supplements rich in methionine.
  • Note: In children, regular protein intake is recommended for adequate growth.
Cystine-binding medications Tiopronin
  • 600-800 mg/day divided into 3 doses in adults
  • 15 mg/kg/day divided into 3 doses in children
  • Starting dose should be adjusted until urinary cystine concentration is <1 mmol/L.
  • Doses >1 g/day do not show further reduction in urinary free cystine concentration.
D-penicillamine
  • 0.5-2 g/day divided into 3-4 doses in adults
  • 20-40 mg/kg/day divided into 3-4 doses (max: 1.2 g/day) in children
1.

Dosage information is consistent with those reported in the clinical practice recommendations published after a consensus conference in January 2019 involving experts in cystinuria and the Metabolic Nephropathy Joint Working Group of the European Reference Network for Rare Kidney Diseases (ERKNet) and eUROGEN members [Servais et al 2021].

Urinary alkalinization. Urinary pH should be >7.5 to induce a threefold increase in cystine solubility compared with its solubility at physiologic urinary pH. To achieve this, affected individuals should take potassium citrate or potassium bicarbonate orally, with a starting dose of 20 mEq three times daily (10 mEq three times daily in children), adjusting the dose until the therapeutic target is reached. The last daily dose should be taken at bedtime for adequate urinary alkalinization overnight.

Urinary volume expansion. To reduce urinary cystine concentration to <1 mmol/L (250 mg/L), it is essential to guarantee a urinary volume ≥3 L/day (>2 L/day in children) and a specific gravity ≤1.005 [Prot-Bertoye et al 2019, Servais et al 2021]. Individuals should drink liquids upon awakening in the morning, throughout the day, and also at night upon each awakening. All fluids can be chosen, avoiding high sugar and sodium beverages [Ferraro et al 2013].

Sodium and protein restriction. A sodium intake <1-1.5 mEq/kg (~6 g per day of sodium chloride) is advisable to reduce cystine excretion [Goldfarb et al 2006].

Individuals with cystinuria should reduce animal protein consumption to 0.8-1 g/kg per day to achieve both an adequate nutritional intake and reduced cystine excretion due to a lower methionine concentration (precursor of cystine) [D'Ambrosio et al 2022]. In children, normal protein intake is recommended for optimal growth.

Thiol-containing drugs for resistant disease. In individuals with persistently high urinary cystine excretion and/or recurrent kidney stones, a thiol-containing drug (cystine-binding agent) should be introduced if alkalinization and other conservative measures are ineffective or limited by reduced adherence after three months of therapy [Barbey et al 2000].

Tiopronin (2-mercaptopropionylglycine) and D-penicillamine are sulfhydryls that cleave the disulfide bond of cystine, then bind cysteine to form a mixed-drug cysteine disulfide, 50-fold more soluble than cystine [Chillarón et al 2010].

Tiopronin initial dose should be 600-800 mg per day in three divided doses in adults (in children, 15 mg/kg per day in three divided doses), while D-penicillamine initial dose should be 0.5-2 g per day divided in three to four doses (in children, 20-40 mg/kg per day in three to four divided doses, with a maximum of 1.2 g per day).

The starting dose should be adjusted to reach the therapeutic urinary cystine concentration target (<1 mmol/L). However, it is crucial to highlight that doses >1 g per day do not show further reduction in urinary free cystine concentration [Worcester et al 2006] and that most individuals cannot achieve the recommended target [Pietrow et al 2003]. Both drugs are associated with adverse events [Zisman 2017, Prot-Bertoye et al 2019, D'Ambrosio et al 2022, Micallef et al 2022], such as the following:

  • Arthritis
  • Immune-mediated diseases
  • Proteinuria (reaching nephrotic syndrome range of ≥3.5 g per day, due to immunocomplex causing a membranous glomerulopathy)
  • Mucocutaneous lesions
  • Cutaneous rash
  • Vitamin B6 deficiency
  • Neutropenia, thrombocytopenia, or aplastic anemia
  • Gastrointestinal intolerance
  • Hepatotoxicity
  • Altered taste

In particular, D-penicillamine was associated with rapidly progressive glomerulonephritis [Ntoso et al 1986, Macarrón et al 1992], while tiopronin has been rarely associated with glomerulopathies (minimal change disease [Zhong et al 2019]). Currently, tiopronin is preferred for the reduced incidence of adverse effects, despite controversial reports [Prot-Bertoye et al 2015, Prot-Bertoye et al 2019].

In individuals on long-term cystine-binding treatment, pyridoxine supplementation is necessary (50 mg per day) due to the risk of vitamin B6 deficiency [Knoll et al 1988].

