Entry - *300008 - CHLORIDE CHANNEL 5; CLCN5 - OMIM
* 300008

CHLORIDE CHANNEL 5; CLCN5


Alternative titles; symbols

CHLORIDE CHANNEL, VOLTAGE-GATED, K2; CLCK2
CLC5


HGNC Approved Gene Symbol: CLCN5

Cytogenetic location: Xp11.23     Genomic coordinates (GRCh38): X:49,922,596-50,099,230 (from NCBI)


Gene-Phenotype Relationships
Location Phenotype Phenotype
MIM number
Inheritance Phenotype
mapping key
Xp11.23 Dent disease 1 300009 XLR 3
Hypophosphatemic rickets 300554 XLR 3
Nephrolithiasis, type I 310468 XLR 3
Proteinuria, low molecular weight, with hypercalciuric nephrocalcinosis 308990 XLR 3

TEXT

Description

The CLCN5 gene encodes a voltage-gated chloride ion channel that belongs to a distinct branch of the chloride channel (CLC) family, which also includes CLCN3 (600580) and CLCN4 (302910) (Fisher et al., 1995).


Cloning and Expression

By positional cloning of a microdeletion at chromosome Xp11.22 identified in a family with Dent disease (DENT1; 300009), Fisher et al. (1994) isolated a coding sequence from a human kidney cDNA library. Sequence analysis suggested that CLCN5, which they termed CLCK2, encoded a new member of the CLC family of voltage-gated chloride channels. A 9.5-kb mRNA transcript was expressed predominantly in the kidney.

Fisher et al. (1995) described the isolation and characterization of the complete open reading frame of CLCN5, which encodes a deduced 746-amino acid protein with significant homology to all known members of the family of voltage-gated chloride channels.


Gene Structure

Fisher et al. (1995) determined that the CLCN5 gene contains 12 exons and spans 25 to 30 kb of genomic DNA.


Mapping

By positional cloning, Fisher et al. (1994) identified the CLCN5 gene within the minimum candidate region for Dent disease (DENT1; 300009) on Xp11.22.

In the course of high-resolution comparative mapping of the proximal region of the mouse X chromosome, Blair et al. (1995) demonstrated the location of the Clcn5 gene in relation to others.


Biochemical Features

Dutzler et al. (2002) presented the x-ray structures of 2 prokaryotic CLC chloride channels, from Salmonella typhimurium and E. coli, at 3.0 and 3.5 angstroms, respectively. Both structures revealed 2 identical pores, each pore being formed by a separate subunit contained within a homodimeric membrane protein.


Gene Function

Gunther et al. (1998) showed that the CLCN5 gene was expressed in renal proximal tubule cells, which normally endocytose proteins passing the glomerular filter. Expression was highest below the brush border in a region densely packed with endocytotic vesicles, where CLC5 colocalizes with the H(+)-ATPase and with internalized proteins early after uptake. CLCN5 localized to apical intracellular vesicles in intercalated cells of the collecting duct, and colocalized with the proton pump in alpha-intercalated cells. In transfected cells, CLC5 colocalized with endocytosed alpha-2-macroglobulin. Cotransfection with a GTPase-deficient rab5 mutant led to enlarged early endosomes that stained for CLC5. Gunther et al. (1998) suggested that CLC5 may be essential for proximal tubular endocytosis by providing an electrical shunt necessary for the efficient acidification of vesicles in the endocytotic pathway, explaining the proteinuria observed in Dent disease.

Devuyst et al. (1999) raised specific antisera against human CLC5 and identified by immunoblotting an 83-kD band corresponding to CLC5 in human kidney cortex and medulla. Immunohistochemistry revealed CLC5 expression in the epithelial cells lining the proximal tubules and the thick ascending limbs of the Henle loop, and in the intercalated cells of the collecting ducts. Subcellular fractionation studies of human kidney established that CLC5 distribution was most closely associated with that of Rab4, a marker of recycling early endosomes. Confocal microscopy using the proximal tubular cell model of opossum kidney cells, which endogenously express CLC5, revealed that CLC5 colocalized with the albumin-containing endocytic vesicles that form part of the receptor-mediated endocytic pathway. The expression of CLC5 at multiple sites in the kidney explained the proteinuria and hypercalciuria which characterize Dent disease.

As described by Novarino et al. (2010), CLC5 is a 2-chloride (Cl-)/proton (H+) exchanger rather than a chloride channel (see Picollo and Pusch, 2005, Scheel et al., 2005, and Zifarelli and Pusch, 2009).


Molecular Genetics

Lloyd et al. (1996) identified 11 mutations in the CLCN5 gene in affected members of 8 kindreds with Dent disease-1 (300009) (see, e.g., 300008.0001-300008.0004), 2 families with X-linked recessive nephrolithiasis (XRN; 310468; 300008.0005-300008.0006), and 1 family with X-linked recessive hypophosphatemic rickets (300554; 300008.0007). All 4 missense mutations were confined to the predicted transmembrane domains. In vitro functional expression studies showed that the mutations markedly reduced or abolished outwardly rectifying chloride currents.

In affected members from 4 unrelated Japanese kindreds with low molecular weight proteinuria (308990), Lloyd et al. (1997) identified 4 different mutations in the CLCN5 gene (300008.0001; 300008.0008-300008.0010). Nakazato et al. (1997) identified mutations in the CLCN5 gene in affected members of 2 Japanese families with low molecular weight proteinuria. Akuta et al. (1997) identified mutations in the CLCN5 gene in 7 of 10 unrelated Japanese patients with low molecular weight proteinuria, hypercalciuria, and nephrocalcinosis. They estimated that over 70% of Japanese patients with the disorder have mutations in the CLCN5 gene.

In 8 unrelated patients with Dent disease, Cox et al. (1999) found 3 nonsense mutations, 4 deletions of single codons, and 1 acceptor splice consensus sequence mutation in the CLCN5 gene. None of these mutations was found in a study of unrelated normal individuals. All of the mutations predicted truncated chloride channels that were likely to result in a functional loss.

After heterologous expression of various mutant CLCN5 cDNAs in Xenopus oocytes, Ludwig et al. (2005) observed that except for the R516W and R648X (300008.0002) variants, none of the mutated proteins induced functional chloride currents or reached the plasma membrane. The tested missense mutations were distributed over different transmembrane regions, implying that correct channel structure and orientation in the membrane is not only a prerequisite for proper CLCN5 function but also for Golgi exit. The R648X mutant, although functionally compromised (30% of wildtype current), displayed a significant increase in surface expression.

Tosetto et al. (2009) identified mutations in the CLCN5 gene, including 15 novel mutations (see, e.g., 300008.0014), in 16 (53%) of 30 mostly Italian patients with a clinical suspicion of Dent disease. Most of the missense mutations were predicted to occur in the helix regions involved in the CLCN5 dimer interface.


Animal Model

Piwon et al. (2000) created a mouse model of Dent disease by targeted disruption of the Clcn5 gene. Clcn5 -/- mice had proteinuria due to strong reduction of apical proximal tubular endocytosis. Both receptor-mediated and fluid-phase endocytosis were affected, and the internalization of the apical transporters NaPi2 and Nhe3 (182307) was slowed. At steady state, however, both proteins were redistributed from the plasma membrane to intracellular vesicles. Piwon et al. (2000) postulated that this may have been caused by an increased stimulation of luminal parathyroid hormone (PTH; 168450) receptors (see 168468) owing to the observed decreased tubular endocytosis of PTH. The rise in luminal PTH concentration should also have stimulated the hydroxylation of 25-hydroxyvitamin D3 to the active hormone. However, this would be counteracted by a urinary loss of the precursor 25-hydroxyvitamin D3. The balance between these opposing effects, both of which are secondary to the defect in proximal tubular endocytosis, probably determined whether there would be hypercalciuria and kidney stones. Piwon et al. (2000) showed that CLC5 is crucial for efficient endocytosis in the proximal tubule. CLC5 was the first intracellular chloride channel for which a role in vesicle trafficking was established. Piwon et al. (2000) argued that their mouse model strongly suggested that alterations in hormones involved in calcium homeostasis, and hyperphosphaturia and hypocalciuria, are indirect effects of defective apical endocytosis of PTH and 25-hydroxyvitamin D3; this may explain how a defect in a chloride channel could lead to kidney stones.

