Entry - *606272 - CYSTINOSIN; CTNS - OMIM
* 606272

CYSTINOSIN; CTNS


HGNC Approved Gene Symbol: CTNS

Cytogenetic location: 17p13.2     Genomic coordinates (GRCh38): 17:3,636,459-3,663,103 (from NCBI)


Gene-Phenotype Relationships
Location Phenotype Phenotype
MIM number
Inheritance Phenotype
mapping key
17p13.2 Cystinosis, atypical nephropathic 219800 AR 3
Cystinosis, late-onset juvenile or adolescent nephropathic 219900 AR 3
Cystinosis, nephropathic 219800 AR 3
Cystinosis, ocular nonnephropathic 219750 AR 3

TEXT

Cloning and Expression

Town et al. (1998) identified a novel gene, CTNS, within the deletion interval on chromosome 17 in patients with nephropathic cystinosis (219800). They found that CTNS encodes an integral membrane protein, which they designated cystinosin, that has features of a lysosomal membrane protein. CTNS, a putative cystine transporter, contains 367 amino acids and 7 transmembrane domains. A 2.7-kb transcript of the CTNS gene was strongly expressed in pancreas, kidney (mature and fetal), skeletal muscle, to a lesser extent in placenta and heart, and weakly in lung and liver.


Gene Structure

Town et al. (1998) determined that the CTNS gene has 12 exons. Phornphutkul et al. (2001) identified the CTNS promoter as the region encompassing nucleotides -316 to +1 with respect to the transcription start site. This region contains an Sp-1 regulatory element at positions -299 to -293 which, as shown by electrophoretic mobility shift assays, binds Sp-1. The CTNS promoter region shares 41 nucleotides with the promoter region of an adjacent gene, CARKL (SHPK; 605060), whose start site is 501 bp from the CTNS start site. CARKL is aligned on the other DNA strand in the other direction.


Mapping

Town et al. (1998) found that the marker locus D17S829 was homozygously deleted in 23 of 70 patients with nephropathic cystinosis and mapped a novel gene, CTNS, to the deletion interval.


Molecular Genetics

Town et al. (1998) identified 11 different mutations in the CTNS gene (see, e.g., 606272.0001-606272.0005), all predicted to cause loss of function of the protein, segregating with nephropathic cystinosis. The most common mutation was a 65-kb deletion (606272.0005), found in 23 (33%) of 70 patients.

Shotelersuk et al. (1998) performed mutation analysis of 108 American-based nephropathic cystinosis patients and found that 48 (44%) were homozygous for the 'European' 65-kb deletion, 2 had a smaller major deletion, 11 were homozygous and 3 were heterozygous for 753G-A (W138X; 606272.0003), and 24 had 21 other mutations. In 20 patients (19%), no mutations were found. Of 82 alleles bearing the 65-kb deletion, 38 derived from Germany, 28 from the British Isles, and 4 from Iceland. The 18 new mutations identified in this study included the first reported missense mutation, 2 in-frame deletions, and mutations in patients of African American, Mexican, and Indian ancestry. CTNS mutations were spread throughout the leader sequence, transmembrane, and nontransmembrane regions. According to a cystinosis clinical severity score, homozygotes for the 65-kb deletion and for W138X had average disease, whereas mutations involving the first amino acids prior to transmembrane domains were associated with mild disease. By Northern blot analysis, CTNS was not expressed in patients homozygous for the 65-kb deletion but was expressed in all 15 other patients tested.

Structure predictions suggested that cystinosin is a novel integral lysosomal membrane protein. Attard et al. (1999) examined the predicted effects of mutations on this model of cystinosin. They screened patients with infantile nephropathic cystinosis, those with late-onset cystinosis, and patients whose phenotype did not fit the classic definitions. They identified 23 different mutations in the CTNS gene, 14 of which were novel. Of 25 patients with infantile nephropathic cystinosis, 12 had 2 severely truncating mutations, consistent with a loss of functional protein, and 13 had missense or in-frame deletions, which would result in disruption of transmembrane domains and loss of protein function. Mutations identified in 2 late-onset patients (see, e.g., 606272.0008) affected functionally unimportant regions of cystinosin, accounting for the patients' milder phenotype. For 3 patients, the age of onset of cystinosis was under 7 years, but the course of the disease was milder than the infantile nephropathic form. This suggested that the missense mutations identified in these individuals (see, e.g., 606272.0007) allowed production of a functional protein and may also indicate regions of cystinosin that are not functionally important.

As indicated earlier, identification of the CTNS gene was facilitated by the detection of deletions spanning the cystinosis locus in affected individuals. Two types of deletions were detected, one of approximately 65 kb, which was found in homozygous state in nearly one-third of cystinotic individuals, and a smaller one of 9.5 to 16 kb, which was carried by a single family. Both the larger and the smaller deletion span the 5-prime end of the CTNS gene, covering exons 1 to 10 and 1 to 3, respectively; STS analysis indicated that the larger deletion was the same size in all patients. Forestier et al. (1999) characterized the deletion breakpoints and demonstrated that, although both deletions occur in regions of repetitive sequences, they are the result of nonhomologous recombination. This type of mechanism suggested that the deletion of approximately 65 kb is not a recurrent mutation, and the results confirmed that it is identical in all patients. Haplotype analysis showed that this large deletion is due to a founder effect that occurred in a white individual, and that it probably arose in the middle of the first millennium. Forestier et al. (1999) also described a rapid PCR-based assay that will accurately detect both homozygous and heterozygous deletions. They used this assay to show that the 65-kb deletion is present in either the homozygous or the heterozygous state in 76% of cystinotic patients of European origin.

Touchman et al. (2000) sequenced 200 kb surrounding the CTNS gene and found that the common cystinosis deletion (606272.0005) is approximately 57 rather than 65 kb. The authors identified SHPK, which they designated CARKL, within this deleted region. The findings indicated that patients with the 57-kb deletion in CTNS also have a deletion of CARKL, which may account for phenotypic variability.

Phornphutkul et al. (2001) identified mutations in the CTNS promoter region in 3 patients with cystinosis (606272.0012-606272.0014). Each of the promoter mutations drastically reduced CAT activity when inserted into a reporter construct and failed either to cause a mobility shift when exposed to nuclear extract or to compete with the normal oligonucleotide's mobility shift. These mutations had no effect on promoter activity of the CARKL gene.

Gahl et al. (2002) stated that more than 50 different CTNS mutations had been described in homozygous form in cystinosis. The most common mutation is the 57,257-bp deletion, which is found in homozygous state in approximately 50% of cystinosis patients of northern European descent. The deletion is an ancient founder mutation; more recent CTNS mutations involve alterations in the promoter region, leader sequence, transmembrane domains, or nontransmembrane regions. Mutations include small deletions and insertions and nonsense, missense, and splicing mutations.

Gahl et al. (2002) stated that patients with intermediate cystinosis (219900) and patients with ocular, or nonnephropathic, cystinosis (219750) generally have 1 severe CTNS mutation (e.g., the 57-kb deletion or a nonsense mutation) and 1 mild mutation, so that part of the transport function of cystinosin is retained. However, homozygosity for a mutation of a conserved amino acid (N323K; 606272.0016) was observed in 2 sibs in Taiwan with intermediate cystinosis (Thoene et al., 1999), indicating presumably that the mutation allowed for some residual cystine transport, accounting for the mild clinical presentation.

Mason et al. (2003) analyzed the CTNS gene in 42 Italian patients with nephropathic cystinosis and found that the mutation spectrum in this population differed from that previously reported for the northern European population: the 57-kb deletion was present in a lower percentage (17%) and splicing mutations represented 30% of the mutations detected.

By screening for mutations in the CTNS exons and promoter region, Kalatzis et al. (2002) identified 14 novel mutations associated with cystinosis: 11 underlying infantile cystinosis, 2 juvenile cystinosis, and 1 associated with an atypical form of the disease (606272.0017). These mutations, all situated in the exons or immediately flanking intronic sequences, comprised in-frame insertions and deletions, as well as missense, nonsense, and putative splice site mutations. Since the cloning of CTNS, the authors had screened for mutations in 108 affected individuals, with a high mutation detection rate of 95.8%. The few undetectable mutant alleles segregated mostly in the noninfantile forms, suggesting that these individuals carried mutations either in the introns or in unidentified regulatory sequences.