Supportive Care

Supportive care to improve quality of life, preserve kidney function, and reduce complications is recommended. This ideally involves multidisciplinary care by specialists in relevant fields (see Table 6).

Table 6.

Cystinuria: Treatment of Manifestations

Manifestation/ConcernTreatmentConsiderations/Other
Acute symptoms of renal colic Appropriate analgesic medicationConsider nonsteroidal anti-inflammatory drugs, only if there are no contraindications
Kidney stones Surgical approaches: ureteroscopic removal using holmium laser 1 or percutaneous nephrolithotomy w/ultrasonic or laser lithotripsy (for larger stones) 2
  • Most persons expel stones spontaneously.
  • In those w/refractory pain or stones wedged in, a surgical approach should be considered. Urgent decompression through stent or nephrostomy may be necessary. 3
Additional treatment as needed in those w/other types of kidney stones (calcium oxalate, calcium phosphate) due to coexisting metabolic abnormalities (e.g., hypercalciuria & hypocitraturia) 4
Recurrent UTIs
  • Antibiotic therapy
  • Evaluate/educate re factors or habits that ↑ risk of UTIs
Antibiotic therapy should be based on antibiogram.
CKD Identify & manage potential risk factors related to CKD progressionMost conservative measures are helpful in slowing CKD progression (such as ↑ fluid intake & ↓ dietary intake of protein & salt). 5
Hypertension Antihypertensive therapyEssential to prevent hypertension from further contributing to CKD

Surveillance

To monitor existing manifestations, the individual's response to supportive care, and the emergence of new manifestations, the evaluations summarized in Table 7 are recommended.

Agents/Circumstances to Avoid

Foods containing methionine such as liver, poultry and horse meat, sardines and tuna in oil, dried cod, and crayfish should be avoided [Bouzidi & Daudon 2007]. Dietary and hair supplements with a high methionine concentration should be avoided [Gillion et al 2021, Spasiano et al 2023].

Evaluation of Relatives at Risk

It is appropriate to clarify the status of apparently asymptomatic older and younger at-risk relatives of an affected individual in order to identify as early as possible those who would benefit from prompt initiation of treatment and preventive measures. Evaluations can include:

See Genetic Counseling for issues related to testing of at-risk relatives for genetic counseling purposes.

Pregnancy Management

Assessment of kidney stones before pregnancy is recommended. Pregnancy is a risk factor for kidney stone disease due to anatomic and physiologic factors and high urine calcium [Lee et al 2021]. Cystine-binding drugs are contraindicated during pregnancy, but urinary alkalinization is considered safe and should be maintained if needed [Pedro et al 2016]. See MotherToBaby for further information on medication use during pregnancy.

Therapies Under Investigation

Nutritional supplements containing alpha-lipoic acid (ALA) induced a reduction in cystine stone formation in murine models due to antioxidant activities [Zee et al 2017]. These findings were confirmed in a few reports in humans [Cil & Perwad 2020]. A randomized, double-blind, placebo-controlled trial evaluated twice-daily 600 mg of ALA in adults with cystinuria (NCT02910531; trial still ongoing). Preliminary results suggest reduced stone burden in 40% of ALA-treated individuals versus 14% with placebo, with minimal adverse effects and no change in urinary cystine. These findings indicate ALA may be a promising alternative therapy [Chi et al 2024].

L-cystine crystallization inhibitors inhibit in vitro crystal growth, distorting the hexagonal structure of cystine. Several studies on animal models demonstrated the ability of such agents to reduce incidence and size of kidney stones [Lee et al 2015, Azer & Goldfarb 2023].

Tolvaptan reduced incidence of calculi in short-term studies inducing urine dilution [Nelson et al 2020, Bai et al 2021].

A small study reported lower crystal volumes after selenium intake [Mohammadi et al 2018].

Glucose may theoretically interfere with urinary cystine binding. Consequently, sodium/glucose cotransporter 2 inhibitors (SGLT2i) have been investigated as a potential therapy for cystinuria. An initial observational series of ten individuals treated off-label with dapagliflozin reported fewer stone events and stable or reduced stone growth in most individuals over a median follow up of 13.5 months with minimal side effects [Sui et al 2024]. A Phase II clinical trial was proposed to evaluate the efficacy of dapagliflozin in individuals with cystinuria (NCT05058859). However, the study was never initiated due to unfulfilled funding requirements and has been officially abandoned.