In Xenopus oocytes, Schwake et al. (2001) found that mutations introduced into the C-terminal internalization PY motif of the Clcn5 gene increased surface expression and currents of the channel by about 2-fold. Further studies with the wildtype and mutant ubiquitin-protein ligase WWP2 (602308) and Rab5 (179512) indicated that the prolonged surface expression of PY-mutant Clcn5 resulted from changes in cellular trafficking of the channel, and that endocytosis of Clcn5 depended on the interaction of the internalization signal with these other endocytic proteins.

Christensen et al. (2003) tested whether the endocytic failure that results from loss of the CLCN5 channel in Dent disease and knockout mice primarily reflects a loss of reabsorption by the multiligand receptors megalin (600073) and cubilin (602997) caused by a trafficking defect. Impaired protein endocytosis in kidney proximal tubule cells of Clcn5 knockout mice was demonstrated by a major decreased uptake of (125)I-labeled beta-2-microglobulin (109700), but not of the fluid-phase tracer FITC-dextran; reduced labeling of endosomes by injected peroxidase and reduced labeling for the endogenous megalin/cubilin ligands vitamin D- and retinol-binding proteins; and urinary appearance of low molecular mass proteins and the selective cubilin ligand transferrin (190000). An overall decrease of megalin and cubilin in proximal tubule cells and their selective loss at the brush border was demonstrated. In contrast, total contents of the rate-limiting endocytic catalysts Rab5a and Rab7 (602298) were unaffected. Thus, impaired protein endocytosis caused by invalidation of Clcn5 primarily reflects a trafficking defect of megalin and cubilin in proximal tubule cells.

Novarino et al. (2010) generated mice that carry the uncoupling E211A mutation that converts ClC5 into a pure chloride conductor. ATP-dependent acidification of renal endosomes was reduced in mice in which ClC5 was knocked out, but normal in mice carrying the E211A mutation. However, their proximal tubular endocytosis was also impaired. Novarino et al. (2010) concluded that endosomal chloride concentration, which is raised by ClC5 in exchange for protons accumulated by the proton ATPase, may play a role in endocytosis.

Alex et al. (2010) showed that loss of Clcn5 in mice exacerbated dextran sodium sulfate (DSS)-induced ulcerative colitis (266600), as measured by disease and histologic activity indices and myeloperoxidase (MPO; 606989) activity. Multiplex serum cytokine analysis, as well as immunofluorescence and Western blot analyses of colonic mucosa, demonstrated a heightened Th1/Th17 profile with increased systemic and local expression of Tnfa (191160), Il6 (147620), and Il17 (603149) in Clcn5 -/- mice with DSS-induced ulcerative colitis. Baseline Il6 and phospho-Ikb (NFKBIA; 164008) were high in Clcn5 -/- mice. Colitis in Clcn5 -/- mice could be attenuated by a high vitamin D diet. Alex et al. (2010) concluded that CLCN5 is involved in the immunopathogenesis of ulcerative colitis.


ALLELIC VARIANTS ( 14 Selected Examples):

.0001 DENT DISEASE 1

PROTEINURIA, LOW MOLECULAR WEIGHT, WITH HYPERCALCIURIA AND NEPHROCALCINOSIS, INCLUDED
CLCN5, TRP279TER
  
RCV000012563...

In affected members of a family with Dent disease (DENT1; 300009), Lloyd et al. (1996) identified a G-to-A transition in the CLCN5 gene, resulting in a trp279-to-ter (W279X) substitution. The mutation was predicted to result in a loss of 469 amino acids from the D6 region to the C terminus.

Lloyd et al. (1997) identified the W279X mutation in affected members of a Japanese family with idiopathic low molecular weight proteinuria associated with hypercalciuric nephrocalcinosis (308990).


.0002 DENT DISEASE 1

CLCN5, ARG648TER
  
RCV000012565...

In affected members of a family with Dent disease (DENT1; 300009), Lloyd et al. (1996) identified a C-to-T transition in the CLCN5 gene, resulting in an arg648-to-ter (R648X) substitution. The mutation was predicted to result in a loss of 100 amino acids from the cytoplasmic C terminus of the protein, deleting domain D13, which is conserved in all eukaryotic chloride channel proteins.

Lloyd et al. (1997) identified the R648X mutation in another family with Dent disease.


.0003 DENT DISEASE 1

CLCN5, LEU200ARG
  
RCV000012566

In affected members of a family with Dent disease (DENT1; 300009), Lloyd et al. (1996) identified a T-to-G transversion in the CLCN5 gene, resulting in a leu200-to-arg (L200R) substitution. The mutation was predicted to disrupt the charge distribution within domain D3 of the protein.


.0004 DENT DISEASE 1

CLCN5, SER520PRO
  
RCV000012567

In affected members of a family with Dent disease (DENT1; 300009), Lloyd et al. (1996) identified a T-to-C transition in the CLCN5 gene, resulting in a ser520-to-pro (S520P) substitution. The mutation was predicted to disrupt a helix in D11.


.0005 NEPHROLITHIASIS, X-LINKED RECESSIVE

CLCN5, ARG704TER
  
RCV001004890...

In affected members of a family with X-linked recessive nephrolithiasis (XRN; 310468), Lloyd et al. (1996) identified a C-to-T transition in the CLCN5 gene, resulting in an arg704-to-ter (R704X) substitution. The mutation was predicted to result in a loss of 42 amino acids from the cytoplasmic C terminus of the protein, deleting domain D13, which is conserved in all eukaryotic chloride channel proteins.


.0006 NEPHROLITHIASIS, X-LINKED RECESSIVE

CLCN5, GLY506GLU
  
RCV002266901...

In affected members of a family with X-linked recessive nephrolithiasis, Lloyd et al. (1996) identified a G-to-A transition in the CLCN5 gene, resulting in a gly506-to-glu (G506E) substitution. The mutation was predicted to disrupt a charge within domain D11.


.0007 HYPOPHOSPHATEMIC RICKETS, X-LINKED RECESSIVE

CLCN5, SER244LEU
  
RCV000012570...

In affected members of an Italian family with X-linked recessive hypophosphatemic rickets (300554) reported by Bolino et al. (1993), Lloyd et al. (1996) identified a C-to-T transition in the CLCN5 gene, resulting in a ser244-to-leu (S244L) substitution. The mutation was predicted to disrupt a helix in D5. Functional expression studies showed that the mutant S244L channel had reduced, but not abolished, chloride conductance.

Oudet et al. (1997) reported a second family with the S244L mutation but with a milder phenotype than that in the family reported by Lloyd et al. (1996). The family reported by Oudet et al. (1997) had neither nephrocalcinosis nor nephrolithiasis. However, the affected individuals were significantly younger than those of the family reported by Lloyd et al. (1996).


.0008 PROTEINURIA, LOW MOLECULAR WEIGHT, WITH HYPERCALCIURIA AND NEPHROCALCINOSIS

CLCN5, TRP343TER
  
RCV000012571

In affected members of a Japanese family with low molecular weight proteinuria associated with hypercalciuria and nephrocalcinosis (308990), Lloyd et al. (1997) identified a G-to-A transition in the CLCN5 gene, resulting in a trp343-to-ter (W343X) substitution.


.0009 PROTEINURIA, LOW MOLECULAR WEIGHT, WITH HYPERCALCIURIA AND NEPHROCALCINOSIS

CLCN5, 1-BP DEL, 2085C
  
RCV000012572

In affected members of a Japanese family with idiopathic low molecular weight proteinuria associated with hypercalciuric nephrocalcinosis (308990), Lloyd et al. (1997) identified a 1-bp deletion (2085delC) in the CLCN5 gene, resulting in a frameshift and premature termination of the protein at codon 699.


.0010 PROTEINURIA, LOW MOLECULAR WEIGHT, WITH HYPERCALCIURIA AND NEPHROCALCINOSIS

CLCN5, ARG280PRO
  
RCV000012573

In affected members of a Japanese family with idiopathic low molecular weight proteinuria associated with hypercalciuric nephrocalcinosis (308990), Lloyd et al. (1997) identified an arg280-to-pro (R280P) mutation in the CLCN5 gene. Heterologous expression of this mutation in Xenopus oocytes demonstrated a 70% reduction in channel activity when compared with the wildtype.


