Haploinsufficiency of FOXF1 causes alveolar capillary dysplasia with misalignment of pulmonary veins (ACDMPV), a lethal neonatal lung developmental disorder. We describe two similar heterozygous CNV deletions involving the FOXF1 enhancer and re-analyze FOXF1 missense mutation, all associated with an unexpectedly mitigated disease phenotype. In one case, the deletion of the maternal allele of the FOXF1 enhancer caused pulmonary hypertension and histopathologically diagnosed MPV without the typical ACD features. In the second case, the deletion of the paternal enhancer resulted in ACDMPV rather than the expected neonatal lethality. In both cases, FOXF1 expression in lung tissue was higher than usually seen or expected in patients with similar deletions, suggesting an increased activity of the remaining allele of the enhancer. Sequencing of these alleles revealed two rare SNVs, rs150502618-A and rs79301423-T, mapping to the partially overlapping binding sites for TFAP2s and CTCF in the core region of the enhancer. Moreover, in a family with three histopathologically-diagnosed ACDMPV siblings whose missense FOXF1 mutation was inherited from the healthy non-mosaic carrier mother, we have identified a rare SNV rs28571077-A within 2-kb of the above-mentioned non-coding SNVs in the FOXF1 enhancer in the mother, that was absent in the affected newborns and 13 unrelated ACDMPV patients with CNV deletions of this genomic region. Based on the low population frequencies of these three variants, their absence in ACDMPV patients, the results of reporter assay, RNAi and EMSA experiments, and in silico predictions, we propose that the described SNVs might have acted on FOXF1 enhancer as hypermorphs.

Children's Hospital of Philadelphia Philadelphia PA USA

CHU Sainte Justine Montreal Québec Canada

Department of Genetics and Pharmaceutical Microbiology Poznan University of Medical Sciences Poznan Poland

Department of Human Genetics Radboud University Medical Center Nijmegen The Netherlands

Department of Medical Genetics Masaryk University and University Hospital Brno Brno Czech Republic

Department of Molecular and Human Genetics Baylor College of Medicine Houston TX USA

Department of Nursing and Midwifery Masaryk University Brno Czech Republic

Department of Obstetrics and Gynecology Masaryk University and University Hospital Brno Brno Czech Republic

Department of Pathology and Immunology Baylor College of Medicine Houston TX USA

Department of Pathology and Laboratory Medicine Perelman School of Medicine Philadelphia PA USA

Department of Pathology Masaryk University and University Hospital Brno Brno Czech Republic

Department of Pathology Université de Montréal Montreal Québec Canada

Department of Pediatrics Université de Montréal Montreal Québec Canada

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