Phenotypic variation is often observed in individuals with the same mutation. However, the mechanisms that contribute to this variation remain largely unknown. Fibronectin mutants in both mouse and zebrafish fail to form a functional cardiovascular system, although the penetrance and expressivity of this phenotype vary depending on the genetic background. Here we investigate the variation of the zebrafish natter phenotype, which is caused by a nonsense mutation in fibronectin 1a (fn1a). natter/fn1a mutants exhibit incompletely penetrant cardia bifida, a phenotype caused by the failure of cardiac progenitors to migrate to the midline. To examine whether this variation is related to the nonsense mutation, we first generated a large deletion in fn1a that removes the proximal promoter and first 17 exons. Characterisation of this allele found that mutants display variable cardiac phenotypes indistinguishable from those observed in natter/fn1a mutants. As phenotypic variation is often associated with changes in paralogous gene expression, we next examined the expression of the fn1a paralogue, fn1b, and observed its upregulation specifically in the natter/fn1a mutants that exhibit a severe phenotype. However, overexpression and double mutant analyses suggest that fn1b expression levels do not modulate the natter/fn1a mutant phenotype. During these studies, we observed a small proportion of natter/fn1a mutants with a wild-type (WT)-like phenotype. Selectively raising WT looking mutant larvae increased the proportion of natter/fn1a mutants displaying the WT-like phenotype from 1.7% to 38.6% in just three generations, indicating the selection of a genetic modifier of the mutant phenotype. We mapped this modifier to the integrin alpha 5 (itgα5) locus through whole-genome sequencing. Furthermore, we found that manipulating itgα5 expression influenced the severity of the fn1a mutant phenotype, and that the variance in itgα5 expression was increased in fn1a mutants exhibiting a severe phenotype. Taken together, these results indicate that itgα5 modifies the fn1a mutant phenotype.