Kalatzis et al. (2004) studied the relationship between transport activity and intracellular localization of cystinosin mutants and their associated clinical phenotype. Thirty-one pathogenic mutations (24 missense mutations, 7 in-frame deletions or insertions) were analyzed. Most of the mutations did not alter the lysosomal localization of cystinosin, although 3 partially mislocalized the protein independently of its C-terminal sorting motif, thus confirming the presence of an additional sorting mechanism. Sixteen of 19 mutations associated with infantile cystinosis abolished transport, whereas 3 of 5 mutations associated with juvenile or ocular forms strongly reduced transport. Five atypical, unclassified, or misclassified mutations could be clarified using the transport data and additional genetic information. The authors concluded that impaired transport is the most frequent cause of pathogenicity, with infantile cystinosis generally resulting from a total loss of activity.

Macias-Vidal et al. (2009) analyzed the CTNS gene in 32 unrelated cystinosis patients, 27 Spanish and 5 Moroccan, and identified homozygous or compound heterozygous mutations in 28 of them; only 1 mutation was detected in 4 patients. All but 2 of the patients had the infantile form of cystinosis and had truncating mutations or mutations affecting conserved amino acids associated with transmembrane regions of the protein. The 2 juvenile cystinosis patients were both compound heterozygotes for a truncating mutation (606272.0004 and 606272.0005, respectively) and a missense mutation (S139F; 606272.0018) in the CTNS gene; the latter had previously been found in a patient with a 'nonclassic,' milder form of nephropathic cystinosis by Attard et al. (1999), who suggested that the S139F mutation might allow production of functional protein or be located in a region of cystinosin that was not functionally important.


Animal Model

Using a promoter trap approach, Cherqui et al. (2002) created mice expressing a truncated cystinosin protein. In wildtype mice, cystinosin localized to lysosomes and transported cystine at acidic pH, whereas the truncated cystinosin mislocalized to the plasma membrane and lost its cystine transport function. These Ctns -/- mice accumulated cystine in all organs tested, and cystine crystals, pathognomonic for cystinosis, were observed. Ctns -/- mice developed ocular changes similar to those observed in affected individuals, bone defects, and behavioral anomalies. However, Ctns -/- mice did not develop proximal tubulopathy or renal failure. As in cystinosis patients, cysteamine administration aided cystine clearance in Ctns -/- mice.

Goodman et al. (2021) transplanted hematopoietic stem and progenitor cells (HSPCs) from a Shpk -/- mouse into a Ctns -/- mouse. The treated Ctns -/- mice had a significant reduction in cystine load in multiple tissues and restoration of Ctns expression compared to untreated mice. The treated mice also had improved kidney morphologic structure compared to untreated Ctns -/- mice. Goodman et al. (2021) concluded that absence of SHPK does not alter the ability of HSPCs to recue cystinosis, and that patients with cystinosis who are homozygous for a common 57-kb deletion (606272.0005) on chromosome 17p13, which includes both the CTNS and SHPK genes, would likely benefit from ex vivo gene therapy approaches.


ALLELIC VARIANTS ( 18 Selected Examples):

.0001 CYSTINOSIS, NEPHROPATHIC

CTNS, GLY95TER
  
RCV000004691

In 2 consanguineous families from Pakistan, Town et al. (1998) found that nephropathic cystinosis (219800) was associated with a gly95-to-ter (G95X) mutation in the CTNS gene. Analysis of 5 microsatellites covering a 4-cM interval showed a common haplotype, suggesting that these families may be related. The mutation was a G-to-T transversion at nucleotide 622, which converted GGA (gly) to TGA (stop).


.0002 CYSTINOSIS, NEPHROPATHIC

CTNS, 2-BP DEL, 397TG
  
RCV000004692

In 2 families from central France, Town et al. (1998) found that nephropathic cystinosis (219800) was associated with hemizygosity for the same 2-bp deletion of the CTNS gene: deletion of TG at 397/399 resulted in a stop codon at the site of the mutation. The 2 families shared a common haplotype that segregated with the deletion. Deletion of the second allele was present in affected members of each family.


.0003 CYSTINOSIS, NEPHROPATHIC

CTNS, TRP138TER
  
RCV000004693...

One family from Northern Ireland and one from Eire were found by Town et al. (1998) to have the same mutation as the basis of nephropathic cystinosis (219800): a TGG-to-TGA transition at nucleotide 753 resulting in a trp138-to-ter (W138X) nonsense mutation.

McGowan-Jordan et al. (1999) found the W138X mutation in 21/40 French Canadian cystinosis chromosomes. In all cases the mutation was on a distinctive haplotype. They found the same haplotype in 2 Irish families with this mutation, supporting the hypothesis that Celtic chromosomes represent an extensive portion of cystinosis chromosomes in French Canada. The studies also suggested a frequently unrecognized contribution from non-Gallic sources in the French Canadian population.


.0004 CYSTINOSIS, NEPHROPATHIC

CYSTINOSIS, LATE-ONSET JUVENILE OR ADOLESCENT NEPHROPATHIC TYPE, INCLUDED
CTNS, 4-BP DEL, 18GACT
  
RCV000004695...

In 4 families from 3 different continents, Town et al. (1998) found that nephropathic cystinosis (219800) was associated with deletion of 4 nucleotides, GACT, at nucleotide 357 of the CTNS gene. This resulted in frameshift and a premature termination. The 4 families did not share a common haplotype, indicating a recurrent mutation. Macias-Vidal et al. (2009) noted that based on numbering from the ATG initiation codon the deletion occurs at nucleotide 18.

In a Spanish patient with juvenile-onset nephropathic cystinosis (219900), Macias-Vidal et al. (2009) identified compound heterozygosity for a 416C-T transition in the CTNS gene, resulting in a ser139-to-phe (S139F; 606272.0018) substitution, and the 4-bp deletion.


.0005 CYSTINOSIS, NEPHROPATHIC

CYSTINOSIS, LATE-ONSET JUVENILE OR ADOLESCENT NEPHROPATHIC TYPE, INCLUDED
CYSTINOSIS, OCULAR NONNEPHROPATHIC, INCLUDED
CTNS, 57-KB DEL
   RCV000004696...

This common mutation in nephropathic cystinosis (219800) was originally reported as a 65-kb deletion. Touchman et al. (2000) sequenced 200 kb surrounding the CTNS gene and found that the deletion is approximately 57 rather than 65 kb. The authors identified SHPK (605060), which they designated CARKL, within this deleted region. The findings indicated that the 57-kb deletion includes deletion of CARKL in addition to CTNS, which may account for phenotypic variability in patients.

In a French/British report (Town et al., 1998), 23 (33%) of 70 patients with nephropathic cystinosis had a 65-kb deletion in the CTNS gene. Among American-based patients studied by Shotelersuk et al. (1998), 48 (44%) of 108 were homozygous for the 65-kb 'European' deletion. Of 96 alleles from these patients, 82 were assigned a nation of origin; 38 (46%) derived from Germany and 28 (34%) arose from the British Isles. Two apparently unrelated patients with homozygous deletions came from Iceland. In addition to the 48 patients homozygous for the 65-kb deletion, many of the patients may have a single copy of the deletion. An upstream deletion breakpoint needed to be determined before a PCR-based test of heterozygosity for the deletion could be developed.

Gahl et al. (2002) stated that the 57-kb deletion is found in the homozygous state in approximately 50% of patients of northern European descent who have cystinosis. This founder mutation, which removes the first 10 exons of CTNS and eliminates expression of the protein, apparently occurred in Germany in approximately 500 A.D. (Shotelersuk et al., 1998) and spread by migration to other regions, including Iceland.

Bendavid et al. (2004) described a FISH method permitting cytogenetic laboratories to test for the 57-kb deletion, which is found in approximately 60% of patients with cystinosis in the United States and northern Europe.

Wamelink et al. (2008) found that cystinosis patients homozygous for the 57-kb deletion had increased urinary sedoheptulose and erythritol compared to patients with other CTNS mutations. Enzyme studies of cultured fibroblasts revealed an 80% reduction in sedoheptulose phosphorylating activity compared to cystinosis patients with other mutations and controls. The findings indicated that the CARKL gene encodes sedoheptulokinase, which functions in the pentose phosphate pathway.

