Subependymal giant cell astrocytomas (SEGAs) are neoplasms that exhibit slow growth patterns and are closely associated with tuberous sclerosis complex (TSC). Recent research indicates that TFE3/TFEB-targeted biomarker glycoprotein nonmetastatic B (GPNMB) is upregulated inTSC1/2-related tumours. In this study, we performed molecular analysis on SEGAs and analyzed GPNMB expression in 6 SEGAs, 10 PXAs, 9 GBMs, 8 eGBMs, 8 diffuse astrocytomas, 8 oligodendrogliomas and 7 glioneuronal tumours through immunohistochemistry, 100 % (6/6) of the SEGA cases exhibited positive GPNMB expression, whereas it was negative in all other CNS tumours. The results indicated that GPNMB is specifically expressed in all SEGAs, distinguishing it from other morphologically similar tumours. The findings demonstrate specific GPNMB expression in SEGA, underscoring its promise as a diagnostic biomarker.