Disruption of the ATE1 and SLC12A1 Genes by Balanced Translocation in a Boy with Non-Syndromic Hearing Loss

Abstract

We report on a boy with non-syndromic hearing loss and an apparently balanced translocation t(10;15)(q26.13;q21.1). The same translocation was found in the normally hearing brother, father and paternal grandfather; however, this does not exclude its involvement in disease pathogenesis, for example, by unmasking a second mutation. Breakpoint analysis via FISH with BAC clones and long-range PCR products revealed a disruption of the arginyltransferase 1 (ATE1) gene on translocation chromosome 10 and the solute carrier family 12, member 1 gene (SLC12A1) on translocation chromosome 15. SNP array analysis revealed neither loss nor gain of chromosomal regions in the affected child, and a targeted gene enrichment panel consisting of 130 known deafness genes was negative for pathogenic mutations. The expression patterns in zebrafish and humans did not provide evidence for ear-specific functions of the ATE1 and SLC12A1 genes. Sanger sequencing of the 2 genes in the boy and 180 GJB2 mutation-negative hearing-impaired individuals did not detect homozygous or compound heterozygous pathogenic mutations. Our study demonstrates the many difficulties in unraveling the molecular causes of a heterogeneous phenotype. We cannot directly implicate disruption of ATE1 and/or SLC12A1 to the abnormal hearing phenotype; however, mutations in these genes may have a role in polygenic or multifactorial forms of hearing impairment. On the other hand, it is conceivable that our patient carries a disease-causing mutation in a so far unidentified deafness gene. Evidently, disruption of ATE1 and/or SLC12A1 gene function alone does not have adverse effects.

Keywords: ATE1; Disease-associated balanced chromosome rearrangement; Non-syndromic hearing impairment; Reciprocal translocation; SLC12A1.

Fig. 1

Chromosome banding and FISH analysis of breakpoint regions. a G-banded karyotype of the index patient showing the apparently balanced derivative chromosomes. b G-banding pattern as well as corresponding ideograms showing the normal and derivative chromosomes resulting from the t(10;15)(q26.13;q21.1) translocation. Arrowheads indicate the translocation breakpoints. c DAPI-stained (blue) metaphase spread of the index patient hybridized with digoxigenin-labeled (red) BAC RP11-78A18. The breakpoint-spanning BAC highlights the ATE1 gene on the normal chromosome 10 as well as the 2 derivative chromosomes 10 and 15.

Fig. 2

Graphic illustrations showing a translocation-mediated disruption of the ATE1 and SLC12A1 genes. The upper part shows a BAC (green) contig covering the ATE1 breakpoint region on chromosome 10. Bars represent 20 kb. An expanded representation of the breakpoint including exon 12 with the end of the coding region and the 3′ UTR region is shown in dark blue, and comprises a 10.1-kb interval. The bottom part shows a BAC contig covering the SLC12A1 breakpoint on chromosome 15. An expanded representation of the breakpoint spanning introns 17-19 and exons 18 and 19 in light blue and dark blue, respectively, comprise an 8.7-kb interval.

Fig. 3

Whole-mount in situ hybridization of wild-type zebrafish embryos shows the expression pattern of ate1 and slc12a1 during embryogenesis. a 91-hpf lateral view depicting strong ate1 expression in the fin bud (arrow) and heart (filled arrowhead) with minor expression in neuromasts (open arrowheads). b A polar view of the 15-16-hpf somite stage with slc12a1 expression in the distal early pronephros (bracket).