Buntinx et al. (2016) noted that the most common mutation in Northern European patients with cystinosis is the 57-kb deletion in the CTNS gene. This deletion extends into the noncoding region upstream of the start codon of the TRPV1 gene (602076), which encodes a capsaicin- and heat-sensitive ion channel. Buntinx et al. (2016) found that patients heterozygous for the deletion showed normal sensory responses, whereas patients homozygous for the mutation exhibited a 60% reduction in vasodilation and pain evoked by capsaicin, as well as an increase in heat detection threshold. Responses to cold, mechanical stimuli, or cinnamaldehyde, a TRPA1 (604775) agonist, were unaltered. Buntinx et al. (2016) concluded that cystinosis patients homozygous for the 57-kb CTNS deletion have a strong reduction of TRPV1 function, possibly accounting for sensory alterations and thermoregulatory deficits in these patients.

Compound Heterozygosity for the 57-kb Deletion

In a 38-year-old woman who presented with photophobia at 38 years of age but had suffered chronic sensitivity to light (219750), Anikster et al. (2000) identified compound heterozygosity for the 57-kb deletion and a 928G-A transition, resulting in a glycine to arginine substitution at codon 197 (G197R; 606272.0011). Compound heterozygosity was also found in 2 additional patients from the same family with ocular cystinosis.

In a Spanish patient with juvenile-onset nephropathic cystinosis (219900), Macias-Vidal et al. (2009) identified compound heterozygosity for a 416C-T transition in the CTNS gene, resulting in a ser139-to-phe (S139F; 606272.0018) substitution, and the 57-kb deletion.


.0006 CYSTINOSIS, NEPHROPATHIC

CTNS, GLY169ASP
  
RCV000004699...

One of 7 missense mutations in the CTNS gene discovered by Shotelersuk et al. (1998) in patients with nephropathic cystinosis (219800) was a gly169-to-asp (G169D) amino acid substitution. Significant CTNS expression was associated with homozygosity of this mutation. All 7 missense mutations gave rise to amino acid changes either inside a transmembrane domain or in the first amino acid prior to a transmembrane domain.


.0007 CYSTINOSIS, ATYPICAL NEPHROPATHIC

CTNS, VAL42ILE
  
RCV000004700...

In 3 patients, Attard et al. (1999) found an atypical presentation of cystinosis (see 219800). Although onset was less than 7 years of age, the course was atypically mild. One of the 3 patients (L18) was homozygous for a G-to-A transition in the CTNS gene, resulting in a val42-to-ile (V42I) substitution in the nonconserved region toward the N terminus. This part of the protein is predicted to lie within the lumen of the lysosome, and the mutation was adjacent to, but would not affect, a potential N-glycosylation site. Thus, the location of the mutation was consistent with a milder phenotype.


.0008 CYSTINOSIS, LATE-ONSET JUVENILE OR ADOLESCENT NEPHROPATHIC TYPE

CTNS, IVS7AS, C-G, -10
  
RCV001836614...

In a patient typical of late-onset cystinosis (219900), Attard et al. (1999) identified an intronic mutation of the CTNS gene, a C-to-G transversion at nucleotide 801 -10. This resulted in the formation of an alternative splice site upstream of the normal site. Sequencing across the exon 7-8 boundary in cDNA showed the homozygous insertion of 9 bases, which would result in the addition of 3 amino acids, pro-cys-ser, at a point immediately adjacent to the second transmembrane domain. Although this occurred in a conserved region, the first cytosolic domain is very small (normally 4 amino acids) and consequently may not be functionally important. The addition of the imino group of proline at this point might be expected to cause disruption of the folding of the polypeptide chain, but is unlikely to enter or interfere with the transmembrane domain.


.0009 CYSTINOSIS, OCULAR NONNEPHROPATHIC

CTNS, IVS10AS, C-G, -3
  
RCV000004702

In a 26-year-old male with ocular nonnephropathic cystinosis (219750), Anikster et al. (2000) reported a C-to-G transversion at the -3 position of the acceptor splice site of IVS10 of the CTNS gene. This mutation was found in compound heterozygosity with a TCCTT deletion at nucleotide 545.


.0010 CYSTINOSIS, NEPHROPATHIC

CTNS, 5-BP DEL, NT545
  
RCV000004703...

Shotelersuk et al. (1998) identified a 5-bp deletion starting at nucleotide 545 resulting in an I69R amino acid substitution and a stop codon at position 73 of the CTNS gene in a patient with classic cystinosis (219800).


.0011 CYSTINOSIS, OCULAR NONNEPHROPATHIC

CTNS, GLY197ARG
  
RCV000004704...

In a 38-year-old woman who presented with photophobia at 38 years of age but had suffered chronic sensitivity to light (219750), Anikster et al. (2000) identified a G-to-A transition at nucleotide 928, resulting in a glycine to arginine substitution at codon 197 (G197R). The patient was compound heterozygous for the 57-kb deletion (606272.0005). This mutation was also found in 2 additional patients from the same family with ocular cystinosis. Both patients were compound heterozygous for the G197R mutation and the 57-kb deletion.


.0012 CYSTINOSIS, NEPHROPATHIC

CTNS, -295G-C, PROMOTER
  
RCV001655746...

In a woman of Scottish-Irish and Puerto Rican descent with nephropathic cystinosis (219800), Phornphutkul et al. (2001) identified heterozygosity for a 57-kb deletion (606272.0005) and a promoter mutation, a G-to-C change at nucleotide -295, involving the Sp-1 regulatory element, in the CTNS gene. The latter mutation was tested for its effect on promoter activity by generation of a -348 to +1 CTNS-CAT construct and was found to produce 19% of the wildtype CAT activity when transfected in HeLa cells.


.0013 CYSTINOSIS, OCULAR NONNEPHROPATHIC

CTNS, -303G-T, PROMOTER
  
RCV000004706

In a girl of German/Norwegian heritage with ocular cystinosis (219750), Phornphutkul et al. (2001) identified heterozygosity for a G197R mutation (606272.0011) and a promoter mutation, a G-to-T transversion at nucleotide -303, in the CTNS gene. The latter mutation was tested for its effect on promoter activity by generation of a -348 to +1 CTNS-CAT construct and was found to produce 5% of the wildtype CAT activity when transfected in HeLa cells.


.0014 CYSTINOSIS, OCULAR NONNEPHROPATHIC

CTNS, 1-BP INS, -303T, PROMOTER
   RCV000004707

In a woman with ocular cystinosis (219750) reported by Anikster et al. (2000), Phornphutkul et al. (2001) identified heterozygosity for a G197R mutation (606272.0011) and a promoter mutation, insertion of a T after position -303, in the CTNS gene. The latter mutation was tested for its effect on promoter activity by generation of a -348 to +1 CTNS-CAT construct and was found to produce 16% of the wildtype CAT activity when transfected in HeLa cells.


.0015 CYSTINOSIS, NEPHROPATHIC

CTNS, GLY339ARG
  
RCV000004708...

In 4 children with nephropathic cystinosis (219800) in the Old Order Amish population in southwestern Ohio, Rupar et al. (2001) identified a G-to-A transition at nucleotide 1354. This transition resulted in a glycine-to-arginine substitution at residue 339 (G339R). It was found in homozygous form in affected children and in heterozygous form in an unaffected sib.


.0016 CYSTINOSIS, LATE-ONSET JUVENILE OR ADOLESCENT NEPHROPATHIC TYPE

CTNS, ASN323LYS
  
RCV000004709...

Thoene et al. (1999) described 2 sibs in Taiwan with intermediate cystinosis (219900) who had linear growth and weight gain within 2 standard deviations of the mean for their ethnic group until the ages of 13 and 14 years when their plasma creatinine concentrations were 1.2 mg per deciliter and 3.3 mg per deciliter, respectively. They were found to be homozygous for a 1308C-G mutation in the CTNS gene, resulting in the substitution of lysine for the conserved asparagine at position 323 (N323K). Presumably, this mutation allowed for some residual cystine transport, accounting for the mild clinical presentation.