.0011 NEPHROLITHIASIS, X-LINKED RECESSIVE

CLCN5, GLY57VAL
  
RCV002468923

In 2 half-brothers, born of the same mother, with X-linked recessive nephrolithiasis (XRN; 310468), Schurman et al. (1998) identified a mutation in the CLCN5 gene, resulting in a gly57-to-val (G57V) substitution. The boys had been referred because of microhematuria and proteinuria noted on screening urinalysis. Family history showed renal failure after recurrent nephrolithiasis in a maternal grandfather and male cousin, and recurrent nephrolithiasis in an older brother.


.0012 DENT DISEASE 1

CLCN5, ALU INS, EX11
   RCV000012575

Claverie-Martin et al. (2003) studied a Spanish patient with Dent disease (DENT1; 300009) and found, by PCR amplification of the CLCN5 exons, an abnormally large exon 11. Sequence analysis showed an insertion in codon 650 of a 345-bp Alu element that had arisen de novo on the maternal chromosome. Polymorphism analysis indicated that the insertion occurred in the germline of the maternal grandfather. The presence of a long poly(A) tract and evidence for a 16-bp target-site duplication implied that the Alu element was integrated by retrotransposition. The mutation predicted a truncated CLC5 protein.

Claverie-Martin et al. (2005) reported further studies of the Alu insertion in the family previously reported by Claverie-Martin et al. (2003). PCR amplification of blood DNA showed that the Alu insertion resulted in aberrant splicing of the CLCN5 pre-mRNA and skipping of exon 11. The resultant truncated protein lacks part of the C terminus, including the PY and CBS2 domains, which are critical for sorting and chloride channel function. In addition, there were 2 conserved exonic splicing enhancer sequences in the site of insertion.


.0013 DENT DISEASE 1

CLCN5, GLY260VAL
  
RCV000012576

Tosetto et al. (2006) identified a 1070G-T transversion in exon 7 of the CLCN5 gene, resulting in a gly260-to-val (G260V) substitution, in 1 of 25 men from northern Italy with end-stage renal disease and renal stones. The findings were consistent with Dent disease (DENT1; 300009). Examination of the family identified the G260V mutation in 2 additional young male relatives. Both had mild proteinuria, and one also had hypercalciuria.


.0014 DENT DISEASE 1

CLCN5, IVS8DS, G-T, +1
  
RCV000012577

In a patient with Dent disease (DENT1; 300009), Tosetto et al. (2009) identified a G-to-T transversion in intron 8 of the CLCN5, resulting in a splice site mutation and generation of an mRNA transcript lacking part of exon 8, which was confirmed by RT-PCR analysis. The mutation truncated the protein at codon 361.


REFERENCES

  1. Akuta, N., Lloyd, S. E., Igarashi, T., Shiraga, H., Matsuyama, T., Yokoro, S., Cox, J. P. D., Thakker, R. V. Mutations of CLCN5 in Japanese children with idiopathic low molecular weight proteinuria, hypercalciuria and nephrocalcinosis. Kidney Int. 52: 911-916, 1997. [PubMed: 9328929, related citations] [Full Text]

  2. Alex, P., Ye, M., Zachos, N. C., Sipes, J., Nguyen, T., Suhodrev, M., Gonzales, L., Arora, Z., Zhang, T., Centola, M., Guggino, S. E., Li, X. Clcn5 knockout mice exhibit novel immunomodulatory effects and are more susceptible to dextran sulfate sodium-induced colitis. J. Immun. 184: 3988-3996, 2010. [PubMed: 20181886, images, related citations] [Full Text]

  3. Blair, H. J., Ho, M., Monaco, A. P., Fisher, S., Craig, I. W., Boyd, Y. High-resolution comparative mapping of the proximal region of the mouse X chromosome. Genomics 28: 305-310, 1995. [PubMed: 8530041, related citations] [Full Text]

  4. Bolino, A., Devoto, M., Enia, G., Zoccali, C., Weissenbach, J., Romeo, G. Genetic mapping in the Xp11.2 region of a new form of X-linked hypophosphatemic rickets. Europ. J. Hum. Genet. 1: 269-279, 1993. [PubMed: 7915957, related citations] [Full Text]

  5. Christensen, E. I., Devuyst, O., Dom, G., Nielsen, R., Van Der Smissen, P., Verroust, P., Leruth, M., Guggino, W. B., Courtoy, P. J. Loss of chloride channel ClC-5 impairs endocytosis by defective trafficking of megalin and cubilin in kidney proximal tubules. Proc. Nat. Acad. Sci. 100: 8472-8477, 2003. [PubMed: 12815097, images, related citations] [Full Text]

  6. Claverie-Martin, F., Flores, C., Anton-Gamero, M., Gonzalez-Acosta, H., Garcia-Nieto, V. The Alu insertion in the CLCN5 gene of a patient with Dent's disease leads to exon 11 skipping. J. Hum. Genet. 50: 370-374, 2005. [PubMed: 16041495, related citations] [Full Text]

  7. Claverie-Martin, F., Gonzalez-Acosta, H., Flores, C., Anton-Gamero, M., Garcia-Nieto, V. De novo insertion of an Alu sequence in the coding region of the CLCN5 gene results in Dent's disease. Hum. Genet. 113: 480-485, 2003. [PubMed: 14569459, related citations] [Full Text]

  8. Cox, J. P. D., Yamamoto, K., Christie, P. T., Wooding, C., Feest, T., Flinter, F. A., Goodyer, P. R., Leumann, E., Neuhaus, T., Reid, C., Williams, P. F., Wrong, O., Thakker, R. V. Renal chloride channel, CLCN5, mutations in Dent's disease. J. Bone Miner. Res. 14: 1536-1542, 1999. [PubMed: 10469281, related citations] [Full Text]

  9. Devuyst, O., Christie, P. T., Courtoy, P. J., Beauwens, R., Thakker, R. V. Intra-renal and subcellular distribution of the human chloride channel, CLC-5, reveals a pathophysiological basis for Dent's disease. Hum. Molec. Genet. 8: 247-257, 1999. [PubMed: 9931332, related citations] [Full Text]

  10. Dutzler, R., Campbell, E. B., Cadene, M., Chait, B. T., MacKinnon, R. X-ray structure of a ClC chloride channel at 3.0 angstrom reveals the molecular basis of anion selectivity. Nature 415: 287-294, 2002. [PubMed: 11796999, related citations] [Full Text]

  11. Fisher, S. E., Black, G. C. M., Lloyd, S. E., Hatchwell, E., Wrong, O., Thakker, R. V., Craig, I. W. Isolation and partial characterization of a chloride channel gene which is expressed in kidney and is a candidate for Dent's disease (an X-linked hereditary nephrolithiasis). Hum. Molec. Genet. 3: 2053-2059, 1994. [PubMed: 7874126, related citations]

  12. Fisher, S. E., Van Bakel, I., Lloyd, S. E., Pearce, S. H. S., Thakker, R. V., Craig, I. W. Cloning and characterization of CLCN5, the human kidney chloride channel gene implicated in Dent disease (an X-linked hereditary nephrolithiasis). Genomics 29: 598-606, 1995. [PubMed: 8575751, related citations] [Full Text]

  13. Gunther, W., Luchow, A., Cluzeaud, F., Vandewalle, A., Jentsch, T. J. ClC-5, the chloride channel mutated in Dent's disease, colocalizes with the proton pump in endocytotically active kidney cells. Proc. Nat. Acad. Sci. 95: 8075-8080, 1998. [PubMed: 9653142, images, related citations] [Full Text]

  14. Lloyd, S. E., Gunther, W., Pearce, S. H. S., Thomson, A., Bianchi, M. L., Bosio, M., Craig, I. W., Fisher, S. E., Scheinman, S. J., Wrong, O., Jentsch, T. J., Thakker, R. V. Characterisation of renal chloride channel, CLCN5, mutations in hypercalciuric nephrolithiasis (kidney stones) disorders. Hum. Molec. Genet. 6: 1233-1239, 1997. [PubMed: 9259268, related citations] [Full Text]

  15. Lloyd, S. E., Pearce, S. H. S., Fisher, S. E., Steinmeyer, K., Schwappach, B., Scheinman, S. J., Harding, B., Bolino, A., Devoto, M., Goodyer, P., Rigden, S. P. A., Wrong, O., Jentsch, T. J., Craig, I. W., Thakker, R. V. A common molecular basis for three inherited kidney stone diseases. Nature 379: 445-449, 1996. [PubMed: 8559248, related citations] [Full Text]

