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Fanconi anemia (FA) is a rare genetic disorder caused by pathogenic variants (PV) in at least 22 genes, which cooperate in the Fanconi anemia/Breast Cancer (FA/BRCA) pathway to maintain genome stability. PV in <i>FANCA</i>, <i>FANCC</i>, and <i>FANCG</i> account for most cases (~90%). This study evaluated the chromosomal, molecular, and physical phenotypic findings of a novel founder <i>FANCG</i> PV, identified in three patients with FA from the <i>Mixe</i> community of Oaxaca, Mexico. All patients presented chromosomal instability and a homozygous PV, <i>FANCG</i>: c.511-3_511-2delCA, identified by next-generation sequencing analysis. Bioinformatic predictions suggest that this deletion disrupts a splice acceptor site promoting the exon 5 skipping. Analysis of Cytoscan 750 K arrays for haplotyping and global ancestry supported the Mexican origin and founder effect of the variant, reaffirming the high frequency of founder PV in <i>FANCG</i>. The degree of bone marrow failure and physical findings (described through the acronyms VACTERL-H and PHENOS) were used to depict the phenotype of the patients. Despite having a similar frequency of chromosomal aberrations and genetic constitution, the phenotype showed a wide spectrum of severity. The identification of a founder PV could help for a systematic and accurate genetic screening of patients with FA suspicion in this population.