.0017 CYSTINOSIS, ATYPICAL NEPHROPATHIC

CTNS, GLY110VAL
  
RCV000004710

In a patient who had atypical nephropathic cystinosis (see 219800), presenting with Fanconi syndrome (134600) and end-stage renal disease, but surprisingly without extrarenal symptoms even late in life, Kalatzis et al. (2002) detected a gly110-to-val (G110V) mutation situated in the N-terminal region of the CTNS gene. As this substitution affected a nonconserved residue, it was not expected to have a significant effect, but it involved the last nucleotide of exon 6 and affected CTNS splicing. Aberrant transcripts were produced that induced a frameshift at amino acid position 111 and led to premature protein termination prior to the seventh transmembrane segment; no correctly spliced CTNS transcript could be detected. However, only leukocyte RNA was studied and it was considered possible that G110V did not lead to the same splicing events in all tissues. Misspliced transcripts in the kidney might account for the severe renal phenotype, whereas the presence of a correctly spliced form, even in small amounts, in other organs could explain the lack of extrarenal disorders.


.0018 CYSTINOSIS, LATE-ONSET JUVENILE OR ADOLESCENT NEPHROPATHIC TYPE

CYSTINOSIS, ATYPICAL NEPHROPATHIC, INCLUDED
CTNS, SER139PHE
  
RCV000004711...

In 2 unrelated Spanish patients with juvenile-onset nephropathic cystinosis (219900), Macias-Vidal et al. (2009) identified compound heterozygosity for a 416C-T transition in the CTNS gene, resulting in a ser139-to-phe (S139F) substitution, and a 4-bp deletion (606272.0004) and a 57-kb deletion (606272.0005), respectively. The S139F mutation had previously been identified in a patient with 'nonclassic' cystinosis (see 219800), with onset before age 7 years but a milder course of disease than the infantile nephropathic form, by Attard et al. (1999), who suggested that the mutation might allow production of functional protein or be located in a region of cystinosin that was not functionally important.


See Also:

REFERENCES

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  2. Attard, M., Jean, G., Forestier, L., Cherqui, S., van't Hoff, W., Broyer, M., Antignac, C., Town, M. Severity of phenotype in cystinosis varies with mutations in the CTNS gene: predicted effect on the model of cystinosin. Hum. Molec. Genet. 8: 2507-2514, 1999. [PubMed: 10556299, related citations] [Full Text]

  3. Bendavid, C., Kleta, R., Long, R., Ouspenskaia, M., Muenke, M., Haddad, B. R., Gahl, W. A. FISH diagnosis of the common 57-kb deletion in CTNS causing cystinosis. Hum. Genet. 115: 510-514, 2004. [PubMed: 15365816, related citations] [Full Text]

  4. Bois, E., Feingold, J., Frenay, P., Briard, M.-L. Infantile cystinosis in France: genetics, incidence, geographic distribution. J. Med. Genet. 13: 434-438, 1976. [PubMed: 1018302, related citations] [Full Text]

  5. Buntinx, L., Voets, T., Morlion, B., Vangeel, L., Janssen, M., Cornelissen, E., Vriens, J., de Hoon, J., Levtchenko, E. TRPV1 dysfunction in cystinosis patients harboring the homozygous 57 kb deletion. Sci. Rep. 6: 35395, 2016. Note: Electronic Article. [PubMed: 27734949, images, related citations] [Full Text]

  6. Cherqui, S., Sevin, C., Hamard, G., Kalatzis, V., Sich, M., Pequignot, M. O., Gogat, K., Abitbol, M., Broyer, M., Gubler, M.-C., Antignac, C. Intralysosomal cystine accumulation in mice lacking cystinosin, the protein defective in cystinosis. Molec. Cell. Biol. 22: 7622-7632, 2002. [PubMed: 12370309, images, related citations] [Full Text]

  7. Forestier, L., Jean, G., Attard, M., Cherqui, S., Lewis, C., van't Hoff, W., Broyer, M., Town, M., Antignac, C. Molecular characterization of CTNS deletions in nephropathic cystinosis: development of a PCR-based detection assay. Am. J. Hum. Genet. 65: 353-359, 1999. [PubMed: 10417278, related citations] [Full Text]

  8. Gahl, W. A., Thoene, J. G., Schneider, J. A. Cystinosis. New Eng. J. Med. 347: 111-121, 2002. [PubMed: 12110740, related citations] [Full Text]

  9. Goodman, S., Khan, M., Sharma, J., Li, Z., Cano, J., Castellanos, C., Estrada, M. V., Gertsman, I., Cherqui, S. Deficiency of the sedoheptulose kinase (Shpk) does not alter the ability of hematopoietic stem cells to rescue cystinosis in the mouse model. Molec. Genet. Metab. 134: 309-316, 2021. [PubMed: 34823997, related citations] [Full Text]

  10. Kalatzis, V., Cohen-Solal, L., Cordier, B., Frishberg, Y., Kemper, M., Nuutinen, E. M., Legrand, E., Cochat, P., Antignac, C. Identification of 14 novel CTNS mutations and characterization of seven splice site mutations associated with cystinosis. Hum. Mutat. 20: 439-446, 2002. [PubMed: 12442267, related citations] [Full Text]

  11. Kalatzis, V., Nevo, N., Cherqui, S., Gasnier, B., Antignac, C. Molecular pathogenesis of cystinosis: effect of CTNS mutations on the transport activity and subcellular localization of cystinosin. Hum. Molec. Genet. 13: 1361-1371, 2004. [PubMed: 15128704, related citations] [Full Text]

  12. Macias-Vidal, J., Rodes, M., Hernandez-Perez, J. M., Vilaseca, M. A., Coll, M. J. Analysis of the CTNS gene in 32 cystinosis patients from Spain. (Letter) Clin. Genet. 76: 486-489, 2009. [PubMed: 19863563, related citations] [Full Text]

  13. Mason, S., Pepe, G., Dall'Amico, R., Tartaglia, S., Casciani, S., Greco, M., Bencivenga, P., Murer, L., Rizzoni, G., Tenconi, R., Clementi, M. Mutational spectrum of the CTNS gene in Italy. Europ. J. Hum. Genet. 11: 503-508, 2003. [PubMed: 12825071, related citations] [Full Text]

  14. McGowan-Jordan, J., Stoddard, K., Podolsky, L., Orrbine, E., McLaine, P., Town, M., Goodyer, P., MacKenzie, A., Heick, H. Molecular analysis of cystinosis: probable Irish origin of the most common French Canadian mutation. Europ. J. Hum. Genet. 7: 671-678, 1999. [PubMed: 10482956, related citations] [Full Text]

  15. Phornphutkul, C., Anikster, Y., Huizing, M., Braun, P., Brodie, C., Chou, J. Y., Gahl, W. A. The promoter of a lysosomal membrane transporter gene, CTNS, binds Sp-1, shares sequences with the promoter of an adjacent gene, CARKL, and causes cystinosis if mutated in a critical region. Am. J. Hum. Genet. 69: 712-721, 2001. [PubMed: 11505338, images, related citations] [Full Text]

  16. Rupar, C. A., Matsell, D., Surry, S., Siu, V. A G339R mutation in the CTNS gene is a common cause of nephropathic cystinosis in the south western Ontario Amish Mennonite population. (Letter) J. Med. Genet. 38: 615-616, 2001. [PubMed: 11565547, related citations] [Full Text]

  17. Shotelersuk, V., Larson, D., Anikster, Y., McDowell, G., Lemons, R., Bernardini, I., Guo, J., Thoene, J., Gahl, W. A. CTNS mutations in an American-based population of cystinosis patients. Am. J. Hum. Genet. 63: 1352-1362, 1998. [PubMed: 9792862, related citations] [Full Text]

  18. Thoene, J., Lemons, R., Anikster, Y., Mullet, J., Paelicke, K., Lucero, C., Gahl, W., Schneider, J., Shu, S. G., Campbell, H. T. Mutations of CTNS causing intermediate cystinosis. Molec. Genet. Metab. 67: 283-293, 1999. [PubMed: 10444339, related citations] [Full Text]

