Calcium pyrophosphate deposition (CPPD) disease is a common crystal arthropathy in the elderly, but its early-onset forms are rare. While secondary hypomagnesemia is a recognized contributor to CCPD, inherited renal magnesium-wasting syndromes remain underdiagnosed. Here we performed a whole exome sequencing (ES) in order to detect pathogenic variants in a 58-year-old male patient with early and severe, refractory CPPD disease. We conducted a comprehensive clinical, biochemical, radiological, and genetic evaluation of the patient. ES was performed and filtered for rare, likely pathogenic variants following ACMG/AMP criteria. Cascade genetic testing was performed in family members. Hypomagnesemia with inappropriate renal magnesium loss was found. Radiographs revealed diffuse chondrocalcinosis ES identified a novel heterozygous Cyclin and CBS Domain Divalent Metal Cation Transport Mediator (CNNM2) missense variant (c.319G>C; p.Gly107Arg), absent from population databases and predicted deleterious (REVEL 0.82). This variant affects a highly conserved residue in the extracellular β-barrel domain. Family screening revealed two additional carriers with isolated hypomagnesemia, consistent with autosomal dominant inheritance. CNNM2 encodes a basolateral magnesium transporter in the tubule. This is the first reported case of CPPD linked to a CNNM2 variant through persistent hypomagnesemia. Its variants have been linked to renal hypomagnesemia, neurological comorbidities, but no link to CPPD has been described. This expands the phenotypic spectrum of CNNM2-related disorders and highlights the relevance of genetic testing in CPPD cases with unexplained hypomagnesemia. Building on published functional studies and domain-level protein modeling, we propose a simplified three-tier classification scheme that organizes CNNM2 variants into clinically meaningful categories.