A splicing mutation (891+4A-->G) in SLC3A1 leads to exon 4 skipping and causes cystinuria in a Moslem Arab family

Analysis of SLC7A9 gene mutations among Jordanian patients with cystinuria

Background

Cystinuria is known as a heritable disorder affecting the cysteine reabsorption by renal system as well as the reabsorption of dibasic amino acids. The main objectives of the present study were to identify genetic mutations in SLC7A9 gene associated with cystinuria.

Methods

A cross sectional study design was conducted. A total of 28 patients diagnosed with cystinuria were included. Molecular techniques were applied to identify genetic mutations in SLC7A9 gene.

Results

The mean age of study participants was 31.57 ± 2.88 years, and slightly more than two thirds of participants were males. Mutations of SLC 7A9 gene showed that the majority of cases (57.1%) were homogeneous, (7.1%) heterogeneous, and slightly more than one third of patients had no mutations. There was no statistically significant relationship between mutations for the SLC7A9 gene and gender (p = 0.249).

Conclusion

Mutations in the SLC7A9 gene are prevalent and can be used as molecular tools to diagnose cystinuria.

•

Cystinuria is an inherited disorder of dibasic amino acid as cystine transport in kidney.

•

SLC7A9 Cystinuria gene was recently isolated in many cystinuria patient from different racial populations.

•

Mutations in the SLC7A9 gene are prevalent in Jordanian (Arab) populations.

Clinical and molecular characterization of cystinuria in a French cohort: relevance of assessing large-scale rearrangements and splicing variants

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.

Management of Cystinuria

Cystinuria is a monogenic disorder in which there is a transepithelial transport defect of di-basic amino acids, including cystine, ornithine, lysine, and arginine (COLA). This results in diminished reabsorption of these amino acids in both the intestine and renal proximal tubule. This article describes the disorder, reviews the mechanisms of normal COLA renal transport, and summarizes issues related to the disorder, such as the role of mutations, associated diseases, clinical manifestations, therapies, the renal impact, and handling of pediatric patients.

Molecular Genetic Analysis of SLC3A1 and SLC7A9 Genes in Czech and Slovak Cystinuric Patients

Cystinuria is a frequently inherited metabolic disorder in the Czech population (frequency 1/5,600) caused by a defect in the renal transport of cystine and dibasic amino acids (arginine, lysine and ornithine). The disease is characterized by increased urinary excretion of the amino acids and often leads to recurrent nephrolithiasis. Cystinuria is classified into two subtypes (type I and type non-I). Type I is caused predominantly by mutations in the SLC3A1 gene (2p16.3), encoding heavy subunit (rBAT) of the heterodimeric transporter. Cystinuria non-I type is caused by mutations in the SLC7A9 gene (19q13.1). In this study, we present results of molecular genetic analysis of the SLC3A1 and the SLC7A9 genes in 24 unrelated cystinuria families. Individual exons of the SLC3A1 and SLC7A9 genes were analyzed by direct sequencing. We found ten different mutations in the SLC3A1 gene including six novel ones: three missense mutations (G140R), D179Y and R365P), one splice site mutation (1137-2A>G), one deletion (1515_1516delAA), and one nonsense mutation (Q119X). The most frequent mutation, M467T; was detected in 36% of all type I classified alleles. In the SLC7A9 gene we found six mutations including three new ones: one missense mutation (G319R), one insertion (611_612insA) and one deletion (205_206delTG). One patient was compound heterozygote for one SLC3A1 and one SLC7A9 mutation. Our results confirm that cystinuria is a heterogeneous disorder at the molecular level, and contribute to the understanding of the distribution and frequency of mutations causing cystinuria in the Caucasian population.

Molecular basis of autosomal recessive diseases among the Palestinian Arabs

In the review of the literature, 71 different autosomal recessive diseases have been delineated that are relatively frequent among Palestinian Arabs. Among those, in 40 the mutation(s) responsible for the diseases are known. Fourteen of these disorders were caused by a single mutation, while the other 26 were due to multiple mutations. Most of the mutations were found in homozygosity among the affected patients. It is probable that the high frequency of most of the genetic diseases among the Palestinian Arabs is due to a founder effect as the result of the high consanguinity rates in this population. However, in some cases the high frequency was demonstrated to be secondary to the presence of multiple mutations, either allelic or in different genes in a small geographic region. This phenomenon remains unexplained but may be secondary to a selective advantage to the carriers, either specific to the region or to the population.