  19. Touchman, J. W., Anikster, Y., Dietrich, N. L., Braden Maduro, V. V., McDowell, G., Shotelersuk, V., Bouffard, G. G., Beckstrom-Sternberg, S. M., Gahl, W. A., Green, E. D. The genomic region encompassing the nephropathic cystinosis gene (CTNS): complete sequencing of a 200-kb segment and discovery of a novel gene within the common cystinosis-causing deletion. Genome Res. 10: 165-173, 2000. [PubMed: 10673275, images, related citations] [Full Text]

  20. Town, M., Jean, G., Cherqui, S., Attard, M., Forestier, L., Whitmore, S. A., Callen, D. F., Gribouval, O., Broyer, M., Bates, G. P., van't Hoff, W., Antignac, C. A novel gene encoding an integral membrane protein is mutated in nephropathic cystinosis. Nature Genet. 18: 319-324, 1998. [PubMed: 9537412, related citations] [Full Text]

  21. Wamelink, M. M. C., Struys, E. A., Jansen, E. E. W., Levtchenko, E. N., Zijlstra, F. S. M., Engelke, U., Blom, H. J., Jakobs, C., Wevers, R. A. Sedoheptulokinase deficiency due to a 57-kb deletion in cystinosis patients causes urinary accumulation of sedoheptulose: elucidation of the CARKL gene. Hum. Mutat. 29: 532-536, 2008. [PubMed: 18186520, related citations] [Full Text]


Hilary J. Vernon - updated : 03/17/2022
Paul J. Converse - updated : 08/23/2017
Marla J. F. O'Neill - updated : 1/13/2010
Cassandra L. Kniffin - updated : 7/28/2008
George E. Tiller - updated : 9/13/2006
Patricia A. Hartz - updated : 3/28/2006
Victor A. McKusick - updated : 4/27/2005
Marla J. F. O'Neill - updated : 11/3/2004
Victor A. McKusick - updated : 1/2/2003
Victor A. McKusick - updated : 8/26/2002
Michael J. Wright - updated : 7/31/2002
Deborah L. Stone - updated : 11/7/2001
Creation Date:
Ada Hamosh : 9/20/2001
carol : 03/17/2022
alopez : 12/11/2017
mgross : 08/23/2017
mcolton : 04/17/2015
wwang : 3/19/2010
wwang : 1/26/2010
terry : 1/13/2010
wwang : 7/29/2008
ckniffin : 7/28/2008
terry : 11/16/2006
alopez : 9/13/2006
mgross : 3/31/2006
terry : 3/28/2006
tkritzer : 5/10/2005
terry : 4/27/2005
carol : 11/4/2004
carol : 11/4/2004
tkritzer : 11/3/2004
carol : 7/29/2003
tkritzer : 1/7/2003
tkritzer : 1/6/2003
terry : 1/2/2003
terry : 11/22/2002
tkritzer : 9/6/2002
tkritzer : 8/29/2002
terry : 8/26/2002
cwells : 8/1/2002
terry : 7/31/2002
carol : 11/7/2001
carol : 9/25/2001
carol : 9/25/2001
carol : 9/25/2001

* 606272

CYSTINOSIN; CTNS


HGNC Approved Gene Symbol: CTNS

SNOMEDCT: 22830006, 62332007;  


Cytogenetic location: 17p13.2     Genomic coordinates (GRCh38): 17:3,636,459-3,663,103 (from NCBI)


Gene-Phenotype Relationships

Location Phenotype Phenotype
MIM number
Inheritance Phenotype
mapping key
17p13.2 Cystinosis, atypical nephropathic 219800 Autosomal recessive 3
Cystinosis, late-onset juvenile or adolescent nephropathic 219900 Autosomal recessive 3
Cystinosis, nephropathic 219800 Autosomal recessive 3
Cystinosis, ocular nonnephropathic 219750 Autosomal recessive 3

TEXT

Cloning and Expression

Town et al. (1998) identified a novel gene, CTNS, within the deletion interval on chromosome 17 in patients with nephropathic cystinosis (219800). They found that CTNS encodes an integral membrane protein, which they designated cystinosin, that has features of a lysosomal membrane protein. CTNS, a putative cystine transporter, contains 367 amino acids and 7 transmembrane domains. A 2.7-kb transcript of the CTNS gene was strongly expressed in pancreas, kidney (mature and fetal), skeletal muscle, to a lesser extent in placenta and heart, and weakly in lung and liver.


Gene Structure

Town et al. (1998) determined that the CTNS gene has 12 exons. Phornphutkul et al. (2001) identified the CTNS promoter as the region encompassing nucleotides -316 to +1 with respect to the transcription start site. This region contains an Sp-1 regulatory element at positions -299 to -293 which, as shown by electrophoretic mobility shift assays, binds Sp-1. The CTNS promoter region shares 41 nucleotides with the promoter region of an adjacent gene, CARKL (SHPK; 605060), whose start site is 501 bp from the CTNS start site. CARKL is aligned on the other DNA strand in the other direction.


Mapping

Town et al. (1998) found that the marker locus D17S829 was homozygously deleted in 23 of 70 patients with nephropathic cystinosis and mapped a novel gene, CTNS, to the deletion interval.


Molecular Genetics

Town et al. (1998) identified 11 different mutations in the CTNS gene (see, e.g., 606272.0001-606272.0005), all predicted to cause loss of function of the protein, segregating with nephropathic cystinosis. The most common mutation was a 65-kb deletion (606272.0005), found in 23 (33%) of 70 patients.

Shotelersuk et al. (1998) performed mutation analysis of 108 American-based nephropathic cystinosis patients and found that 48 (44%) were homozygous for the 'European' 65-kb deletion, 2 had a smaller major deletion, 11 were homozygous and 3 were heterozygous for 753G-A (W138X; 606272.0003), and 24 had 21 other mutations. In 20 patients (19%), no mutations were found. Of 82 alleles bearing the 65-kb deletion, 38 derived from Germany, 28 from the British Isles, and 4 from Iceland. The 18 new mutations identified in this study included the first reported missense mutation, 2 in-frame deletions, and mutations in patients of African American, Mexican, and Indian ancestry. CTNS mutations were spread throughout the leader sequence, transmembrane, and nontransmembrane regions. According to a cystinosis clinical severity score, homozygotes for the 65-kb deletion and for W138X had average disease, whereas mutations involving the first amino acids prior to transmembrane domains were associated with mild disease. By Northern blot analysis, CTNS was not expressed in patients homozygous for the 65-kb deletion but was expressed in all 15 other patients tested.

Structure predictions suggested that cystinosin is a novel integral lysosomal membrane protein. Attard et al. (1999) examined the predicted effects of mutations on this model of cystinosin. They screened patients with infantile nephropathic cystinosis, those with late-onset cystinosis, and patients whose phenotype did not fit the classic definitions. They identified 23 different mutations in the CTNS gene, 14 of which were novel. Of 25 patients with infantile nephropathic cystinosis, 12 had 2 severely truncating mutations, consistent with a loss of functional protein, and 13 had missense or in-frame deletions, which would result in disruption of transmembrane domains and loss of protein function. Mutations identified in 2 late-onset patients (see, e.g., 606272.0008) affected functionally unimportant regions of cystinosin, accounting for the patients' milder phenotype. For 3 patients, the age of onset of cystinosis was under 7 years, but the course of the disease was milder than the infantile nephropathic form. This suggested that the missense mutations identified in these individuals (see, e.g., 606272.0007) allowed production of a functional protein and may also indicate regions of cystinosin that are not functionally important.

As indicated earlier, identification of the CTNS gene was facilitated by the detection of deletions spanning the cystinosis locus in affected individuals. Two types of deletions were detected, one of approximately 65 kb, which was found in homozygous state in nearly one-third of cystinotic individuals, and a smaller one of 9.5 to 16 kb, which was carried by a single family. Both the larger and the smaller deletion span the 5-prime end of the CTNS gene, covering exons 1 to 10 and 1 to 3, respectively; STS analysis indicated that the larger deletion was the same size in all patients. Forestier et al. (1999) characterized the deletion breakpoints and demonstrated that, although both deletions occur in regions of repetitive sequences, they are the result of nonhomologous recombination. This type of mechanism suggested that the deletion of approximately 65 kb is not a recurrent mutation, and the results confirmed that it is identical in all patients. Haplotype analysis showed that this large deletion is due to a founder effect that occurred in a white individual, and that it probably arose in the middle of the first millennium. Forestier et al. (1999) also described a rapid PCR-based assay that will accurately detect both homozygous and heterozygous deletions. They used this assay to show that the 65-kb deletion is present in either the homozygous or the heterozygous state in 76% of cystinotic patients of European origin.

