title: 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.
authors.affiliation: Department of Biomedicine, Aarhus University, Aarhus, Denmark; Centre for Integrative Sequencing (iSEQ), Aarhus University, Aarhus, Denmark.
authors.forename: Mette
authors.initials: M
authors.lastname: Nyegaard
authors.affiliation: 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.
authors.forename: Nanna D
authors.initials: ND
authors.lastname: Rendtorff
authors.affiliation: Department of Biomedicine, Aarhus University, Aarhus, Denmark.
authors.forename: Morten S
authors.initials: MS
authors.lastname: Nielsen
authors.affiliation: Department of Biomedicine, Aarhus University, Aarhus, Denmark.
authors.forename: Thomas J
authors.initials: TJ
authors.lastname: Corydon
authors.affiliation: Department of Biomedicine, Aarhus University, Aarhus, Denmark; Centre for Integrative Sequencing (iSEQ), Aarhus University, Aarhus, Denmark.
authors.forename: Ditte
authors.initials: D
authors.lastname: Demontis
authors.affiliation: Department of Biomedicine, Aarhus University, Aarhus, Denmark; Centre for Integrative Sequencing (iSEQ), Aarhus University, Aarhus, Denmark.
authors.forename: Anna
authors.initials: A
authors.lastname: Starnawska
authors.affiliation: Department of Biomedicine, Aarhus University, Aarhus, Denmark; Centre for Integrative Sequencing (iSEQ), Aarhus University, Aarhus, Denmark.
authors.forename: Anne
authors.initials: A
authors.lastname: Hedemand
authors.affiliation: Wolfson Centre for Age-Related Diseases, King's College London, London, United Kingdom.
authors.forename: Annalisa
authors.initials: A
authors.lastname: Buniello
authors.affiliation: Biotech Research & Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark.
authors.forename: Francesco
authors.initials: F
authors.lastname: Niola
authors.affiliation: Department of Chemistry and Bioscience, Aalborg University, Aalborg Ø, Denmark.
authors.forename: Michael T
authors.initials: MT
authors.lastname: Overgaard
authors.affiliation: Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America.
authors.forename: Suzanne M
authors.initials: SM
authors.lastname: Leal
authors.affiliation: Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan.
authors.forename: Wasim
authors.initials: W
authors.lastname: Ahmad
authors.affiliation: Department of Molecular Medicine, Aarhus University Hospital, Skejby, Aarhus, Denmark.
authors.forename: Friedrik P
authors.initials: FP
authors.lastname: Wikman
authors.affiliation: Department of Clinical Genetics, Vejle Hospital, Vejle, Denmark.
authors.forename: Kirsten B
authors.initials: KB
authors.lastname: Petersen
authors.affiliation: Department of Clinical Genetics, Vejle Hospital, Vejle, Denmark.
authors.forename: Dorthe G
authors.initials: DG
authors.lastname: Crüger
authors.affiliation: Department of Otorhinolaryngology, Radboud University Medical Center, Nijmegen, Nijmegen, Netherlands.
authors.forename: Jaap
authors.initials: J
authors.lastname: Oostrik
authors.affiliation: 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.
authors.forename: Hannie
authors.initials: H
authors.lastname: Kremer
authors.affiliation: Wilhelm Johannsen Centre for Functional Genome Research, Department of Cellular and Molecular Medicine (ICMM), The Panum Institute, University of Copenhagen, Copenhagen, Denmark.
authors.forename: Niels
authors.initials: N
authors.lastname: Tommerup
authors.affiliation: Biotech Research & Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark.
authors.forename: Morten
authors.initials: M
authors.lastname: Frödin
authors.affiliation: Wolfson Centre for Age-Related Diseases, King's College London, London, United Kingdom.
authors.forename: Karen P
authors.initials: KP
authors.lastname: Steel
authors.affiliation: 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.
authors.forename: Lisbeth
authors.initials: L
authors.lastname: Tranebjærg
authors.affiliation: Department of Biomedicine, Aarhus University, Aarhus, Denmark; Centre for Integrative Sequencing (iSEQ), Aarhus University, Aarhus, Denmark.
authors.forename: Anders D
authors.initials: AD
authors.lastname: Børglum
mesh_terms: D000818:Animals; D001483:Base Sequence; D002460:Cell Line; D018389:Codon, Nonsense / Q000235:genetics; D003638:Deafness / Q000235:genetics; D003718:Denmark; D051930:Endolyn / Q000235:genetics*; D005190:Family; D005260:Female; D057809:HEK293 Cells; D006801:Humans; D008297:Male; D051379:Mice; D008810:Mice, Inbred C57BL; D018895:Microsatellite Repeats / Q000235:genetics; D009925:Organ of Corti / Q000378:metabolism; D010375:Pedigree; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D017422:Sequence Analysis, DNA
chemical_list: D018389:Codon, Nonsense; D051930:Endolyn