Dyskeratosis congenita (DC) is a rare hereditary telomere biology disorder characterized by bone marrow failure, nail dystrophy, mucosal leukoplakia, and abnormal skin pigmentation. Telomere shortening resulting from defects in telomere maintenance genes is a central pathogenic mechanism of the disease. TERF1-interacting nuclear factor 2 (TIN2), encoded by the TINF2 gene, is a critical component of the shelterin complex that safeguards telomere integrity by coordinating interactions among TRF1, TRF2, and TPP1/POT1. Heterozygous missense mutations in TINF2 are known to cause autosomal dominant dyskeratosis congenita type 3. In this study, a comprehensive in silico analysis was performed to identify deleterious and pathogenic non-synonymous single-nucleotide polymorphisms (nsSNPs) in the TIN2 protein. A total of 271 nsSNPs were subjected to sequence-based prediction tools (SIFT, PROVEAN, PolyPhen-2, Mutation Assessor, and SAAFEC-SEQ). Structure-based stability analyses of 134 variants located within the resolved crystal structure (PDB ID: 5XYF) were conducted using SDM2, DUET, mCSM, and MUpro. High-confidence deleterious and destabilizing mutations were further evaluated for disease association using PMut, PhD-SNP, and Rhapsody. Twelve missense mutations (A16D, V22G, V34G, L38P, V49G, R52P, R56G, E109G, F114S, L121P, Y139C, and L150P) were consistently predicted as pathogenic. Detailed structural characterization revealed significant alterations in protein stability, packing density, accessible surface area, aggregation propensity, and intermolecular noncovalent interactions. Most of these mutations showed increased aggregation tendency or reduced solubility, suggesting disruption of shelterin complex stability. This study provides structural and functional insights into pathogenic TINF2 variants and highlights potential molecular mechanisms underlying autosomal dominant dyskeratosis congenita.