New genetic therapeutic approaches, including nanoparticles and adeno-associated viral vector technologies, are under investigation considering the well-defined molecular basis and the specific target of cystinuria [Peek & Wilson 2022]. While routine genotyping is not currently required for clinical management, identifying the causative variants will be crucial for future gene-targeted therapies, including CRISPR/Cas9-based approaches and other genome-editing strategies [Beckermann et al 2020, Woodard et al 2025].

Search ClinicalTrials.gov in the US and EU Clinical Trials Register in Europe for access to information on clinical studies for a wide range of diseases and conditions.

Genetic Counseling

Genetic counseling is the process of providing individuals and families with information on the nature, mode(s) of inheritance, and implications of genetic disorders to help them make informed medical and personal decisions. The following section deals with genetic risk assessment and the use of family history and genetic testing to clarify genetic status for family members; it is not meant to address all personal, cultural, or ethical issues that may arise or to substitute for consultation with a genetics professional. —ED.

Mode of Inheritance

Cystinuria caused by biallelic pathogenic variants in SLC3A1 (type AA) or SLC7A9 (type BB) is inherited in an autosomal recessive manner.

Cystinuria caused by pathogenic variants in both SLC3A1 and SLC7A9 (type AB) (i.e., a heterozygous pathogenic variant in SLC3A1 and a heterozygous pathogenic variant in SLC7A9) is inherited in a digenic manner.

Cystinuria caused by a heterozygous pathogenic variant in SLC3A1 (type A0) or SLC7A9 (type B0) is inherited in an autosomal dominant manner with reduced penetrance. To date, autosomal dominant inheritance with reduced penetrance of SLC3A1-related cystinuria has only been reported in individuals with a specific tandem duplication in SLC3A1 including exons 5 to 9 [Schmidt et al 2003]. Note: In some individuals with a phenotype consistent with cystinuria and a single identified SLC3A1 or SLC7A9 pathogenic variant, it is possible that an undetected pathogenic variant on the other allele or pathogenic variant(s) in a different gene could be involved.

Autosomal dominant inheritance of cystinuria is reported less commonly than autosomal recessive and digenic inheritance of cystinuria.

Autosomal Recessive Inheritance – Risk to Family Members

Parents of a proband

Sibs of a proband

  • If both parents are known to be heterozygous for an SLC3A1 or SLC7A9 pathogenic variant, each sib of an affected individual has at conception a 25% chance of inheriting biallelic pathogenic variants and being affected, a 50% chance of inheriting one pathogenic variant and being heterozygous, and a 25% chance of inheriting neither of the familial pathogenic variants.
  • Individuals who are heterozygous for an SLC7A9 pathogenic variant or a specific tandem duplication of SLC3A1 including exons 5 to 9 [Schmidt et al 2003] may have higher levels of urinary cystine excretion and are therefore at risk of forming cystine stones over a lifetime (see Clinical Description, Heterozygotes).

Offspring of a proband. Unless an affected individual's reproductive partner also has an SLC3A1 or SLC7A9 pathogenic variant, offspring will be obligate heterozygotes for a pathogenic variant in SLC3A1 or SLC7A9.

Other family members. Each sib of the proband's parents is at a 50% risk of being heterozygous for an SLC3A1 or SLC7A9 pathogenic variant.

Heterozygote detection. Heterozygote testing for at-risk relatives requires prior identification of the cystinuria-related pathogenic variants in the family.

Digenic Inheritance – Risk to Family Members

Parents of a proband

  • Both parents of an individual with cystinuria caused by pathogenic variants in SLC3A1 and SLC7A9 (i.e., a heterozygous pathogenic variant in SLC3A1 and a heterozygous pathogenic variant in SLC7A9) may be heterozygous for a pathogenic variant or one parent may be heterozygous for both pathogenic variants and the other parent has neither of the pathogenic variants.
  • Molecular genetic testing is recommended for the parents of a proband to determine their genetic status and allow reliable recurrence risk assessment.

Sibs of a proband

  • If both parents are heterozygous for an SLC3A1 or SLC7A9 pathogenic variant, each sib at conception has a 25% chance of inheriting both pathogenic variants and having digenic cystinuria, a 50% chance of inheriting one pathogenic variant and being heterozygous, and a 25% chance of inheriting neither of the pathogenic variants.
  • If one parent is heterozygous for pathogenic variants in both SLC3A1 and SLC7A9 (and the other parent has neither of the pathogenic variants), each sib at conception has a 25% chance of inheriting both pathogenic variants and having digenic cystinuria, a 50% chance of one pathogenic variant and being heterozygous, and a 25% chance inheriting neither of the pathogenic variants.
  • Individuals who are heterozygous for an SLC7A9 pathogenic variant or a specific tandem duplication of SLC3A1 including exons 5 to 9 [Schmidt et al 2003] may have higher levels of urinary cystine excretion and are therefore at risk of forming cystine stones over a lifetime (see Clinical Description, Heterozygotes).