Touchman et al. (2000) sequenced 200 kb surrounding the CTNS gene and found that the common cystinosis deletion (606272.0005) is approximately 57 rather than 65 kb. The authors identified SHPK, which they designated CARKL, within this deleted region. The findings indicated that patients with the 57-kb deletion in CTNS also have a deletion of CARKL, which may account for phenotypic variability.

Phornphutkul et al. (2001) identified mutations in the CTNS promoter region in 3 patients with cystinosis (606272.0012-606272.0014). Each of the promoter mutations drastically reduced CAT activity when inserted into a reporter construct and failed either to cause a mobility shift when exposed to nuclear extract or to compete with the normal oligonucleotide's mobility shift. These mutations had no effect on promoter activity of the CARKL gene.

Gahl et al. (2002) stated that more than 50 different CTNS mutations had been described in homozygous form in cystinosis. The most common mutation is the 57,257-bp deletion, which is found in homozygous state in approximately 50% of cystinosis patients of northern European descent. The deletion is an ancient founder mutation; more recent CTNS mutations involve alterations in the promoter region, leader sequence, transmembrane domains, or nontransmembrane regions. Mutations include small deletions and insertions and nonsense, missense, and splicing mutations.

Gahl et al. (2002) stated that patients with intermediate cystinosis (219900) and patients with ocular, or nonnephropathic, cystinosis (219750) generally have 1 severe CTNS mutation (e.g., the 57-kb deletion or a nonsense mutation) and 1 mild mutation, so that part of the transport function of cystinosin is retained. However, homozygosity for a mutation of a conserved amino acid (N323K; 606272.0016) was observed in 2 sibs in Taiwan with intermediate cystinosis (Thoene et al., 1999), indicating presumably that the mutation allowed for some residual cystine transport, accounting for the mild clinical presentation.

Mason et al. (2003) analyzed the CTNS gene in 42 Italian patients with nephropathic cystinosis and found that the mutation spectrum in this population differed from that previously reported for the northern European population: the 57-kb deletion was present in a lower percentage (17%) and splicing mutations represented 30% of the mutations detected.

By screening for mutations in the CTNS exons and promoter region, Kalatzis et al. (2002) identified 14 novel mutations associated with cystinosis: 11 underlying infantile cystinosis, 2 juvenile cystinosis, and 1 associated with an atypical form of the disease (606272.0017). These mutations, all situated in the exons or immediately flanking intronic sequences, comprised in-frame insertions and deletions, as well as missense, nonsense, and putative splice site mutations. Since the cloning of CTNS, the authors had screened for mutations in 108 affected individuals, with a high mutation detection rate of 95.8%. The few undetectable mutant alleles segregated mostly in the noninfantile forms, suggesting that these individuals carried mutations either in the introns or in unidentified regulatory sequences.

Kalatzis et al. (2004) studied the relationship between transport activity and intracellular localization of cystinosin mutants and their associated clinical phenotype. Thirty-one pathogenic mutations (24 missense mutations, 7 in-frame deletions or insertions) were analyzed. Most of the mutations did not alter the lysosomal localization of cystinosin, although 3 partially mislocalized the protein independently of its C-terminal sorting motif, thus confirming the presence of an additional sorting mechanism. Sixteen of 19 mutations associated with infantile cystinosis abolished transport, whereas 3 of 5 mutations associated with juvenile or ocular forms strongly reduced transport. Five atypical, unclassified, or misclassified mutations could be clarified using the transport data and additional genetic information. The authors concluded that impaired transport is the most frequent cause of pathogenicity, with infantile cystinosis generally resulting from a total loss of activity.

Macias-Vidal et al. (2009) analyzed the CTNS gene in 32 unrelated cystinosis patients, 27 Spanish and 5 Moroccan, and identified homozygous or compound heterozygous mutations in 28 of them; only 1 mutation was detected in 4 patients. All but 2 of the patients had the infantile form of cystinosis and had truncating mutations or mutations affecting conserved amino acids associated with transmembrane regions of the protein. The 2 juvenile cystinosis patients were both compound heterozygotes for a truncating mutation (606272.0004 and 606272.0005, respectively) and a missense mutation (S139F; 606272.0018) in the CTNS gene; the latter had previously been found in a patient with a 'nonclassic,' milder form of nephropathic cystinosis by Attard et al. (1999), who suggested that the S139F mutation might allow production of functional protein or be located in a region of cystinosin that was not functionally important.


Animal Model

Using a promoter trap approach, Cherqui et al. (2002) created mice expressing a truncated cystinosin protein. In wildtype mice, cystinosin localized to lysosomes and transported cystine at acidic pH, whereas the truncated cystinosin mislocalized to the plasma membrane and lost its cystine transport function. These Ctns -/- mice accumulated cystine in all organs tested, and cystine crystals, pathognomonic for cystinosis, were observed. Ctns -/- mice developed ocular changes similar to those observed in affected individuals, bone defects, and behavioral anomalies. However, Ctns -/- mice did not develop proximal tubulopathy or renal failure. As in cystinosis patients, cysteamine administration aided cystine clearance in Ctns -/- mice.

Goodman et al. (2021) transplanted hematopoietic stem and progenitor cells (HSPCs) from a Shpk -/- mouse into a Ctns -/- mouse. The treated Ctns -/- mice had a significant reduction in cystine load in multiple tissues and restoration of Ctns expression compared to untreated mice. The treated mice also had improved kidney morphologic structure compared to untreated Ctns -/- mice. Goodman et al. (2021) concluded that absence of SHPK does not alter the ability of HSPCs to recue cystinosis, and that patients with cystinosis who are homozygous for a common 57-kb deletion (606272.0005) on chromosome 17p13, which includes both the CTNS and SHPK genes, would likely benefit from ex vivo gene therapy approaches.


ALLELIC VARIANTS 18 Selected Examples):

.0001   CYSTINOSIS, NEPHROPATHIC

CTNS, GLY95TER
SNP: rs121908124, ClinVar: RCV000004691

In 2 consanguineous families from Pakistan, Town et al. (1998) found that nephropathic cystinosis (219800) was associated with a gly95-to-ter (G95X) mutation in the CTNS gene. Analysis of 5 microsatellites covering a 4-cM interval showed a common haplotype, suggesting that these families may be related. The mutation was a G-to-T transversion at nucleotide 622, which converted GGA (gly) to TGA (stop).


.0002   CYSTINOSIS, NEPHROPATHIC

CTNS, 2-BP DEL, 397TG
SNP: rs1567695026, ClinVar: RCV000004692

In 2 families from central France, Town et al. (1998) found that nephropathic cystinosis (219800) was associated with hemizygosity for the same 2-bp deletion of the CTNS gene: deletion of TG at 397/399 resulted in a stop codon at the site of the mutation. The 2 families shared a common haplotype that segregated with the deletion. Deletion of the second allele was present in affected members of each family.


.0003   CYSTINOSIS, NEPHROPATHIC

CTNS, TRP138TER
SNP: rs113994205, rs121908125, gnomAD: rs113994205, rs121908125, ClinVar: RCV000004693, RCV000630473, RCV000723832, RCV001276658, RCV002512763

One family from Northern Ireland and one from Eire were found by Town et al. (1998) to have the same mutation as the basis of nephropathic cystinosis (219800): a TGG-to-TGA transition at nucleotide 753 resulting in a trp138-to-ter (W138X) nonsense mutation.

McGowan-Jordan et al. (1999) found the W138X mutation in 21/40 French Canadian cystinosis chromosomes. In all cases the mutation was on a distinctive haplotype. They found the same haplotype in 2 Irish families with this mutation, supporting the hypothesis that Celtic chromosomes represent an extensive portion of cystinosis chromosomes in French Canada. The studies also suggested a frequently unrecognized contribution from non-Gallic sources in the French Canadian population.


