PLD sample ID. Germline mutation(s)* Predicted protein effect Somatic mutation* Predicted protein effect Ref. ADPKD1 JHU415 PKD1 c.12378C>G p.Tyr4126X PKD1 c.12551insGC p.His4185Argfs*13 [33] ADPKD1 JHU452 PKD1 c.7165T>C PKD1 c.9047A>G - p.Gln3016Arg PKD1 c.8900C>G PKD1 c.10050+2del20 PKD1 c.8558T>C PKD1 c.7567G>T PKD1 c.8733del16 p.Ser2967X aberrant splicing p.Phe2853Ser p.Glu2523X p.Asp2912Argfs*77 [33] ADPKD2 UT1500 PKD2 c.2152insA p.Asn720Lysfs*5 PKD2 c.710-8del19 aberrant splicing [30] PCLD patient 1 PRKCSH c.1341-2A>G aberrant splicing PRKCSH c.224T>C PRKCSH c.1499G>A p.Phe75Ser p.Cys500Tyr [34] *TranscriptID. PRKCSH (NM_002743.2); PKD1 (L33243.1); PKD2 (NM_000297.2)

Table 1: Somatic mutations with the predicted effect on protein level in liver cyst tissue from PLD patients. Types of somatic hits included 5 substitutions, 3 deletions and 1 insertion mutation at the similar gene locus (GRCh37-hg19). These mutations resulted in pathogenic mis-sense changes or truncated protein products.