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Liu D, Zhao Y, Xue X, Hou X, Xu H, Zhao X, Tian Y, Tang W, Guo J, Xu C. Novel compound heterozygous pathogenic variants in the SLC3A1 gene in a Chinese family with cystinuria. BMC Med Genomics 2023; 16:333. [PMID: 38114997 PMCID: PMC10731833 DOI: 10.1186/s12920-023-01767-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 12/05/2023] [Indexed: 12/21/2023] Open
Abstract
BACKGROUND Cystinuria is an autosomal recessive disorder characterized by a cystine transport deficiency in the renal tubules due to mutations in two genes: SLC3A1 and SLC7A9. Cystinuria can be classified into three forms based on the genotype: type A, due to mutations in the SLC3A1 gene; type B, due to mutations in the SLC7A9 gene; and type AB, due to mutations in both genes. METHODS We report a 12-year-old boy from central China with cystine stones. He was from a non-consanguineous family that had no known history of genetic disease. A physical examination showed normal development and neurological behaviors. Whole-exome and Sanger sequencing were used to identify and verify the suspected pathogenic variants. RESULTS The compound heterozygous variants c.898_905del (p.Arg301AlafsTer6) is located in exon5 and c.1898_1899insAT (p.Asp634LeufsTer46) is located in exon10 of SLC3A1 (NM_000341.4) were deemed responsible for type A cystinuria family. The variant c.898_905del was reported in a Japanese patient in 2000, and the variant c.1898_1899insAT is novel. CONCLUSION A novel pathogenic heterozygous variant pair of the SLC3A1 gene was identified in a Chinese boy with type A cystinuria, enriching the mutational spectrum of the SLC3A1 gene. We attempted to find a pattern for the association between the genotype of SLC3A1 variants and the manifestations of cystinuria in patients with different onset ages. Our findings have important implications for genetic counseling and the early clinical diagnosis of cystinuria.
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Affiliation(s)
- Danhua Liu
- The Research and Application Center of Precision Medicine, The Second Affiliated Hospital, Zhengzhou University, Zhengzhou, 450000, China
| | - Yongli Zhao
- Department of Urology, the Second Affiliated Hospital of Zhengzhou University, NO. 2 Jingba Road, Zhengzhou, 450014, China
| | - Xia Xue
- Henan Key Laboratory of Helicobacter Pylori & Microbiota and Gastrointestinal Cancer, Marshall Medical Research Center, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, 450002, China
| | - Xinyue Hou
- Precision Medicine Center, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450000, China
| | - Hongen Xu
- Precision Medicine Center, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450000, China
| | - Xinghua Zhao
- Department of Urology, the Second Affiliated Hospital of Zhengzhou University, NO. 2 Jingba Road, Zhengzhou, 450014, China
| | - Yongan Tian
- Precision Medicine Center, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450000, China
| | - Wenxue Tang
- The Research and Application Center of Precision Medicine, The Second Affiliated Hospital, Zhengzhou University, Zhengzhou, 450000, China
- Precision Medicine Center, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450000, China
- Henan Institute of Medical and Pharmaceutical Sciences, BGI College, Zhengzhou University, Zhengzhou, 450052, China
| | - Jiancheng Guo
- The Research and Application Center of Precision Medicine, The Second Affiliated Hospital, Zhengzhou University, Zhengzhou, 450000, China
- Precision Medicine Center, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450000, China
- Henan Institute of Medical and Pharmaceutical Sciences, BGI College, Zhengzhou University, Zhengzhou, 450052, China
| | - Changbao Xu
- Department of Urology, the Second Affiliated Hospital of Zhengzhou University, NO. 2 Jingba Road, Zhengzhou, 450014, China.
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Gaildrat P, Lebbah S, Tebani A, Sudrié-Arnaud B, Tostivint I, Bollee G, Tubeuf H, Charles T, Bertholet-Thomas A, Goldenberg A, Barbey F, Martins A, Saugier-Veber P, Frébourg T, Knebelmann B, Bekri S. Clinical and molecular characterization of cystinuria in a French cohort: relevance of assessing large-scale rearrangements and splicing variants. Mol Genet Genomic Med 2017; 5:373-389. [PMID: 28717662 PMCID: PMC5511796 DOI: 10.1002/mgg3.294] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2017] [Revised: 03/27/2017] [Accepted: 04/06/2017] [Indexed: 02/04/2023] Open
Abstract
Background Cystinuria is an autosomal recessive disorder of dibasic amino acid transport in the kidney and the intestine leading to increased urinary cystine excretion and nephrolithiasis. Two genes, SLC3A1 and SLC7A9, coding respectively for rBAT and b0,+AT, account for the genetic basis of cystinuria. Methods This study reports the clinical and molecular characterization of a French cohort including 112 cystinuria patients and 25 relatives from 99 families. Molecular screening was performed using sequencing and Quantitative Multiplex PCR of Short Fluorescent Fragments analyses. Functional minigene‐based assays have been used to characterize splicing variants. Results Eighty‐eight pathogenic nucleotide changes were identified in SLC3A1 (63) and SLC7A9 (25) genes, of which 42 were novel. Interestingly, 17% (15/88) and 11% (10/88) of the total number of variants correspond, respectively, to large‐scale rearrangements and splicing mutations. Functional minigene‐based assays were performed for six variants located outside the most conserved sequences of the splice sites; three variants affect splice sites, while three others modify exonic splicing regulatory elements (ESR), in good agreement with a new in silico prediction based on ΔtESRseq values. Conclusion This report expands the spectrum of SLC3A1 and SLC7A9 variants and supports that digenic inheritance is unlikely. Furthermore, it highlights the relevance of assessing large‐scale rearrangements and splicing mutations to fully characterize cystinuria patients at the molecular level.
