Autophagy serves as a master regulator of cellular homeostasis. Hence, expectedly autophagic dysfunction has been documented in many diseases such as cancer, neurodegeneration and cardiovascular disorders. A novel homozygous mutation in PLEKHM2 gene (mPLEKHM2) resulted in dilated cardiomyopathy with left ventricular noncompaction (DCM-LVNC), probably as result of impaired autophagy due to disruption of lysosomal movement assisted by PLEKHM2. Here we report a generation of three iPSC lines, four clones originated from two patients with homozygous mPLEKHM2 and two from a heterozygote sibling. All generated lines highly expressed pluripotency markers, spontaneously differentiated into three germ layers, retained the mutation after reprogramming and displayed normal karyotypes.