Function and structure of heterodimeric amino acid transporters

Heterodimeric amino acid transporters are comprised of two subunits, a polytopic membrane protein (light chain) and an associated type II membrane protein (heavy chain). The heavy chain rbAT (related to b(0,+) amino acid transporter) associates with the light chain b(0,+)AT (b(0,+) amino acid transporter) to form the amino acid transport system b(0,+), whereas the homologous heavy chain 4F2hc interacts with several light chains to form system L (with LAT1 and LAT2), system y(+)L (with y(+)LAT1 and y(+)LAT2), system x (with xAT), or system asc (with asc1). The association of light chains with the two heavy chains is not unambiguous. rbAT may interact with LAT2 and y(+)LAT1 and vice versa; 4F2hc may interact with b(0,+)AT when overexpressed. 4F2hc is necessary for trafficking of the light chain to the plasma membrane, whereas the light chains are thought to determine the transport characteristics of the respective heterodimer. In contrast to 4F2hc, mutations in rbAT suggest that rbAT itself takes part in the transport besides serving for the trafficking of the light chain to the cell surface. Heavy and light subunits are linked together by a disulfide bridge. The disulfide bridge, however, is not necessary for the trafficking of rbAT or 4F2 heterodimers to the membrane or for the functioning of the transporter. However, there is experimental evidence that the disulfide bridge in the 4F2hc/LAT1 heterodimer plays a role in the regulation of a cation channel. These results highlight complex interactions between the different subunits of heterodimeric amino acid transporters and suggest that despite high grades of homology, the interactions between rbAT and 4F2hc and their respective partners may be different.

Cystinuria type I: identification of eight new mutations in SLC3A1

BACKGROUND

Cystinuria is a heritable disorder of amino acid transport characterized by the defective transport of cystine and the dibasic amino acids through the brush border epithelial cells of the renal tubule and intestine tract. Three types of cystinuria (I, II, and III) have been described based on the urinary excretion of cystine and dibasic amino acids in obligate heterozygotes. The SLC3A1 gene coding for an amino acid transporter named rBAT is responsible for type I cystinuria, whereas the SLC7A9 gene coding for a subunit (b0,+AT) of rBAT is involved in determining non-type I (types II and III) cystinuria.

METHODS

The SLC3A1 gene sequence was investigated in a sample of seven type I/type I, three type I/non-type I, six type I/untyped, and four untyped unrelated cystinuric patients by RNA single-strand conformation polymorphism (RNA-SSCP).

RESULTS

Eight new point mutations (S168X, 765+1G>T, 766-2A>G, R452Q, Y461X, S547W, L564F, and C673W) and seven previously reported mutations were detected. These new mutations increase the number of mutated alleles so far characterized in SLC3A1 to 62.

CONCLUSIONS

We have found SLC3A1 mutations in 0.739 of the type I chromosomes studied. The relatively high proportion of uncharacterized type I chromosomes suggests either that there may be mutations not yet found in SLC3A1 or that many of the assigned type I chromosomes in mixed type I/non-type I patients may have mutations in SLC7A9. If the hypothesis is excluded in the future, we believe that a third gene may be involved in cystinuria.

Detection of two novel large deletions in SLC3A1 by semi-quantitative fluorescent multiplex PCR

Cystinuria is an autosomal recessive aminoaciduria in which two clinical types have been described (type I and non-type I). Cystinuria type I is caused by mutations in SLC3A1, a gene located in 2p16 coding for an amino acid transporter named rBAT. Using multiplex semi-quantitative fluorescent PCR, we amplified the ten exons of SLC3A1 together with exon 5 of DSCR1 (located on chromosome 21) as a double-dose control gene. We detected two large novel deletions in a Belgian family, one comprising exons 2-10 and another one at exon 10. The method described here can be used to detect a range of deletions from single-base differences in size to entire missing exons, making it useful for scanning genes with a small to medium number of exons.

Cystinuria calls for heteromultimeric amino acid transporters

The proteins rBAT (related to bo,+ amino acid transporter) and 4F2hc (the heavy chain of the surface antigen 4F2) are homologous proteins that induce amino acid transport in Xenopus oocytes. The role of rBAT in amino acid transport is substantiated by the fact that mutations in the gene encoding it cause cystinuria, a heritable disease characterised by high concentrations of cystine in the urine. Structural and functional evidence supports the hypothesis that both rBAT and 4F2hc proteins form part of heterodimeric amino acid transporters. There is new evidence that the functional unit of system y+L amino acid transporter is a disulfide bridge-dependent complex of 4F2hc with a Xenopus oocyte plasma membrane protein.