A Novel Locus Harbouring a Functional CD164 Nonsense Mutation Identified in a Large Danish Family with Nonsyndromic Hearing Impairment

Abstract

Nonsyndromic hearing impairment (NSHI) is a highly heterogeneous condition with more than eighty known causative genes. However, in the clinical setting, a large number of NSHI families have unexplained etiology, suggesting that there are many more genes to be identified. In this study we used SNP-based linkage analysis and follow up microsatellite markers to identify a novel locus (DFNA66) on chromosome 6q15-21 (LOD 5.1) in a large Danish family with dominantly inherited NSHI. By locus specific capture and next-generation sequencing, we identified a c.574C>T heterozygous nonsense mutation (p.R192*) in CD164. This gene encodes a 197 amino acid transmembrane sialomucin (known as endolyn, MUC-24 or CD164), which is widely expressed and involved in cell adhesion and migration. The mutation segregated with the phenotype and was absent in 1200 Danish control individuals and in databases with whole-genome and exome sequence data. The predicted effect of the mutation was a truncation of the last six C-terminal residues of the cytoplasmic tail of CD164, including a highly conserved canonical sorting motif (YXXФ). In whole blood from an affected individual, we found by RT-PCR both the wild-type and the mutated transcript suggesting that the mutant transcript escapes nonsense mediated decay. Functional studies in HEK cells demonstrated that the truncated protein was almost completely retained on the plasma cell membrane in contrast to the wild-type protein, which targeted primarily to the endo-lysosomal compartments, implicating failed endocytosis as a possible disease mechanism. In the mouse ear, we found CD164 expressed in the inner and outer hair cells of the organ of Corti, as well as in other locations in the cochlear duct. In conclusion, we have identified a new DFNA locus located on chromosome 6q15-21 and implicated CD164 as a novel gene for hearing impairment.

Translational plasticity facilitates the accumulation of nonsense genetic variants in the human population

“…For example, a recent study identified a novel C-terminal truncating variant in CD164 that segregated with nonsyndromic hearing impairment in an affected family. Only the last six amino acids of CD164 were removed, but without the encoded canonical sorting motif, the truncated protein was trapped on the cell membrane (Nyegaard et al 2015).…”

Microgravity Affects Thyroid Cancer Cells during the TEXUS-53 Mission Stronger than Hypergravity

“…The stained samples were examined using a confocal laser scanning microscope (LSM 780, Zeiss, Jena, Germany) using 40× oil-immersion objective with a NA of 1.3 [74].…”

Translational plasticity facilitates the accumulation of nonsense genetic variants in the human population

“…For example, a recent study identified a novel Cterminal truncating variant in CD164 that segregated with nonsyndromic hearing impairment in an affected family. Only the last six amino acids of CD164 were removed, but without the encoded canonical sorting motif, the truncated protein was trapped on the cell membrane (Nyegaard et al 2015).…”