ObjectiveTo analyze the distribution of common pathogenic variants for hearing loss in children with nonsyndromic hearing loss and relevant high risk population in Shenzhen so as to provide evidence for molecular diagnosis, genetic counseling and epidemiologic study.MethodsMatrixassisted laser desorption ionization time of flight mass spectrometry (MALDITOFMS) technology was used to detect twenty genetic variants in GJB2, GJB3, SLC26A4, and MTRNR1 in 71 children with prelingual hearing loss aged one to six years (hearing loss group), 145 hearing family members as the highrisk population (highrisk group), and 200 irrelevant individuals with normal hearing as controls (control group).ResultsCommon pathogenic variants for hearing loss were detected in 37% (26/71) of children in the hearing loss group, 28% (40/145) of the highrisk group, and 4.5% (9/200) of the control group. The detection rates of GJB2 variants were 18% (13/71) of children in the hearing loss group, 12% (17/145) of the highrisk group, and 2% (4/200) of the control group, while those of SLC26A4 variants were 18% (13/71), 16% (23/145), and 2.5% (5/200) respectively. The detection rates of GJB2 and SLC26A4 in both the hearing loss group and highrisk group were markedly higher than those in the control group (all P<0.0001), while their differences between the hearing loss group and highrisk group were statistically insignificant (P=0.209). GJB2 and SLC26A4 homozygotes and compound heterozygotes constituted 18% (13/71) of children in the hearing loss group. Homozygotes and compound heterozygotes were not detected in the highrisk population or in controls, which was statistically different from children of the hearing loss group (P<0.0001)。GJB3 and MTRNR1 variants were not found in any individuals tested.ConclusionsHomozygosity and compound heterozygosity of common pathogenic variants in GJB2 and SLC26A4 are significant causes of the prelingual hearing loss in Shenzhen, and GJB2:c.235delC and SLC26A4:c.919-2A>G are the most frequently detected variants. If only one heterozygous pathogenic variant is detected in a child with hearing loss, full gene sequencing should be recommended to establish the molecular etiology.