MOTA syndrome, the acronym for Manitoba-oculo-tricho-anal syndrome (OMIM 248450), is a distinct autosomal recessive multiple malformation syndrome caused by mutations in the FREM1 gene (OMIM 608944). Eight patients with MOTA syndrome and a pathogenic FREM1 mutation have previously been documented. We report on a new male patient, 3.5 months old, with MOTA syndrome, who presented with the following features: bilateral incomplete cryptophthalmos with a completely fused, ill-defined upper eyelid and a keratinized cornea, hypertelorism, a broad tip of the nose, a circle-shaped whirl of hair on the forehead, and a low anorectal malformation, which could be corrected on day 2 of life without a colostomy. In expansion to the previously reported phenotype of MOTA syndrome, the patient showed characteristic features reported in patients with Fraser syndrome, including dysplastic ears, cutaneous syndactyly 3/4 of the hands and syndactyly 2/3 of the right foot. Molecular analysis of FREM1 identified compound heterozygosity for a new frameshift deletion in exon 24 (c.4629delC, p.F1544SfsX62) and a previously reported missense mutation in exon 21 (c.3971T>G, p.L1324R). This report further extends the phenotype of MOTA syndrome and underscores the overlapping clinical spectrum of FRAS-FREM complex diseases.