Joubert syndrome (JBTS) is a rare neurodevelopmental ciliopathy characterized by a distinctive \""molar tooth sign\"" on brain MRI. CSPP1 (centrosome and spindle pole-associatedprotein 1) encodes a ciliary protein essential for ciliogenesis and centrosome function, with pathogenic variants causing Joubert syndrome 21. We describe a 5-month-old JBST patient with CSPP1 variants identified by trio whole-exome sequencing. The proband was identified to carry compound heterozygous variants in the CSPP1 gene: a previously reported maternal nonsense variant (c.3127C>T, p.R1043*) and a novel paternal deep intronic variant (c.1215-26A>G). This intronic variant was confirmed by reverse transcription-polymerase chain reaction (RT-PCR) analysis of patient-derived peripheral blood RNA and minigene assays in HEK293T cells, which demonstrated that c.1215-26A>G induces complete skipping of exon 10 (58 bp), resulting in a frameshift and premature termination codon. Clinical presentation included severe global developmental delay (Motor Development Index 0.3rd percentile, Mental Development Index 0.5th percentile), hypotonia, and classic molar tooth sign on MRI, consistent with JBTS21. Functional validation enabled reclassification of c.1215-26A>G from VUS to likely pathogenic according to ACMG guidelines. These findings expand the mutational spectrum of CSPP1-related JBTS and provides diagnostic evidence through integrated computational prediction and experimental validation, underscoring the critical importance of functional studies for resolving deep intronic variants in clinical practice and genetic counseling for rare ciliopathies.