Four children were born to healthy first cousins, three with intractable diarrhea. Sibling A developed hypothyroidism, growth hormone deficiency and subsequently, obesity. Small bowel biopsy in A and D showed a similar non-specific enteropathy.250K SNPs in patients A, B and C were genotyped, and 5 homozygous regions shared by patients A and B that includes 337 protein-coding genes. Whole exome sequencing of patient D sequenced to a coverage of X63, and 97.1%. Of the 1089 on-target variants only 46 variants were homozygous and only 4 were located at the linked regions. We focused on the N309K mutation in the proprotein convertase subtilisin /kexin type 1 (PCSK1) gene, which was predicted as disease-causing. The position of this mutation corresponds to a residue critical to proprotein maturation and enzyme activity, the oxyanion hole transition state-stabilizing amino acid N309. Unexpectedly, the N309K mutant protein exhibited normal prodomain removal and was efficiently secreted from both HEK293 and Neuro2A cells. However, the secreted enzyme showed no catalytic activity, and was not processed into the 66 kDa form in either cell line; the wild-type protein was processed in Neuro2A cells. It was shown that the N309K enzyme is able to cleave its own propeptide but is catalytically inert against in trans substrates. Our findings confirm that the novel mutation N309K in the PCSK1 gene caused the pathology in this family. The failure of enteroendocrine cells caused by mutations in PCSK1 results in severe infantile diarrhea accompanied by multiple endocrine abnormalities.