Genetic heterogeneity between various lesions of one patient with a germline mutation in the MEN1 gene, reflected both in deoxyribonucleic acid (DNA) sequencing and copy number alteration patterns. Germline DNA, extracted from saliva, showing heterogenous MEN1 mutation. The unaffected allele is lost in the pancreatic neuroendocrine tumor (PNET) and the gastric lymph node (LN). In these two lesions, pathogenic variants were detected in the ATRX gene (insertion) and the SETD2 gene (missense), respectively. In addition, an identical copy-number alteration signature is demonstrated for these two lesions. All together, these findings demonstrate the clonality of these two lesions. The other lesions, liver metastasis and duodenal LN, show only the MEN1 heterogenous variant, which may point toward an undetected driver mutation or epimutation, but show again the clonality. The heterogeneity between the two pairs of tumors is also evident.