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

PLoS Genet. 2015 Jul 21;11(7):e1005386. doi: 10.1371/journal.pgen.1005386.

Mette Nyegaard ¹, Nanna D Rendtorff ², Morten S Nielsen ³, Thomas J Corydon ³, Ditte Demontis ¹, Anna Starnawska ¹, Anne Hedemand ¹, Annalisa Buniello ⁴, Francesco Niola ⁵, Michael T Overgaard ⁶, Suzanne M Leal ⁷, Wasim Ahmad ⁸, Friedrik P Wikman ⁹, Kirsten B Petersen ¹⁰, Dorthe G Crüger ¹⁰, Jaap Oostrik ¹¹, Hannie Kremer ¹², Niels Tommerup ¹³, Morten Frödin ⁵, Karen P Steel ⁴, Lisbeth Tranebjærg ², Anders D Børglum ¹

Affiliations

1 Department of Biomedicine, Aarhus University, Aarhus, Denmark; Centre for Integrative Sequencing (iSEQ), Aarhus University, Aarhus, Denmark.
2 Wilhelm Johannsen Centre for Functional Genome Research, Department of Cellular and Molecular Medicine (ICMM), The Panum Institute, University of Copenhagen, Copenhagen, Denmark; Department of Otorhinolaryngology, Head & Neck Surgery and Audiology, Bispebjerg Hospital/Rigshospitalet, Copenhagen, Denmark; Clinical Genetic Clinic, Kennedy Center, Copenhagen University Hospital, Rigshospitalet, Glostrup, Denmark.
3 Department of Biomedicine, Aarhus University, Aarhus, Denmark.
4 Wolfson Centre for Age-Related Diseases, King's College London, London, United Kingdom.
5 Biotech Research & Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark.
6 Department of Chemistry and Bioscience, Aalborg University, Aalborg Ø, Denmark.
7 Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America.
8 Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan.
9 Department of Molecular Medicine, Aarhus University Hospital, Skejby, Aarhus, Denmark.
10 Department of Clinical Genetics, Vejle Hospital, Vejle, Denmark.
11 Department of Otorhinolaryngology, Radboud University Medical Center, Nijmegen, Nijmegen, Netherlands.
12 Department of Otorhinolaryngology, Radboud University Medical Center, Nijmegen, Nijmegen, Netherlands; Department of Human Genetics, Radboud University Medical Center, Nijmegen, Nijmegen, Netherlands; Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Nijmegen, Netherlands.
13 Wilhelm Johannsen Centre for Functional Genome Research, Department of Cellular and Molecular Medicine (ICMM), The Panum Institute, University of Copenhagen, Copenhagen, Denmark.

PMID: 26197441 DOI: 10.1371/journal.pgen.1005386

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.

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