The genomic region encompassing the nephropathic cystinosis gene (CTNS): Complete sequencing of a 200-kb segment and discovery of a novel gene withinthe common cystinosis-causing deletion

Nephropathic cystinosis is an autosomal recessive disorder caused by the de fective transport of cystine our of lysosomes. Recently, the causative gene (CTNS) was identified and presumed to encode an integral membrane protein called cystinosin. Many of the disease-associated mutations in CTNS are del etions, including one >55 kb in size that represents the most common cystin osis allele encountered to date. In an effort to determine the precise geno mic organization of CTNS and to gain sequence-based insight about the DNA w ithin and flanking cystinosis-associated deletions, we mapped and sequenced the region of human chromosome 17p13 encompassing CTNS. Specifically, a ba cterial artificial chromosome (BAC)-based physical map spanning CTNS was co nstructed by sequence-tagged site (STS)-content mapping. The resulting BAC contig provided the relative order of 43 STSs. Two overlapping BACs, which together contain all of the CTNS exons as well as extensive amounts of flan king DNA, were selected and subjected to shotgun sequencing. A total of 200 ,237 bp of contiguous, high-accuracy sequence was generated. Analysis of th e resulting data revealed a number of interesting features about this genom ic region, including the long-range organization of CTNS insight about the breakpoints and intervening DNA associated with the common cystinosis-causi ng deletion, and structural information about Five genes neighboring CTNS ( human ortholog of rat vanilloid receptor subtype 1 gene, CARKL, TIP-1, P2X5 , and HUMINAE). In particular, sequence analysis detected the presence of a novel gene (CARKL) residing within the most common cystinosis-causing dele tion. This gene encodes a previously unknown protein that is predicted to F unction as a carbohydrate kinase. Interestingly, both CTNS and CARKL are ab sent in nearly half of all cystinosis patients (i.e., those homozygous For the common deletion).