  16. Lloyd, S. E., Pearce, S. H. S., Gunther, W., Kawaguchi, H., Igarashi, T., Jentsch, T. J., Thakker, R. V. Idiopathic low molecular weight proteinuria associated with hypercalciuric nephrocalcinosis in Japanese children is due to mutations of the renal chloride channel (CLCN5). J. Clin. Invest. 99: 967-974, 1997. [PubMed: 9062355, related citations] [Full Text]

  17. Ludwig, M., Doroszewicz, J., Seyberth, H. W., Bokenkamp, A., Balluch, B., Nuutinen, M., Utsch, B., Waldegger, S. Functional evaluation of Dent's disease-causing mutations: implications for ClC-5 channel trafficking and internalization. Hum. Genet. 117: 228-237, 2005. [PubMed: 15895257, related citations] [Full Text]

  18. Nakazato, H., Hattori, S., Furuse, A., Kawano, T., Karashima, S., Tsuruta, M., Yoshimuta, J., Endo, F., Matsuda, I. Mutations in the CLCN5 gene in Japanese patients with familial idiopathic low-molecular-weight proteinuria. Kidney Int. 52: 895-900, 1997. [PubMed: 9328927, related citations] [Full Text]

  19. Novarino, G., Weinert, S., Rickheit, G., Jentsch, T. J. Endosomal chloride-proton exchange rather than chloride conductance is crucial for renal endocytosis. Science 328: 1398-1401, 2010. [PubMed: 20430975, related citations] [Full Text]

  20. Oudet, C., Martin-Coignard, D., Pannetier, S., Praud, E., Champion, G., Hanauer, A. A second family with XLRH displays the mutation S244L in the CLCN5 gene. Hum. Genet. 99: 781-784, 1997. [PubMed: 9187673, related citations] [Full Text]

  21. Picollo, A., Pusch, M. Chloride/proton antiporter activity of mammalian CLC proteins ClC-4 and ClC-5. Nature 436: 420-423, 2005. [PubMed: 16034421, related citations] [Full Text]

  22. Piwon, N., Gunther, W., Schwake, M., Bosl, M. R., Jentsch, T. J. ClC-5 Cl(-)-channel disruption impairs endocytosis in a mouse model for Dent's disease. Nature 408: 369-373, 2000. [PubMed: 11099045, related citations] [Full Text]

  23. Scheel, O., Zdebik, A. A., Lourdel, S., Jentsch, T. J. Voltage-dependent electrogenic chloride/proton exchange by endosomal CLC proteins. Nature 436: 424-427, 2005. [PubMed: 16034422, related citations] [Full Text]

  24. Schurman, S. J., Norden, A. G. W., Scheinman, S. J. X-linked recessive nephrolithiasis: presentation and diagnosis in children. J. Pediat. 132: 859-862, 1998. [PubMed: 9602200, related citations] [Full Text]

  25. Schwake, M., Friedrich, T., Jentsch, T. J. An internalization signal in ClC-5, an endosomal Cl- channel mutated in Dent's disease. J. Biol. Chem. 276: 12049-12054, 2001. [PubMed: 11116157, related citations] [Full Text]

  26. Tosetto, E., Ceol, M,, Mezzabotta, F., Ammenti, A., Peruzzi, L., Caruso, M. R., Barbano, G., Vezzoli, G., Colussi, G., Vergine, G., Giordano, M., Glorioso, N., Degortes, S., Soldati, L., Sayer, J., D'Angelo, A., Anglani, F. Novel mutations of the CLCN5 gene including a complex allele and a 5-prime UTR mutation in Dent disease 1. (Letter) Clin. Genet. 76: 413-416, 2009. [PubMed: 19673950, related citations] [Full Text]

  27. Tosetto, E., Graziotto, R., Artifoni, L., Nachtigal, J., Cascone, C., Conz, P., Piva, M., Dell'Aquila, R., De Paoli Vitali, E., Citron, L., Nalesso, F., Antonello, A., Vertolli, U., Zagatti, R., Lupo, A., D'Angelo, A., Anglani, F., Gambaro, G. Dent's disease and prevalence of renal stones in dialysis patients in Northeastern Italy. J. Hum. Genet. 51: 25-30, 2006. [PubMed: 16247550, related citations] [Full Text]

  28. Zifarelli, G., Pusch, G. Conversion of the 2 Cl-/1 H+ antiporter ClC-5 in a NO(3)-/H+ antiporter by a single point mutation. EMBO J. 28: 175-182, 2009. [PubMed: 19131966, images, related citations] [Full Text]


Cassandra L. Kniffin - updated : 12/3/2010
Paul J. Converse - updated : 10/26/2010
Ada Hamosh - updated : 6/30/2010
Cassandra L. Kniffin - updated : 11/17/2008
Cassandra L. Kniffin - updated : 3/1/2006
Cassandra L. Kniffin - updated : 11/8/2005
Cassandra L. Kniffin - updated : 10/13/2005
Cassandra L. Kniffin - reorganized : 9/19/2005
Marla J. F. O'Neill - updated : 7/21/2005
Victor A. McKusick - updated : 11/24/2003
Victor A. McKusick - updated : 8/28/2003
Ada Hamosh - updated : 1/17/2002
Ada Hamosh - updated : 11/14/2000
Victor A. McKusick - updated : 11/9/1999
Ada Hamosh - updated : 4/8/1999
Victor A. McKusick - updated : 9/4/1998
Michael J. Wright - updated : 8/25/1997
Victor A. McKusick - updated : 8/22/1997
Victor A. McKusick - updated : 5/9/1997
Creation Date:
Victor A. McKusick : 1/31/1996
carol : 06/22/2021
joanna : 02/20/2015
wwang : 12/7/2010
ckniffin : 12/3/2010
mgross : 10/27/2010
terry : 10/26/2010
alopez : 7/1/2010
terry : 6/30/2010
wwang : 11/24/2008
ckniffin : 11/17/2008
wwang : 3/7/2006
ckniffin : 3/1/2006
wwang : 11/17/2005
ckniffin : 11/8/2005
wwang : 10/24/2005
ckniffin : 10/13/2005
carol : 9/19/2005
carol : 9/19/2005
ckniffin : 9/7/2005
ckniffin : 9/1/2005
wwang : 7/22/2005
terry : 7/21/2005
terry : 4/21/2005
terry : 6/2/2004
alopez : 11/25/2003
terry : 11/24/2003
tkritzer : 8/28/2003
alopez : 1/22/2002
terry : 1/17/2002
mgross : 11/15/2000
terry : 11/14/2000
carol : 11/16/1999
terry : 11/9/1999
carol : 7/28/1999
kayiaros : 7/13/1999
carol : 5/24/1999
alopez : 4/8/1999
carol : 9/14/1998
terry : 9/4/1998
terry : 6/15/1998
dholmes : 6/10/1998
terry : 6/4/1998
terry : 11/20/1997
terry : 9/4/1997
terry : 8/25/1997
terry : 8/25/1997
terry : 8/25/1997
terry : 8/25/1997
terry : 8/22/1997
terry : 8/11/1997
terry : 8/11/1997
alopez : 6/27/1997
alopez : 5/9/1997
alopez : 5/9/1997
alopez : 5/7/1997
joanna : 2/1/1996
mark : 1/31/1996

* 300008

CHLORIDE CHANNEL 5; CLCN5


Alternative titles; symbols

CHLORIDE CHANNEL, VOLTAGE-GATED, K2; CLCK2
CLC5


HGNC Approved Gene Symbol: CLCN5

SNOMEDCT: 444645005, 717789008;  


Cytogenetic location: Xp11.23     Genomic coordinates (GRCh38): X:49,922,596-50,099,230 (from NCBI)


Gene-Phenotype Relationships

Location Phenotype Phenotype
MIM number
Inheritance Phenotype
mapping key
Xp11.23 Dent disease 1 300009 X-linked recessive 3
Hypophosphatemic rickets 300554 X-linked recessive 3
Nephrolithiasis, type I 310468 X-linked recessive 3
Proteinuria, low molecular weight, with hypercalciuric nephrocalcinosis 308990 X-linked recessive 3

TEXT

Description

The CLCN5 gene encodes a voltage-gated chloride ion channel that belongs to a distinct branch of the chloride channel (CLC) family, which also includes CLCN3 (600580) and CLCN4 (302910) (Fisher et al., 1995).