Offspring of a proband. Assuming that the proband's reproductive partner does not have an SLC3A1 or SLC7A9 pathogenic variant, each child of an affected individual has a 25% chance of inheriting both pathogenic variants and having digenic cystinuria, a 50% chance of inheriting one pathogenic variant and being heterozygous, and a 25% chance of inheriting neither of the pathogenic variants.

Other family members. Each sib of a heterozygous parent has a 50% chance of having either an SLC3A1 or SLC7A9 pathogenic variant.

Autosomal Dominant Inheritance – Risk to Family Members

Parents of a proband

  • Approximately 33% of individuals diagnosed with autosomal dominant cystinuria have an affected parent [Rhodes et al 2015].
  • Some individuals diagnosed with autosomal dominant cystinuria have the disorder as the result of a de novo pathogenic variant.
  • If a molecular diagnosis has been established in the proband and the proband appears to be the only affected family member (i.e., a simplex case), molecular genetic testing is recommended for the parents of the proband to evaluate their genetic status and inform recurrence risk assessment. Note: A proband may appear to be the only affected family member because of failure to recognize the disorder in family members, reduced penetrance, or late onset of the disease in an affected parent. Therefore, de novo occurrence of an SLC3A1 or SLC7A9 pathogenic variant cannot be confirmed unless molecular genetic testing has demonstrated that neither parent is heterozygous for the pathogenic variant.
  • If the pathogenic variant identified in the proband is not identified in either parent and parental identity testing has confirmed biological maternity and paternity, the following possibilities should be considered:

Sibs of a proband. The risk to the sibs of the proband depends on the clinical/genetic status of the proband's parents:

  • If a parent of the proband is affected and/or is known to have the SLC3A1 or SLC7A9 pathogenic variant identified in the proband, the risk to the sibs of inheriting the pathogenic variant is 50%.
  • Penetrance in heterozygotes is reduced. Sibs who inherit an SLC7A9 pathogenic variant or a specific tandem duplication of SLC3A1 including exons 5 to 9 [Schmidt et al 2003] may have higher levels of urinary cystine excretion and are therefore at risk of forming cystine stones over a lifetime (see Clinical Description, Heterozygotes).
  • If the proband has a known SLC3A1 or SLC7A9 pathogenic variant that cannot be detected in the leukocyte DNA of either parent, the recurrence risk to sibs is estimated to be 1% because of the possibility of parental gonadal mosaicism [Rahbari et al 2016].
  • If the parents are clinically unaffected but their genetic status is unknown, the risk to the sibs of a proband appears to be low but increased over that of the general population because of the possibility of reduced penetrance in a heterozygous parent and the possibility of parental gonadal mosaicism.

Offspring of a proband. Each child of an individual with autosomal dominant cystinuria has a 50% chance of inheriting an SLC3A1 or SLC7A9 pathogenic variant.

Other family members. The risk to other family members depends on the status of the proband's parents: if a parent has the pathogenic variant, the parent's family members may be at risk.

Related Genetic Counseling Issues

See Management, Evaluation of Relatives at Risk for information on evaluating at-risk relatives for the purpose of early diagnosis and treatment.

Family planning

  • The optimal time for determination of genetic risk and discussion of the availability of prenatal/preimplantation genetic testing is before pregnancy.
  • It is appropriate to offer genetic counseling (including discussion of potential risks to offspring and reproductive options) to young adults who are affected and/or at risk of having SLC3A1 or SLC7A9 pathogenic variant(s).
  • Heterozygote testing should be considered for the reproductive partners of individuals known to have SLC3A1 or SLC7A9 pathogenic variant(s). SLC3A1 and SLC7A9 founder variants have been identified in several populations (see Table 9).

DNA banking. Because it is likely that testing methodology and our understanding of genes, pathogenic mechanisms, and diseases will improve in the future, consideration should be given to banking DNA from probands in whom a molecular diagnosis has not been confirmed (i.e., the causative pathogenic mechanism is unknown). For more information, see Huang et al [2022].

Prenatal Testing and Preimplantation Genetic Testing

Molecular genetic testing. If the SLC3A1 and/or SLC7A9 pathogenic variant(s) have been identified in an affected family member, prenatal and preimplantation genetic testing are possible.

Prenatal ultrasound. Identification of hyperechoic colon on prenatal ultrasound before 36 weeks' gestation has a high positive predictive value of cystinuria [Tostivint et al 2017, Servais et al 2021]. In pregnancies in which there is no family history of cystinuria but an abnormality such as hyperechoic colon is detected on ultrasound examination, molecular genetic testing is recommended.