.0004   CYSTINOSIS, NEPHROPATHIC

CYSTINOSIS, LATE-ONSET JUVENILE OR ADOLESCENT NEPHROPATHIC TYPE, INCLUDED
CTNS, 4-BP DEL, 18GACT
SNP: rs786204501, ClinVar: RCV000004695, RCV000169183, RCV000258029, RCV000698691, RCV000723831, RCV001843488, RCV002516530, RCV003917579

In 4 families from 3 different continents, Town et al. (1998) found that nephropathic cystinosis (219800) was associated with deletion of 4 nucleotides, GACT, at nucleotide 357 of the CTNS gene. This resulted in frameshift and a premature termination. The 4 families did not share a common haplotype, indicating a recurrent mutation. Macias-Vidal et al. (2009) noted that based on numbering from the ATG initiation codon the deletion occurs at nucleotide 18.

In a Spanish patient with juvenile-onset nephropathic cystinosis (219900), Macias-Vidal et al. (2009) identified compound heterozygosity for a 416C-T transition in the CTNS gene, resulting in a ser139-to-phe (S139F; 606272.0018) substitution, and the 4-bp deletion.


.0005   CYSTINOSIS, NEPHROPATHIC

CYSTINOSIS, LATE-ONSET JUVENILE OR ADOLESCENT NEPHROPATHIC TYPE, INCLUDED
CYSTINOSIS, OCULAR NONNEPHROPATHIC, INCLUDED
CTNS, 57-KB DEL
ClinVar: RCV000004696, RCV000004697, RCV000004698

This common mutation in nephropathic cystinosis (219800) was originally reported as a 65-kb deletion. Touchman et al. (2000) sequenced 200 kb surrounding the CTNS gene and found that the deletion is approximately 57 rather than 65 kb. The authors identified SHPK (605060), which they designated CARKL, within this deleted region. The findings indicated that the 57-kb deletion includes deletion of CARKL in addition to CTNS, which may account for phenotypic variability in patients.

In a French/British report (Town et al., 1998), 23 (33%) of 70 patients with nephropathic cystinosis had a 65-kb deletion in the CTNS gene. Among American-based patients studied by Shotelersuk et al. (1998), 48 (44%) of 108 were homozygous for the 65-kb 'European' deletion. Of 96 alleles from these patients, 82 were assigned a nation of origin; 38 (46%) derived from Germany and 28 (34%) arose from the British Isles. Two apparently unrelated patients with homozygous deletions came from Iceland. In addition to the 48 patients homozygous for the 65-kb deletion, many of the patients may have a single copy of the deletion. An upstream deletion breakpoint needed to be determined before a PCR-based test of heterozygosity for the deletion could be developed.

Gahl et al. (2002) stated that the 57-kb deletion is found in the homozygous state in approximately 50% of patients of northern European descent who have cystinosis. This founder mutation, which removes the first 10 exons of CTNS and eliminates expression of the protein, apparently occurred in Germany in approximately 500 A.D. (Shotelersuk et al., 1998) and spread by migration to other regions, including Iceland.

Bendavid et al. (2004) described a FISH method permitting cytogenetic laboratories to test for the 57-kb deletion, which is found in approximately 60% of patients with cystinosis in the United States and northern Europe.

Wamelink et al. (2008) found that cystinosis patients homozygous for the 57-kb deletion had increased urinary sedoheptulose and erythritol compared to patients with other CTNS mutations. Enzyme studies of cultured fibroblasts revealed an 80% reduction in sedoheptulose phosphorylating activity compared to cystinosis patients with other mutations and controls. The findings indicated that the CARKL gene encodes sedoheptulokinase, which functions in the pentose phosphate pathway.

Buntinx et al. (2016) noted that the most common mutation in Northern European patients with cystinosis is the 57-kb deletion in the CTNS gene. This deletion extends into the noncoding region upstream of the start codon of the TRPV1 gene (602076), which encodes a capsaicin- and heat-sensitive ion channel. Buntinx et al. (2016) found that patients heterozygous for the deletion showed normal sensory responses, whereas patients homozygous for the mutation exhibited a 60% reduction in vasodilation and pain evoked by capsaicin, as well as an increase in heat detection threshold. Responses to cold, mechanical stimuli, or cinnamaldehyde, a TRPA1 (604775) agonist, were unaltered. Buntinx et al. (2016) concluded that cystinosis patients homozygous for the 57-kb CTNS deletion have a strong reduction of TRPV1 function, possibly accounting for sensory alterations and thermoregulatory deficits in these patients.

Compound Heterozygosity for the 57-kb Deletion

In a 38-year-old woman who presented with photophobia at 38 years of age but had suffered chronic sensitivity to light (219750), Anikster et al. (2000) identified compound heterozygosity for the 57-kb deletion and a 928G-A transition, resulting in a glycine to arginine substitution at codon 197 (G197R; 606272.0011). Compound heterozygosity was also found in 2 additional patients from the same family with ocular cystinosis.

In a Spanish patient with juvenile-onset nephropathic cystinosis (219900), Macias-Vidal et al. (2009) identified compound heterozygosity for a 416C-T transition in the CTNS gene, resulting in a ser139-to-phe (S139F; 606272.0018) substitution, and the 57-kb deletion.


.0006   CYSTINOSIS, NEPHROPATHIC

CTNS, GLY169ASP
SNP: rs121908126, ClinVar: RCV000004699, RCV002512764

One of 7 missense mutations in the CTNS gene discovered by Shotelersuk et al. (1998) in patients with nephropathic cystinosis (219800) was a gly169-to-asp (G169D) amino acid substitution. Significant CTNS expression was associated with homozygosity of this mutation. All 7 missense mutations gave rise to amino acid changes either inside a transmembrane domain or in the first amino acid prior to a transmembrane domain.


.0007   CYSTINOSIS, ATYPICAL NEPHROPATHIC

CTNS, VAL42ILE
SNP: rs35086888, gnomAD: rs35086888, ClinVar: RCV000004700, RCV000276289, RCV000333816, RCV000440461, RCV001276655, RCV001699175, RCV002512765, RCV003914807

In 3 patients, Attard et al. (1999) found an atypical presentation of cystinosis (see 219800). Although onset was less than 7 years of age, the course was atypically mild. One of the 3 patients (L18) was homozygous for a G-to-A transition in the CTNS gene, resulting in a val42-to-ile (V42I) substitution in the nonconserved region toward the N terminus. This part of the protein is predicted to lie within the lumen of the lysosome, and the mutation was adjacent to, but would not affect, a potential N-glycosylation site. Thus, the location of the mutation was consistent with a milder phenotype.


.0008   CYSTINOSIS, LATE-ONSET JUVENILE OR ADOLESCENT NEPHROPATHIC TYPE

CTNS, IVS7AS, C-G, -10
SNP: rs765481486, gnomAD: rs765481486, ClinVar: RCV001836614, RCV002567954

In a patient typical of late-onset cystinosis (219900), Attard et al. (1999) identified an intronic mutation of the CTNS gene, a C-to-G transversion at nucleotide 801 -10. This resulted in the formation of an alternative splice site upstream of the normal site. Sequencing across the exon 7-8 boundary in cDNA showed the homozygous insertion of 9 bases, which would result in the addition of 3 amino acids, pro-cys-ser, at a point immediately adjacent to the second transmembrane domain. Although this occurred in a conserved region, the first cytosolic domain is very small (normally 4 amino acids) and consequently may not be functionally important. The addition of the imino group of proline at this point might be expected to cause disruption of the folding of the polypeptide chain, but is unlikely to enter or interfere with the transmembrane domain.


.0009   CYSTINOSIS, OCULAR NONNEPHROPATHIC

CTNS, IVS10AS, C-G, -3
SNP: rs113994210, gnomAD: rs113994210, ClinVar: RCV000004702

In a 26-year-old male with ocular nonnephropathic cystinosis (219750), Anikster et al. (2000) reported a C-to-G transversion at the -3 position of the acceptor splice site of IVS10 of the CTNS gene. This mutation was found in compound heterozygosity with a TCCTT deletion at nucleotide 545.