Cloning and Expression

By positional cloning of a microdeletion at chromosome Xp11.22 identified in a family with Dent disease (DENT1; 300009), Fisher et al. (1994) isolated a coding sequence from a human kidney cDNA library. Sequence analysis suggested that CLCN5, which they termed CLCK2, encoded a new member of the CLC family of voltage-gated chloride channels. A 9.5-kb mRNA transcript was expressed predominantly in the kidney.

Fisher et al. (1995) described the isolation and characterization of the complete open reading frame of CLCN5, which encodes a deduced 746-amino acid protein with significant homology to all known members of the family of voltage-gated chloride channels.


Gene Structure

Fisher et al. (1995) determined that the CLCN5 gene contains 12 exons and spans 25 to 30 kb of genomic DNA.


Mapping

By positional cloning, Fisher et al. (1994) identified the CLCN5 gene within the minimum candidate region for Dent disease (DENT1; 300009) on Xp11.22.

In the course of high-resolution comparative mapping of the proximal region of the mouse X chromosome, Blair et al. (1995) demonstrated the location of the Clcn5 gene in relation to others.


Biochemical Features

Dutzler et al. (2002) presented the x-ray structures of 2 prokaryotic CLC chloride channels, from Salmonella typhimurium and E. coli, at 3.0 and 3.5 angstroms, respectively. Both structures revealed 2 identical pores, each pore being formed by a separate subunit contained within a homodimeric membrane protein.


Gene Function

Gunther et al. (1998) showed that the CLCN5 gene was expressed in renal proximal tubule cells, which normally endocytose proteins passing the glomerular filter. Expression was highest below the brush border in a region densely packed with endocytotic vesicles, where CLC5 colocalizes with the H(+)-ATPase and with internalized proteins early after uptake. CLCN5 localized to apical intracellular vesicles in intercalated cells of the collecting duct, and colocalized with the proton pump in alpha-intercalated cells. In transfected cells, CLC5 colocalized with endocytosed alpha-2-macroglobulin. Cotransfection with a GTPase-deficient rab5 mutant led to enlarged early endosomes that stained for CLC5. Gunther et al. (1998) suggested that CLC5 may be essential for proximal tubular endocytosis by providing an electrical shunt necessary for the efficient acidification of vesicles in the endocytotic pathway, explaining the proteinuria observed in Dent disease.

Devuyst et al. (1999) raised specific antisera against human CLC5 and identified by immunoblotting an 83-kD band corresponding to CLC5 in human kidney cortex and medulla. Immunohistochemistry revealed CLC5 expression in the epithelial cells lining the proximal tubules and the thick ascending limbs of the Henle loop, and in the intercalated cells of the collecting ducts. Subcellular fractionation studies of human kidney established that CLC5 distribution was most closely associated with that of Rab4, a marker of recycling early endosomes. Confocal microscopy using the proximal tubular cell model of opossum kidney cells, which endogenously express CLC5, revealed that CLC5 colocalized with the albumin-containing endocytic vesicles that form part of the receptor-mediated endocytic pathway. The expression of CLC5 at multiple sites in the kidney explained the proteinuria and hypercalciuria which characterize Dent disease.

As described by Novarino et al. (2010), CLC5 is a 2-chloride (Cl-)/proton (H+) exchanger rather than a chloride channel (see Picollo and Pusch, 2005, Scheel et al., 2005, and Zifarelli and Pusch, 2009).


Molecular Genetics

Lloyd et al. (1996) identified 11 mutations in the CLCN5 gene in affected members of 8 kindreds with Dent disease-1 (300009) (see, e.g., 300008.0001-300008.0004), 2 families with X-linked recessive nephrolithiasis (XRN; 310468; 300008.0005-300008.0006), and 1 family with X-linked recessive hypophosphatemic rickets (300554; 300008.0007). All 4 missense mutations were confined to the predicted transmembrane domains. In vitro functional expression studies showed that the mutations markedly reduced or abolished outwardly rectifying chloride currents.

In affected members from 4 unrelated Japanese kindreds with low molecular weight proteinuria (308990), Lloyd et al. (1997) identified 4 different mutations in the CLCN5 gene (300008.0001; 300008.0008-300008.0010). Nakazato et al. (1997) identified mutations in the CLCN5 gene in affected members of 2 Japanese families with low molecular weight proteinuria. Akuta et al. (1997) identified mutations in the CLCN5 gene in 7 of 10 unrelated Japanese patients with low molecular weight proteinuria, hypercalciuria, and nephrocalcinosis. They estimated that over 70% of Japanese patients with the disorder have mutations in the CLCN5 gene.

In 8 unrelated patients with Dent disease, Cox et al. (1999) found 3 nonsense mutations, 4 deletions of single codons, and 1 acceptor splice consensus sequence mutation in the CLCN5 gene. None of these mutations was found in a study of unrelated normal individuals. All of the mutations predicted truncated chloride channels that were likely to result in a functional loss.

After heterologous expression of various mutant CLCN5 cDNAs in Xenopus oocytes, Ludwig et al. (2005) observed that except for the R516W and R648X (300008.0002) variants, none of the mutated proteins induced functional chloride currents or reached the plasma membrane. The tested missense mutations were distributed over different transmembrane regions, implying that correct channel structure and orientation in the membrane is not only a prerequisite for proper CLCN5 function but also for Golgi exit. The R648X mutant, although functionally compromised (30% of wildtype current), displayed a significant increase in surface expression.

Tosetto et al. (2009) identified mutations in the CLCN5 gene, including 15 novel mutations (see, e.g., 300008.0014), in 16 (53%) of 30 mostly Italian patients with a clinical suspicion of Dent disease. Most of the missense mutations were predicted to occur in the helix regions involved in the CLCN5 dimer interface.


Animal Model

Piwon et al. (2000) created a mouse model of Dent disease by targeted disruption of the Clcn5 gene. Clcn5 -/- mice had proteinuria due to strong reduction of apical proximal tubular endocytosis. Both receptor-mediated and fluid-phase endocytosis were affected, and the internalization of the apical transporters NaPi2 and Nhe3 (182307) was slowed. At steady state, however, both proteins were redistributed from the plasma membrane to intracellular vesicles. Piwon et al. (2000) postulated that this may have been caused by an increased stimulation of luminal parathyroid hormone (PTH; 168450) receptors (see 168468) owing to the observed decreased tubular endocytosis of PTH. The rise in luminal PTH concentration should also have stimulated the hydroxylation of 25-hydroxyvitamin D3 to the active hormone. However, this would be counteracted by a urinary loss of the precursor 25-hydroxyvitamin D3. The balance between these opposing effects, both of which are secondary to the defect in proximal tubular endocytosis, probably determined whether there would be hypercalciuria and kidney stones. Piwon et al. (2000) showed that CLC5 is crucial for efficient endocytosis in the proximal tubule. CLC5 was the first intracellular chloride channel for which a role in vesicle trafficking was established. Piwon et al. (2000) argued that their mouse model strongly suggested that alterations in hormones involved in calcium homeostasis, and hyperphosphaturia and hypocalciuria, are indirect effects of defective apical endocytosis of PTH and 25-hydroxyvitamin D3; this may explain how a defect in a chloride channel could lead to kidney stones.

In Xenopus oocytes, Schwake et al. (2001) found that mutations introduced into the C-terminal internalization PY motif of the Clcn5 gene increased surface expression and currents of the channel by about 2-fold. Further studies with the wildtype and mutant ubiquitin-protein ligase WWP2 (602308) and Rab5 (179512) indicated that the prolonged surface expression of PY-mutant Clcn5 resulted from changes in cellular trafficking of the channel, and that endocytosis of Clcn5 depended on the interaction of the internalization signal with these other endocytic proteins.

