Deubiquitinase with endodeubiquitinase activity that specifically interacts with and cleaves 'Lys-63'-linked long polyubiquitin chains. Shows only weak activity against 'Lys-11' and 'Lys-48'-linked chains (PubMed:29476094, PubMed:29563501, PubMed:29576528). Plays an important role in genome stability pathways, functioning to prevent spontaneous DNA damage and also promote cellular survival in response to exogenous DNA damage (PubMed:29576527, PubMed:29576528). Modulates the ubiquitination status of replication protein A (RPA) complex proteins in response to replication stress (PubMed:29563501). {ECO:0000269|PubMed:29476094, ECO:0000269|PubMed:29563501, ECO:0000269|PubMed:29576527, ECO:0000269|PubMed:29576528}. This is the function of ENSG00000153975 (ZUP1, zinc finger containing ubiquitin peptidase 1).