Identification of a Novel Pathogenic Rearrangement Variant of the APC Gene Associated with a Variable Spectrum of Familial Cancer

Abstract

Familial adenomatous polyposis (FAP) is an autosomal-dominant condition characterized by the presence of multiple colorectal adenomas, caused by germline variants in the adenomatous polyposis coli (APC) gene. More than 300 germline variants have been characterized. The detection of novel variants is important to understand the mechanisms of pathophysiology. We identified a novel pathogenic germline variant using next-generation sequencing (NGS) in a proband patient. The variant is a complex rearrangement (c.422+1123_532-577 del ins 423-1933_423-1687 inv) that generates a complete deletion of exon 5 of the APC gene. To study the variant in other family members, we designed an endpoint PCR method followed by Sanger sequencing. The variant was identified in the proband patient’s mother, one daughter, her brother, two cousins, a niece, and a second nephew. In patients where the variant was identified, we found atypical clinical symptoms, including mandibular, ovarian, breast, pancreatic, and gastric cancer. Genetic counseling and cancer prevention strategies were provided for the family. According to the American College of Medical Genetics (ACMG) guidelines, this novel variant is considered a PVS1 variant (very strong evidence of pathogenicity), and it can be useful in association with clinical data for early surveillance and suitable treatment.

Constitutional chromothripsis of the APC locus as a cause of genetic predisposition to colon cancer

“…1 Aside from an abundance of coding variants, several intronic rearrangements, a complex event that generates a complete deletion of exon 5 (c.422+1123_532-577 del ins 423-1933_423-1687 inv), or deep intronic single nucleotide variants have been described for APC. [2][3][4][5][6] The latter loss-of-function mechanisms may frequently escape detection in routine diagnostics.…”

“…Approximately 20% of patients with clinical FAP remain unsolved after routine molecular genetic analysis of the APC and additional polyposis genes, suggesting additional loss-of-function mechanisms 1. Aside from an abundance of coding variants, several intronic rearrangements, a complex event that generates a complete deletion of exon 5 (c.422+1123_532–577 del ins 423–1933_423–1687 inv), or deep intronic single nucleotide variants have been described for APC 2–6. The latter loss-of-function mechanisms may frequently escape detection in routine diagnostics.…”