Christensen et al. (2003) tested whether the endocytic failure that results from loss of the CLCN5 channel in Dent disease and knockout mice primarily reflects a loss of reabsorption by the multiligand receptors megalin (600073) and cubilin (602997) caused by a trafficking defect. Impaired protein endocytosis in kidney proximal tubule cells of Clcn5 knockout mice was demonstrated by a major decreased uptake of (125)I-labeled beta-2-microglobulin (109700), but not of the fluid-phase tracer FITC-dextran; reduced labeling of endosomes by injected peroxidase and reduced labeling for the endogenous megalin/cubilin ligands vitamin D- and retinol-binding proteins; and urinary appearance of low molecular mass proteins and the selective cubilin ligand transferrin (190000). An overall decrease of megalin and cubilin in proximal tubule cells and their selective loss at the brush border was demonstrated. In contrast, total contents of the rate-limiting endocytic catalysts Rab5a and Rab7 (602298) were unaffected. Thus, impaired protein endocytosis caused by invalidation of Clcn5 primarily reflects a trafficking defect of megalin and cubilin in proximal tubule cells.

Novarino et al. (2010) generated mice that carry the uncoupling E211A mutation that converts ClC5 into a pure chloride conductor. ATP-dependent acidification of renal endosomes was reduced in mice in which ClC5 was knocked out, but normal in mice carrying the E211A mutation. However, their proximal tubular endocytosis was also impaired. Novarino et al. (2010) concluded that endosomal chloride concentration, which is raised by ClC5 in exchange for protons accumulated by the proton ATPase, may play a role in endocytosis.

Alex et al. (2010) showed that loss of Clcn5 in mice exacerbated dextran sodium sulfate (DSS)-induced ulcerative colitis (266600), as measured by disease and histologic activity indices and myeloperoxidase (MPO; 606989) activity. Multiplex serum cytokine analysis, as well as immunofluorescence and Western blot analyses of colonic mucosa, demonstrated a heightened Th1/Th17 profile with increased systemic and local expression of Tnfa (191160), Il6 (147620), and Il17 (603149) in Clcn5 -/- mice with DSS-induced ulcerative colitis. Baseline Il6 and phospho-Ikb (NFKBIA; 164008) were high in Clcn5 -/- mice. Colitis in Clcn5 -/- mice could be attenuated by a high vitamin D diet. Alex et al. (2010) concluded that CLCN5 is involved in the immunopathogenesis of ulcerative colitis.


ALLELIC VARIANTS 14 Selected Examples):

.0001   DENT DISEASE 1

PROTEINURIA, LOW MOLECULAR WEIGHT, WITH HYPERCALCIURIA AND NEPHROCALCINOSIS, INCLUDED
CLCN5, TRP279TER
SNP: rs151340620, ClinVar: RCV000012563, RCV000012564

In affected members of a family with Dent disease (DENT1; 300009), Lloyd et al. (1996) identified a G-to-A transition in the CLCN5 gene, resulting in a trp279-to-ter (W279X) substitution. The mutation was predicted to result in a loss of 469 amino acids from the D6 region to the C terminus.

Lloyd et al. (1997) identified the W279X mutation in affected members of a Japanese family with idiopathic low molecular weight proteinuria associated with hypercalciuric nephrocalcinosis (308990).


.0002   DENT DISEASE 1

CLCN5, ARG648TER
SNP: rs151340621, gnomAD: rs151340621, ClinVar: RCV000012565, RCV001723558

In affected members of a family with Dent disease (DENT1; 300009), Lloyd et al. (1996) identified a C-to-T transition in the CLCN5 gene, resulting in an arg648-to-ter (R648X) substitution. The mutation was predicted to result in a loss of 100 amino acids from the cytoplasmic C terminus of the protein, deleting domain D13, which is conserved in all eukaryotic chloride channel proteins.

Lloyd et al. (1997) identified the R648X mutation in another family with Dent disease.


.0003   DENT DISEASE 1

CLCN5, LEU200ARG
SNP: rs151340622, ClinVar: RCV000012566

In affected members of a family with Dent disease (DENT1; 300009), Lloyd et al. (1996) identified a T-to-G transversion in the CLCN5 gene, resulting in a leu200-to-arg (L200R) substitution. The mutation was predicted to disrupt the charge distribution within domain D3 of the protein.


.0004   DENT DISEASE 1

CLCN5, SER520PRO
SNP: rs151340623, ClinVar: RCV000012567

In affected members of a family with Dent disease (DENT1; 300009), Lloyd et al. (1996) identified a T-to-C transition in the CLCN5 gene, resulting in a ser520-to-pro (S520P) substitution. The mutation was predicted to disrupt a helix in D11.


.0005   NEPHROLITHIASIS, X-LINKED RECESSIVE

CLCN5, ARG704TER
SNP: rs151340624, ClinVar: RCV001004890, RCV003904829

In affected members of a family with X-linked recessive nephrolithiasis (XRN; 310468), Lloyd et al. (1996) identified a C-to-T transition in the CLCN5 gene, resulting in an arg704-to-ter (R704X) substitution. The mutation was predicted to result in a loss of 42 amino acids from the cytoplasmic C terminus of the protein, deleting domain D13, which is conserved in all eukaryotic chloride channel proteins.


.0006   NEPHROLITHIASIS, X-LINKED RECESSIVE

CLCN5, GLY506GLU
SNP: rs151340625, ClinVar: RCV002266901, RCV002468922

In affected members of a family with X-linked recessive nephrolithiasis, Lloyd et al. (1996) identified a G-to-A transition in the CLCN5 gene, resulting in a gly506-to-glu (G506E) substitution. The mutation was predicted to disrupt a charge within domain D11.


.0007   HYPOPHOSPHATEMIC RICKETS, X-LINKED RECESSIVE

CLCN5, SER244LEU
SNP: rs151340626, ClinVar: RCV000012570, RCV000192274, RCV000485318, RCV002482856, RCV003398487

In affected members of an Italian family with X-linked recessive hypophosphatemic rickets (300554) reported by Bolino et al. (1993), Lloyd et al. (1996) identified a C-to-T transition in the CLCN5 gene, resulting in a ser244-to-leu (S244L) substitution. The mutation was predicted to disrupt a helix in D5. Functional expression studies showed that the mutant S244L channel had reduced, but not abolished, chloride conductance.

Oudet et al. (1997) reported a second family with the S244L mutation but with a milder phenotype than that in the family reported by Lloyd et al. (1996). The family reported by Oudet et al. (1997) had neither nephrocalcinosis nor nephrolithiasis. However, the affected individuals were significantly younger than those of the family reported by Lloyd et al. (1996).


.0008   PROTEINURIA, LOW MOLECULAR WEIGHT, WITH HYPERCALCIURIA AND NEPHROCALCINOSIS

CLCN5, TRP343TER
SNP: rs151340627, ClinVar: RCV000012571

In affected members of a Japanese family with low molecular weight proteinuria associated with hypercalciuria and nephrocalcinosis (308990), Lloyd et al. (1997) identified a G-to-A transition in the CLCN5 gene, resulting in a trp343-to-ter (W343X) substitution.


.0009   PROTEINURIA, LOW MOLECULAR WEIGHT, WITH HYPERCALCIURIA AND NEPHROCALCINOSIS

CLCN5, 1-BP DEL, 2085C
SNP: rs1569540520, ClinVar: RCV000012572

In affected members of a Japanese family with idiopathic low molecular weight proteinuria associated with hypercalciuric nephrocalcinosis (308990), Lloyd et al. (1997) identified a 1-bp deletion (2085delC) in the CLCN5 gene, resulting in a frameshift and premature termination of the protein at codon 699.


.0010   PROTEINURIA, LOW MOLECULAR WEIGHT, WITH HYPERCALCIURIA AND NEPHROCALCINOSIS

CLCN5, ARG280PRO
SNP: rs151340628, gnomAD: rs151340628, ClinVar: RCV000012573

In affected members of a Japanese family with idiopathic low molecular weight proteinuria associated with hypercalciuric nephrocalcinosis (308990), Lloyd et al. (1997) identified an arg280-to-pro (R280P) mutation in the CLCN5 gene. Heterologous expression of this mutation in Xenopus oocytes demonstrated a 70% reduction in channel activity when compared with the wildtype.


.0011   NEPHROLITHIASIS, X-LINKED RECESSIVE

CLCN5, GLY57VAL
SNP: rs151340629, ClinVar: RCV002468923

In 2 half-brothers, born of the same mother, with X-linked recessive nephrolithiasis (XRN; 310468), Schurman et al. (1998) identified a mutation in the CLCN5 gene, resulting in a gly57-to-val (G57V) substitution. The boys had been referred because of microhematuria and proteinuria noted on screening urinalysis. Family history showed renal failure after recurrent nephrolithiasis in a maternal grandfather and male cousin, and recurrent nephrolithiasis in an older brother.


