Introduction: Familial adenomatous polyposis (FAP) caused by a de novo 5q chromosomal deletion is rare, and precise cytogenetic analysis utilizing comparative genomic hybridization (CGH) arrays have been performed in few cases. Case presentation: We herein present the case of a 38-year-old man with advanced rectal and duodenal cancer, FAP, and severe mental retardation caused by a de novo chromosomal deletion at 5q14-22. He was referred to our outpatient clinic because of a positive fecal occult blood test result. He was found to have advanced rectal cancer, with over 200 colorectal polyps, and duodenal cancer. He underwent laparoscopic total proctocolectomy with definitive ileostomy followed by partial resection of the duodenum. Comparative genomic hybridization to characterize deleted genes identified a large 5q deletion expanding approximately 24.9 Mbp, including the APC gene. Conclusion: Patients who harbor a chromosomal deletion involving 5q21 are at risk of developing rectal cancer and polyposis. Therefore, such patients need early cancer screening following the availability of genetic information.

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