A novel pathogenic APC variant identified in a Chinese pedigree with familial adenomatous polyposis

Background Familial adenomatous polyposis (FAP) is an autosomal dominant genetic disorder characterized by the development of numerous colorectal polyps and a high predisposition to colorectal cancer, primarily caused by germline variants in the APC gene. This study aimed to identify and functionally validate a novel APC variant in a Chinese FAP pedigree. Methods A three-generation Chinese FAP pedigree was recruited. Peripheral blood samples were collected from family members to extract genomic DNA. Whole-exome sequencing (WES) was performed to screen candidate variants, and Sanger sequencing was used for verification. SW480 cells (endogenously deficient in functional APC) were divided into three groups: empty vector group, APC-wild-type (APC-WT) group, and APC-mutant group. Western blot analysis was conducted to detect β-catenin protein expression levels, to evaluate the functional impact of the identified variant. Results The proband’s FAP-associated colorectal cancer was identified as exhibiting microsatellite instability high (MSI-H) with a classic MLH1/PMS2 dual loss pattern. A novel germline variant APC c.3799dup was identified in all affected family members but was absent in unaffected individuals. Western blot analysis showed that β-catenin protein levels in the APC-WT group were significantly lower than those in the APC-Mutant group (P < 0.05) and the empty vector group (P < 0.01). This indicated that the c.3799 dup variant abolished APC’s ability to promote β-catenin degradation, leading to sustained activation of the Wnt/β-catenin pathway. Conclusion The novel APC variant c.3799 dup is a pathogenic variant associated with FAP. Our findings expand the spectrum of known APC variants and provide functional evidence for the pathogenicity of this variant. The rare co-occurrence of FAP and MSI-H in the proband enriches the molecular phenotypic spectrum of FAP-related tumors.