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Abstract Cystinosis is a rare lysosomal storage disorder caused by a variant in the CTNS gene that leads to the accumulation of cystine in the body’s tissues. It has been classified into three subtypes based on its clinical presentation: severe infantile nephropathic cystinosis, intermediate mild form, and ocular non-nephropathic adult form. We report a teenage girl who presented with end stage kidney disease as her first presentation and was found to have corneal cystine crystals upon ophthalmic evaluation. Genetic testing confirmed that she has a CTNS variant, a CTNS variant c.520A > C p.(Ser174Arg) never described in the literature previously. Full family genetic screening supported the diagnosis. She was started on oral and ocular cysteamine and maintained on peritoneal dialysis for a few months and eventually underwent a successful deceased donor kidney transplantation. These findings expand the spectrum of CTNS gene variants and highlight the potential of atypical and severe presentations of this variant during adolescence.