.0010   CYSTINOSIS, NEPHROPATHIC

CTNS, 5-BP DEL, NT545
SNP: rs879758262, ClinVar: RCV000004703, RCV001358753, RCV002527666

Shotelersuk et al. (1998) identified a 5-bp deletion starting at nucleotide 545 resulting in an I69R amino acid substitution and a stop codon at position 73 of the CTNS gene in a patient with classic cystinosis (219800).


.0011   CYSTINOSIS, OCULAR NONNEPHROPATHIC

CTNS, GLY197ARG
SNP: rs113994207, gnomAD: rs113994207, ClinVar: RCV000004704, RCV000169004, RCV000514820, RCV000763395, RCV001844005, RCV002512766

In a 38-year-old woman who presented with photophobia at 38 years of age but had suffered chronic sensitivity to light (219750), Anikster et al. (2000) identified a G-to-A transition at nucleotide 928, resulting in a glycine to arginine substitution at codon 197 (G197R). The patient was compound heterozygous for the 57-kb deletion (606272.0005). This mutation was also found in 2 additional patients from the same family with ocular cystinosis. Both patients were compound heterozygous for the G197R mutation and the 57-kb deletion.


.0012   CYSTINOSIS, NEPHROPATHIC

CTNS, -295G-C, PROMOTER
SNP: rs112140949, gnomAD: rs112140949, ClinVar: RCV001655746, RCV001826361, RCV001836615, RCV002568019

In a woman of Scottish-Irish and Puerto Rican descent with nephropathic cystinosis (219800), Phornphutkul et al. (2001) identified heterozygosity for a 57-kb deletion (606272.0005) and a promoter mutation, a G-to-C change at nucleotide -295, involving the Sp-1 regulatory element, in the CTNS gene. The latter mutation was tested for its effect on promoter activity by generation of a -348 to +1 CTNS-CAT construct and was found to produce 19% of the wildtype CAT activity when transfected in HeLa cells.


.0013   CYSTINOSIS, OCULAR NONNEPHROPATHIC

CTNS, -303G-T, PROMOTER
SNP: rs887657778, ClinVar: RCV000004706

In a girl of German/Norwegian heritage with ocular cystinosis (219750), Phornphutkul et al. (2001) identified heterozygosity for a G197R mutation (606272.0011) and a promoter mutation, a G-to-T transversion at nucleotide -303, in the CTNS gene. The latter mutation was tested for its effect on promoter activity by generation of a -348 to +1 CTNS-CAT construct and was found to produce 5% of the wildtype CAT activity when transfected in HeLa cells.


.0014   CYSTINOSIS, OCULAR NONNEPHROPATHIC

CTNS, 1-BP INS, -303T, PROMOTER
ClinVar: RCV000004707

In a woman with ocular cystinosis (219750) reported by Anikster et al. (2000), Phornphutkul et al. (2001) identified heterozygosity for a G197R mutation (606272.0011) and a promoter mutation, insertion of a T after position -303, in the CTNS gene. The latter mutation was tested for its effect on promoter activity by generation of a -348 to +1 CTNS-CAT construct and was found to produce 16% of the wildtype CAT activity when transfected in HeLa cells.


.0015   CYSTINOSIS, NEPHROPATHIC

CTNS, GLY339ARG
SNP: rs121908127, gnomAD: rs121908127, ClinVar: RCV000004708, RCV001193377, RCV001781181, RCV002512767, RCV003904807

In 4 children with nephropathic cystinosis (219800) in the Old Order Amish population in southwestern Ohio, Rupar et al. (2001) identified a G-to-A transition at nucleotide 1354. This transition resulted in a glycine-to-arginine substitution at residue 339 (G339R). It was found in homozygous form in affected children and in heterozygous form in an unaffected sib.


.0016   CYSTINOSIS, LATE-ONSET JUVENILE OR ADOLESCENT NEPHROPATHIC TYPE

CTNS, ASN323LYS
SNP: rs121908128, gnomAD: rs121908128, ClinVar: RCV000004709, RCV002512768, RCV003466816

Thoene et al. (1999) described 2 sibs in Taiwan with intermediate cystinosis (219900) who had linear growth and weight gain within 2 standard deviations of the mean for their ethnic group until the ages of 13 and 14 years when their plasma creatinine concentrations were 1.2 mg per deciliter and 3.3 mg per deciliter, respectively. They were found to be homozygous for a 1308C-G mutation in the CTNS gene, resulting in the substitution of lysine for the conserved asparagine at position 323 (N323K). Presumably, this mutation allowed for some residual cystine transport, accounting for the mild clinical presentation.


.0017   CYSTINOSIS, ATYPICAL NEPHROPATHIC

CTNS, GLY110VAL
SNP: rs121908129, ClinVar: RCV000004710

In a patient who had atypical nephropathic cystinosis (see 219800), presenting with Fanconi syndrome (134600) and end-stage renal disease, but surprisingly without extrarenal symptoms even late in life, Kalatzis et al. (2002) detected a gly110-to-val (G110V) mutation situated in the N-terminal region of the CTNS gene. As this substitution affected a nonconserved residue, it was not expected to have a significant effect, but it involved the last nucleotide of exon 6 and affected CTNS splicing. Aberrant transcripts were produced that induced a frameshift at amino acid position 111 and led to premature protein termination prior to the seventh transmembrane segment; no correctly spliced CTNS transcript could be detected. However, only leukocyte RNA was studied and it was considered possible that G110V did not lead to the same splicing events in all tissues. Misspliced transcripts in the kidney might account for the severe renal phenotype, whereas the presence of a correctly spliced form, even in small amounts, in other organs could explain the lack of extrarenal disorders.


.0018   CYSTINOSIS, LATE-ONSET JUVENILE OR ADOLESCENT NEPHROPATHIC TYPE

CYSTINOSIS, ATYPICAL NEPHROPATHIC, INCLUDED
CTNS, SER139PHE
SNP: rs267606754, gnomAD: rs267606754, ClinVar: RCV000004711, RCV000004712, RCV000169140, RCV000258030, RCV002243621, RCV002512769

In 2 unrelated Spanish patients with juvenile-onset nephropathic cystinosis (219900), Macias-Vidal et al. (2009) identified compound heterozygosity for a 416C-T transition in the CTNS gene, resulting in a ser139-to-phe (S139F) substitution, and a 4-bp deletion (606272.0004) and a 57-kb deletion (606272.0005), respectively. The S139F mutation had previously been identified in a patient with 'nonclassic' cystinosis (see 219800), with onset before age 7 years but a milder course of disease than the infantile nephropathic form, by Attard et al. (1999), who suggested that the mutation might allow production of functional protein or be located in a region of cystinosin that was not functionally important.


See Also:

Bois et al. (1976)

REFERENCES

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Contributors:
Hilary J. Vernon - updated : 03/17/2022
Paul J. Converse - updated : 08/23/2017
Marla J. F. O'Neill - updated : 1/13/2010
Cassandra L. Kniffin - updated : 7/28/2008
George E. Tiller - updated : 9/13/2006
Patricia A. Hartz - updated : 3/28/2006
Victor A. McKusick - updated : 4/27/2005
Marla J. F. O'Neill - updated : 11/3/2004
Victor A. McKusick - updated : 1/2/2003
Victor A. McKusick - updated : 8/26/2002
Michael J. Wright - updated : 7/31/2002
Deborah L. Stone - updated : 11/7/2001

Creation Date:
Ada Hamosh : 9/20/2001

Edit History:
carol : 03/17/2022
alopez : 12/11/2017
mgross : 08/23/2017
mcolton : 04/17/2015
wwang : 3/19/2010
wwang : 1/26/2010
terry : 1/13/2010
wwang : 7/29/2008
ckniffin : 7/28/2008
terry : 11/16/2006
alopez : 9/13/2006
mgross : 3/31/2006
terry : 3/28/2006
tkritzer : 5/10/2005
terry : 4/27/2005
carol : 11/4/2004
carol : 11/4/2004
tkritzer : 11/3/2004
carol : 7/29/2003
tkritzer : 1/7/2003
tkritzer : 1/6/2003
terry : 1/2/2003
terry : 11/22/2002
tkritzer : 9/6/2002
tkritzer : 8/29/2002
terry : 8/26/2002
cwells : 8/1/2002
terry : 7/31/2002
carol : 11/7/2001
carol : 9/25/2001
carol : 9/25/2001
carol : 9/25/2001