.0012   DENT DISEASE 1

CLCN5, ALU INS, EX11
ClinVar: RCV000012575

Claverie-Martin et al. (2003) studied a Spanish patient with Dent disease (DENT1; 300009) and found, by PCR amplification of the CLCN5 exons, an abnormally large exon 11. Sequence analysis showed an insertion in codon 650 of a 345-bp Alu element that had arisen de novo on the maternal chromosome. Polymorphism analysis indicated that the insertion occurred in the germline of the maternal grandfather. The presence of a long poly(A) tract and evidence for a 16-bp target-site duplication implied that the Alu element was integrated by retrotransposition. The mutation predicted a truncated CLC5 protein.

Claverie-Martin et al. (2005) reported further studies of the Alu insertion in the family previously reported by Claverie-Martin et al. (2003). PCR amplification of blood DNA showed that the Alu insertion resulted in aberrant splicing of the CLCN5 pre-mRNA and skipping of exon 11. The resultant truncated protein lacks part of the C terminus, including the PY and CBS2 domains, which are critical for sorting and chloride channel function. In addition, there were 2 conserved exonic splicing enhancer sequences in the site of insertion.


.0013   DENT DISEASE 1

CLCN5, GLY260VAL
SNP: rs151340630, ClinVar: RCV000012576

Tosetto et al. (2006) identified a 1070G-T transversion in exon 7 of the CLCN5 gene, resulting in a gly260-to-val (G260V) substitution, in 1 of 25 men from northern Italy with end-stage renal disease and renal stones. The findings were consistent with Dent disease (DENT1; 300009). Examination of the family identified the G260V mutation in 2 additional young male relatives. Both had mild proteinuria, and one also had hypercalciuria.


.0014   DENT DISEASE 1

CLCN5, IVS8DS, G-T, +1
SNP: rs1569540382, ClinVar: RCV000012577

In a patient with Dent disease (DENT1; 300009), Tosetto et al. (2009) identified a G-to-T transversion in intron 8 of the CLCN5, resulting in a splice site mutation and generation of an mRNA transcript lacking part of exon 8, which was confirmed by RT-PCR analysis. The mutation truncated the protein at codon 361.


REFERENCES

  1. Akuta, N., Lloyd, S. E., Igarashi, T., Shiraga, H., Matsuyama, T., Yokoro, S., Cox, J. P. D., Thakker, R. V. Mutations of CLCN5 in Japanese children with idiopathic low molecular weight proteinuria, hypercalciuria and nephrocalcinosis. Kidney Int. 52: 911-916, 1997. [PubMed: 9328929] [Full Text: https://doi.org/10.1038/ki.1997.412]

  2. Alex, P., Ye, M., Zachos, N. C., Sipes, J., Nguyen, T., Suhodrev, M., Gonzales, L., Arora, Z., Zhang, T., Centola, M., Guggino, S. E., Li, X. Clcn5 knockout mice exhibit novel immunomodulatory effects and are more susceptible to dextran sulfate sodium-induced colitis. J. Immun. 184: 3988-3996, 2010. [PubMed: 20181886] [Full Text: https://doi.org/10.4049/jimmunol.0901657]

  3. Blair, H. J., Ho, M., Monaco, A. P., Fisher, S., Craig, I. W., Boyd, Y. High-resolution comparative mapping of the proximal region of the mouse X chromosome. Genomics 28: 305-310, 1995. [PubMed: 8530041] [Full Text: https://doi.org/10.1006/geno.1995.1146]

  4. Bolino, A., Devoto, M., Enia, G., Zoccali, C., Weissenbach, J., Romeo, G. Genetic mapping in the Xp11.2 region of a new form of X-linked hypophosphatemic rickets. Europ. J. Hum. Genet. 1: 269-279, 1993. [PubMed: 7915957] [Full Text: https://doi.org/10.1159/000472424]

  5. Christensen, E. I., Devuyst, O., Dom, G., Nielsen, R., Van Der Smissen, P., Verroust, P., Leruth, M., Guggino, W. B., Courtoy, P. J. Loss of chloride channel ClC-5 impairs endocytosis by defective trafficking of megalin and cubilin in kidney proximal tubules. Proc. Nat. Acad. Sci. 100: 8472-8477, 2003. [PubMed: 12815097] [Full Text: https://doi.org/10.1073/pnas.1432873100]

  6. Claverie-Martin, F., Flores, C., Anton-Gamero, M., Gonzalez-Acosta, H., Garcia-Nieto, V. The Alu insertion in the CLCN5 gene of a patient with Dent's disease leads to exon 11 skipping. J. Hum. Genet. 50: 370-374, 2005. [PubMed: 16041495] [Full Text: https://doi.org/10.1007/s10038-005-0265-5]

  7. Claverie-Martin, F., Gonzalez-Acosta, H., Flores, C., Anton-Gamero, M., Garcia-Nieto, V. De novo insertion of an Alu sequence in the coding region of the CLCN5 gene results in Dent's disease. Hum. Genet. 113: 480-485, 2003. [PubMed: 14569459] [Full Text: https://doi.org/10.1007/s00439-003-0991-8]

  8. Cox, J. P. D., Yamamoto, K., Christie, P. T., Wooding, C., Feest, T., Flinter, F. A., Goodyer, P. R., Leumann, E., Neuhaus, T., Reid, C., Williams, P. F., Wrong, O., Thakker, R. V. Renal chloride channel, CLCN5, mutations in Dent's disease. J. Bone Miner. Res. 14: 1536-1542, 1999. [PubMed: 10469281] [Full Text: https://doi.org/10.1359/jbmr.1999.14.9.1536]

  9. Devuyst, O., Christie, P. T., Courtoy, P. J., Beauwens, R., Thakker, R. V. Intra-renal and subcellular distribution of the human chloride channel, CLC-5, reveals a pathophysiological basis for Dent's disease. Hum. Molec. Genet. 8: 247-257, 1999. [PubMed: 9931332] [Full Text: https://doi.org/10.1093/hmg/8.2.247]

  10. Dutzler, R., Campbell, E. B., Cadene, M., Chait, B. T., MacKinnon, R. X-ray structure of a ClC chloride channel at 3.0 angstrom reveals the molecular basis of anion selectivity. Nature 415: 287-294, 2002. [PubMed: 11796999] [Full Text: https://doi.org/10.1038/415287a]

  11. Fisher, S. E., Black, G. C. M., Lloyd, S. E., Hatchwell, E., Wrong, O., Thakker, R. V., Craig, I. W. Isolation and partial characterization of a chloride channel gene which is expressed in kidney and is a candidate for Dent's disease (an X-linked hereditary nephrolithiasis). Hum. Molec. Genet. 3: 2053-2059, 1994. [PubMed: 7874126]

  12. Fisher, S. E., Van Bakel, I., Lloyd, S. E., Pearce, S. H. S., Thakker, R. V., Craig, I. W. Cloning and characterization of CLCN5, the human kidney chloride channel gene implicated in Dent disease (an X-linked hereditary nephrolithiasis). Genomics 29: 598-606, 1995. [PubMed: 8575751] [Full Text: https://doi.org/10.1006/geno.1995.9960]

  13. Gunther, W., Luchow, A., Cluzeaud, F., Vandewalle, A., Jentsch, T. J. ClC-5, the chloride channel mutated in Dent's disease, colocalizes with the proton pump in endocytotically active kidney cells. Proc. Nat. Acad. Sci. 95: 8075-8080, 1998. [PubMed: 9653142] [Full Text: https://doi.org/10.1073/pnas.95.14.8075]

  14. Lloyd, S. E., Gunther, W., Pearce, S. H. S., Thomson, A., Bianchi, M. L., Bosio, M., Craig, I. W., Fisher, S. E., Scheinman, S. J., Wrong, O., Jentsch, T. J., Thakker, R. V. Characterisation of renal chloride channel, CLCN5, mutations in hypercalciuric nephrolithiasis (kidney stones) disorders. Hum. Molec. Genet. 6: 1233-1239, 1997. [PubMed: 9259268] [Full Text: https://doi.org/10.1093/hmg/6.8.1233]