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Affiliation(s)
- Pascaline Gaildrat
- Inserm U1245UNIROUENNormandie UnivNormandy Centre for Genomic and Personalized MedicineRouenFrance
| | - Said Lebbah
- Department of NephrologyNecker HospitalParisFrance
| | - Abdellah Tebani
- Inserm U1245UNIROUENNormandie UnivNormandy Centre for Genomic and Personalized MedicineRouenFrance.,Department of Metabolic BiochemistryRouen University HospitalRouenFrance
| | | | | | | | - Hélène Tubeuf
- Inserm U1245UNIROUENNormandie UnivNormandy Centre for Genomic and Personalized MedicineRouenFrance.,Interactive BiosoftwareRouenFrance
| | | | | | | | - Frederic Barbey
- Department of TransplantationCHUV Department of PediatricsLausanne University HospitalLausanneSwitzerland
| | - Alexandra Martins
- Inserm U1245UNIROUENNormandie UnivNormandy Centre for Genomic and Personalized MedicineRouenFrance
| | - Pascale Saugier-Veber
- Inserm U1245UNIROUENNormandie UnivNormandy Centre for Genomic and Personalized MedicineRouenFrance.,Department of GeneticsRouen University HospitalRouenFrance
| | - Thierry Frébourg
- Inserm U1245UNIROUENNormandie UnivNormandy Centre for Genomic and Personalized MedicineRouenFrance.,Department of GeneticsRouen University HospitalRouenFrance
| | | | - Soumeya Bekri
- Inserm U1245UNIROUENNormandie UnivNormandy Centre for Genomic and Personalized MedicineRouenFrance.,Department of Metabolic BiochemistryRouen University HospitalRouenFrance
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Abstract
Cystinuria is an aminoaciduria caused by mutations in the genes that encode the two subunits of the amino acid transport system b0,+, responsible for the renal reabsorption of cystine and dibasic amino acids. The clinical symptoms of cystinuria relate to nephrolithiasis, due to the precipitation of cystine in urine. Mutations in SLC3A1, which codes for the heavy subunit rBAT, cause cystinuria type A, whereas mutations in SLC7A9, which encodes the light subunit b0,+AT, cause cystinuria type B. By crossing Slc3a1-/- with Slc7a9-/- mice we generated a type AB cystinuria mouse model to test digenic inheritance of cystinuria. The 9 genotypes obtained have been analyzed at early (2- and 5-months) and late stage (8-months) of the disease. Monitoring the lithiasic phenotype by X-ray, urine amino acid content analysis and protein expression studies have shown that double heterozygous mice (Slc7a9+/-Slc3a1+/-) present lower expression of system b0,+ and higher hyperexcretion of cystine than single heterozygotes (Slc7a9+/-Slc3a1+/+ and Slc7a9+/+Slc3a1+/-) and give rise to lithiasis in 4% of the mice, demonstrating that cystinuria has a digenic inheritance in this mouse model. Moreover in this study it has been demonstrated a genotype/phenotype correlation in type AB cystinuria mouse model providing new insights for further molecular and genetic studies of cystinuria patients.
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Mutation analysis of SLC3A1 and SLC7A9 genes in patients with cystinuria. Urolithiasis 2015; 43:447-53. [PMID: 26123750 DOI: 10.1007/s00240-015-0794-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2014] [Accepted: 06/15/2015] [Indexed: 10/23/2022]
Abstract
Cystinuria is an autosomal inherited disorder of renal reabsorption of cystine, arginine, lysine, and ornithine. Increased urinary excretion of cystine results in the formation of kidney stones. Considering the few studies on the genetic basis of the cystinuria in the Middle East and the population-specific distribution of mutations in the SLC3A1 and SLC7A9 genes, in the present study, mutation analysis of these two genes was performed in a cohort of Iranian patients with cystinuria. Thirty unrelated cystinuria patients were analyzed for four of the most common mutations using ARMS-PCR (M467T, T216M) and RFLP-PCR (G105R, R333W) methods. For negative sample, two exons of both genes, which harbor many mutations, were subject to DNA sequencing. Eight variants were identified including missense, polymorphism, intron variant, and a novel variant. The most frequent mutations were not detected in our patients and only G105R was found. Since the molecular genetic testing results may influence the therapy and prognosis of cystinuria, this paper contributes to understanding of the molecular basis of cystinuria in the Iranian patients.
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