Novel Fanci Mutations in Fanconi Anemia with Vacterl Association

Introduction: Fanconi anemia (FA) is associated with mutations in at least 18 genes in the FA/BRCA DNA repair pathway. Some patients with FA have features of the VACTERL association (vertebral anomalies, anal atresia, congenital heart disease, trachea-esophageal fistula, esophageal atresia, renal, and limb anomalies [radius and/or thumb]). Any three anomalies are required to be classified as VACTERL association. The presence of this association among cases with FA is considered to be 5%; the frequency of FA among those with VACTERL association is unknown.

Objective: To determine the genotype in previously uncharacterized patients with FA and to examine the relationship between genotype and features of VACTERL association.

Methods: The NCI FA cohort included 18 unrelated patients with the VACTERL association, among 54 FA patients who had comprehensive examinations including radiologic and ultrasound studies at the NIH Clinical Center (33%). DNA from patients with unknown genotypes was subjected to whole exome sequencing (WES) at the NCI's Cancer Genomic Research Laboratory; one patient's DNA was also studied by sequencing the coding regions of all known FA genes (Haloplex sequencing) at Vrije Universiteit.

Results: Mutations in FANCI were identified in three of the 18 patients with the VACTERL association, two at the NCI and the third patient at Vrije Universiteit; there were no FANCI patients among those without the VACTERL association. Mutations in the others with VACTERL were A (N=6), C (N=4), D2 (N=2), J (N=2), and unknown (N=1).

NCI-82-1 had multiple birth defects. At 5 9/12 years she had extreme short stature, microcephaly, triangular face, and VACTERL features (fused cervical vertebrae, atrial septal defect [ASD], ventricular septal defect [VSD], duodenal atresia, small kidneys, and absent thumbs). Progressive cytopenias led to stem cell transplantation at age 10 1/2 years, with death a year later from multi-organ failure. WES data identified FANCI mutations: one deletion (p.Ser1268Argfs*5) and one insertion (p.Asp1301Glyfs*3) resulting in premature stop codons.

NCI-253-1 was born at 34 weeks with multiple birth defects. At age 3 she had marked short stature, microcephaly, triangular face, and VACTERL features (cervical vertebral anomaly, VSD, patent foramen ovale, horseshoe kidney, and dangling thumb). Haploplex sequencing revealed one novel mutation in FANCI (p.Cys1014Tyr) and one previously reported mutation (p.Tyr487X).

NCI 309-1 was one of fraternal twins conceived by in vitro fertilization and delivered at 32 weeks by C-section. At age 8 she had microcephaly, a small, triangular face, small eyes, Chiari malformation, and a small pituitary gland with poorly visualized pituitary stalk. Her VACTERL features included small neck, narrow C5 vertebra, bilaterally hypoplastic thumbs, absent radial pulses, and bilateral ureteric reimplantation for reflux. Her FANCI WES identified two mutations, p.Ser347Pro and p.Gly401Glufs*3.

Conclusion: These three cases with FANCI, plus four among 13 with FANCI in the literature constitute seven of 16 cases with FANCI with VACTERL features (44%), significantly higher than the predicted 5%. Recent studies demonstrated that VACTERL features were more frequent than the expected 5% in individuals with FANCB, D1, D2, J, N, and O (Alter and Rosenberg, Mol Syndromol 2013) and L (Vetro et al, Hum Mut 2015). Mutations in FANCI should be added to the genotypes with a very high frequency of the VACTERL phenotype.