  15. Lloyd, S. E., Pearce, S. H. S., Fisher, S. E., Steinmeyer, K., Schwappach, B., Scheinman, S. J., Harding, B., Bolino, A., Devoto, M., Goodyer, P., Rigden, S. P. A., Wrong, O., Jentsch, T. J., Craig, I. W., Thakker, R. V. A common molecular basis for three inherited kidney stone diseases. Nature 379: 445-449, 1996. [PubMed: 8559248] [Full Text: https://doi.org/10.1038/379445a0]

  16. Lloyd, S. E., Pearce, S. H. S., Gunther, W., Kawaguchi, H., Igarashi, T., Jentsch, T. J., Thakker, R. V. Idiopathic low molecular weight proteinuria associated with hypercalciuric nephrocalcinosis in Japanese children is due to mutations of the renal chloride channel (CLCN5). J. Clin. Invest. 99: 967-974, 1997. [PubMed: 9062355] [Full Text: https://doi.org/10.1172/JCI119262]

  17. Ludwig, M., Doroszewicz, J., Seyberth, H. W., Bokenkamp, A., Balluch, B., Nuutinen, M., Utsch, B., Waldegger, S. Functional evaluation of Dent's disease-causing mutations: implications for ClC-5 channel trafficking and internalization. Hum. Genet. 117: 228-237, 2005. [PubMed: 15895257] [Full Text: https://doi.org/10.1007/s00439-005-1303-2]

  18. Nakazato, H., Hattori, S., Furuse, A., Kawano, T., Karashima, S., Tsuruta, M., Yoshimuta, J., Endo, F., Matsuda, I. Mutations in the CLCN5 gene in Japanese patients with familial idiopathic low-molecular-weight proteinuria. Kidney Int. 52: 895-900, 1997. [PubMed: 9328927] [Full Text: https://doi.org/10.1038/ki.1997.410]

  19. Novarino, G., Weinert, S., Rickheit, G., Jentsch, T. J. Endosomal chloride-proton exchange rather than chloride conductance is crucial for renal endocytosis. Science 328: 1398-1401, 2010. [PubMed: 20430975] [Full Text: https://doi.org/10.1126/science.1188070]

  20. Oudet, C., Martin-Coignard, D., Pannetier, S., Praud, E., Champion, G., Hanauer, A. A second family with XLRH displays the mutation S244L in the CLCN5 gene. Hum. Genet. 99: 781-784, 1997. [PubMed: 9187673] [Full Text: https://doi.org/10.1007/s004390050448]

  21. Picollo, A., Pusch, M. Chloride/proton antiporter activity of mammalian CLC proteins ClC-4 and ClC-5. Nature 436: 420-423, 2005. [PubMed: 16034421] [Full Text: https://doi.org/10.1038/nature03720]

  22. Piwon, N., Gunther, W., Schwake, M., Bosl, M. R., Jentsch, T. J. ClC-5 Cl(-)-channel disruption impairs endocytosis in a mouse model for Dent's disease. Nature 408: 369-373, 2000. [PubMed: 11099045] [Full Text: https://doi.org/10.1038/35042597]

  23. Scheel, O., Zdebik, A. A., Lourdel, S., Jentsch, T. J. Voltage-dependent electrogenic chloride/proton exchange by endosomal CLC proteins. Nature 436: 424-427, 2005. [PubMed: 16034422] [Full Text: https://doi.org/10.1038/nature03860]

  24. Schurman, S. J., Norden, A. G. W., Scheinman, S. J. X-linked recessive nephrolithiasis: presentation and diagnosis in children. J. Pediat. 132: 859-862, 1998. [PubMed: 9602200] [Full Text: https://doi.org/10.1016/s0022-3476(98)70318-x]

  25. Schwake, M., Friedrich, T., Jentsch, T. J. An internalization signal in ClC-5, an endosomal Cl- channel mutated in Dent's disease. J. Biol. Chem. 276: 12049-12054, 2001. [PubMed: 11116157] [Full Text: https://doi.org/10.1074/jbc.M010642200]

  26. Tosetto, E., Ceol, M,, Mezzabotta, F., Ammenti, A., Peruzzi, L., Caruso, M. R., Barbano, G., Vezzoli, G., Colussi, G., Vergine, G., Giordano, M., Glorioso, N., Degortes, S., Soldati, L., Sayer, J., D'Angelo, A., Anglani, F. Novel mutations of the CLCN5 gene including a complex allele and a 5-prime UTR mutation in Dent disease 1. (Letter) Clin. Genet. 76: 413-416, 2009. [PubMed: 19673950] [Full Text: https://doi.org/10.1111/j.1399-0004.2009.01212.x]

  27. Tosetto, E., Graziotto, R., Artifoni, L., Nachtigal, J., Cascone, C., Conz, P., Piva, M., Dell'Aquila, R., De Paoli Vitali, E., Citron, L., Nalesso, F., Antonello, A., Vertolli, U., Zagatti, R., Lupo, A., D'Angelo, A., Anglani, F., Gambaro, G. Dent's disease and prevalence of renal stones in dialysis patients in Northeastern Italy. J. Hum. Genet. 51: 25-30, 2006. [PubMed: 16247550] [Full Text: https://doi.org/10.1007/s10038-005-0317-x]

  28. Zifarelli, G., Pusch, G. Conversion of the 2 Cl-/1 H+ antiporter ClC-5 in a NO(3)-/H+ antiporter by a single point mutation. EMBO J. 28: 175-182, 2009. [PubMed: 19131966] [Full Text: https://doi.org/10.1038/emboj.2008.284]


Contributors:
Cassandra L. Kniffin - updated : 12/3/2010
Paul J. Converse - updated : 10/26/2010
Ada Hamosh - updated : 6/30/2010
Cassandra L. Kniffin - updated : 11/17/2008
Cassandra L. Kniffin - updated : 3/1/2006
Cassandra L. Kniffin - updated : 11/8/2005
Cassandra L. Kniffin - updated : 10/13/2005
Cassandra L. Kniffin - reorganized : 9/19/2005
Marla J. F. O'Neill - updated : 7/21/2005
Victor A. McKusick - updated : 11/24/2003
Victor A. McKusick - updated : 8/28/2003
Ada Hamosh - updated : 1/17/2002
Ada Hamosh - updated : 11/14/2000
Victor A. McKusick - updated : 11/9/1999
Ada Hamosh - updated : 4/8/1999
Victor A. McKusick - updated : 9/4/1998
Michael J. Wright - updated : 8/25/1997
Victor A. McKusick - updated : 8/22/1997
Victor A. McKusick - updated : 5/9/1997

Creation Date:
Victor A. McKusick : 1/31/1996

Edit History:
carol : 06/22/2021
joanna : 02/20/2015
wwang : 12/7/2010
ckniffin : 12/3/2010
mgross : 10/27/2010
terry : 10/26/2010
alopez : 7/1/2010
terry : 6/30/2010
wwang : 11/24/2008
ckniffin : 11/17/2008
wwang : 3/7/2006
ckniffin : 3/1/2006
wwang : 11/17/2005
ckniffin : 11/8/2005
wwang : 10/24/2005
ckniffin : 10/13/2005
carol : 9/19/2005
carol : 9/19/2005
ckniffin : 9/7/2005
ckniffin : 9/1/2005
wwang : 7/22/2005
terry : 7/21/2005
terry : 4/21/2005
terry : 6/2/2004
alopez : 11/25/2003
terry : 11/24/2003
tkritzer : 8/28/2003
alopez : 1/22/2002
terry : 1/17/2002
mgross : 11/15/2000
terry : 11/14/2000
carol : 11/16/1999
terry : 11/9/1999
carol : 7/28/1999
kayiaros : 7/13/1999
carol : 5/24/1999
alopez : 4/8/1999
carol : 9/14/1998
terry : 9/4/1998
terry : 6/15/1998
dholmes : 6/10/1998
terry : 6/4/1998
terry : 11/20/1997
terry : 9/4/1997
terry : 8/25/1997
terry : 8/25/1997
terry : 8/25/1997
terry : 8/25/1997
terry : 8/22/1997
terry : 8/11/1997
terry : 8/11/1997
alopez : 6/27/1997
alopez : 5/9/1997
alopez : 5/9/1997
alopez : 5/7/1997
joanna : 2/1/1996
mark : 1/31/1996