Notable variants included frameshift mutations in ALPK3 and KANSL1L and a missense variant in the previously established X-linked deafness gene POU3F. The mutation in ALPK3 was a homozygous 1-bp deletion (ENST00000258888.5: c.2018delC), resulting in a predicted premature termination (ENSP00000258888.5:p.Gln675SerfsX30) (Fig. 1C). Here, ALPK3 is linked to X-linked deafness.