Background Choanal atresia has only been rarely reported in Kabuki syndrome, but is a common feature of CHARGE syndrome. Otherwise, the two conditions have a number of overlapping features, and molecular links between them have recently been elucidated.

Objectives We report a mother and her two children who presented with congenital choanal atresia. All three were found to have a mutation in the KMT2D gene, suggesting that the family has an unusual presentation of Kabuki syndrome.

Design/methods Phenotypic and molecular data on the affected patients was collected. Microarray and CHD7 sequencing were previously normal in the children. Samples from the mother and her unaffected parents were sent as a trio for whole exome sequencing.

Results The facial features in the family were not typical for Kabuki syndrome, but were highly conserved among affected individuals; they included short palpebral fissures, anteverted nares, tall forehead, and prognathism. All three had bilateral choanal atresia, high arched palate, hypodontia, hearing loss, fetal fingertip pads, and speech delay. One or more had mild learning difficulties, bifid uvula, atrialseptal defect, and scoliosis. A de novo dominant missense mutation in KMT2D was found in the mother (p. Q3575H) and confirmed in the two children. This mutation has not been previously reported in the literature or in ExAC Browser.

Conclusions We report a unique phenotype associated with a novel mutation in the KMT2D gene. Our findings further demonstrate the overlap of features of Kabuki and CHARGE syndromes, and reinforce the potential association between these conditions.