Note: Gestational age is expressed as menstrual weeks calculated either from the first day of the last normal menstrual period or by ultrasound measurements.

Differences in perspective may exist among medical professionals and within families regarding the use of prenatal and preimplantation genetic testing. While most health care professionals would consider use of prenatal and preimplantation genetic testing to be a personal decision, discussion of these issues may be helpful.

Resources

GeneReviews staff has selected the following disease-specific and/or umbrella support organizations and/or registries for the benefit of individuals with this disorder and their families. GeneReviews is not responsible for the information provided by other organizations. For information on selection criteria, click here.

Molecular Genetics

Information in the Molecular Genetics and OMIM tables may differ from that elsewhere in the GeneReview: tables may contain more recent information. —ED.

Table A.

Cystinuria: Genes and Databases

Data are compiled from the following standard references: gene from HGNC; chromosome locus from OMIM; protein from UniProt. For a description of databases (Locus Specific, HGMD, ClinVar) to which links are provided, click here.

Table B.

OMIM Entries for Cystinuria (View All in OMIM)

104614SOLUTE CARRIER FAMILY 3 (CYSTINE, DIBASIC, AND NEUTRAL AMINO ACID TRANSPORTER), MEMBER 1; SLC3A1
220100CYSTINURIA
604144SOLUTE CARRIER FAMILY 7 (CATIONIC AMINO ACID TRANSPORTER, y+ SYSTEM), MEMBER 9; SLC7A9

Molecular Pathogenesis

Cystinuria is caused by pathogenic variants in SLC3A1 and/or SLC7A9, which encode the two subunits in the cystine transporters located in the small intestine and on the apical membrane of renal tubular epithelial cells [Chillarón et al 1997, Fernández et al 2002]. Normally, cystine is freely filtered by the glomerulus and reabsorbed in the proximal tubule, a process largely dependent on cystine transporters. This transporter is a heterodimeric complex composed of:

  • The amino acid transport subunit encoded by SLC7A9: b(0,+)-type amino acid transporter 1;
  • A glycoprotein encoded by SLC3A1 that is responsible for the proper localization of b(0,+)AT1: amino acid transporter heavy chain SLC3A1 (also called rBAT).

This system facilitates the sodium-independent reabsorption of cystine and dibasic amino acids (including ornithine, arginine, and lysine).

In individuals with cystinuria, this reabsorption is impaired. While ornithine, arginine, and lysine are highly soluble, cystine has poor solubility at physiologic urine pH. As a result, it becomes supersaturated in the urine, leading to crystal precipitation in the renal tubular lumen and ultimately forming kidney stones [Servais et al 2021].

Mechanism of disease causation. Loss of function

Table 8.

Cystinuria: Gene-Specific Laboratory Considerations

Gene 1Special Consideration
SLC3A1 CNVs are common and have to be covered by appropriate analyses.
SLC7A9
1.

Genes from Table 1 in alphabetic order

Table 9.

Pathogenic Variants Referenced in This GeneReview by Gene

Gene 1Reference SequencesDNA Nucleotide Change
(Alias 2)
Predicted Protein ChangeComment [Reference]
SLC3A1 NM_000341​.4
NP_000332​.2
c.808C>Tp.Arg270TerFounder variant in persons of Ashkenazi Jewish ancestry [Zlotogora et al 2018]
NM_000341​.4 c.1136+2T>C
(IVS6+2T>C)
--Founder variant in persons of Mennonite ancestry (Weaverland & Groffdale) [Strauss & Puffenberger 2009]
NM_000341​.4
NP_000332​.2
c.1354C>Tp.Arg452Trp
SLC7A9 NM_014270​.5
NP_055085​.1
c.508G>Ap.Val170MetFounder variant in persons from Israel of Libyan Jewish ancestry [Lotan et al 2007]
c.1166C>Tp.Thr389MetFounder variant in persons of Mennonite ancestry (Weaverland & Groffdale) [Strauss & Puffenberger 2009]

Variants listed in the table have been provided by the authors. GeneReviews staff have not independently verified the classification of variants.

GeneReviews follows the standard naming conventions of the Human Genome Variation Society (varnomen​.hgvs.org). See Quick Reference for an explanation of nomenclature.

1.

Genes from Table 1 in alphabetic order

2.

Variant designation that does not conform to current naming conventions

Chapter Notes

Revision History

  • 20 November 2025 (sw) Review posted live
  • 2 April 2025 (pmf) Original submission

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