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Usher syndrome 1C (USH1C) is a congenital condition manifesting profound hearing loss, the absence of vestibular function, and eventual retinal degeneration. The USH1C locus has been mapped genetically to a 2- to 3-cM interval in 11p14–15.1 between  D11S899  and D11S861.  In an effort to identify the USH1C disease gene we have isolated the region between these markers in yeast artificial chromosomes (YACs) using a combination of STS content mapping and Alu –PCR hybridization. The YAC contig is ∼3.5 Mb and has located several other loci within this interval, resulting in the order CEN-LDHA-SAA1-TPH-D11S1310-(D11S1888/KCNC1)-MYOD1-D11S902D11S921-D11S1890-TEL. Subsequent haplotyping and homozygosity analysis refined the location of the disease gene to a 400-kb interval between  D11S902  and D11S1890  with all affected individuals being homozygous for the internal marker  D11S921.  To facilitate gene identification, the critical region has been converted into P1 artificial chromosome (PAC) clones using sequence-tagged sites (STSs) mapped to the YAC contig,  Alu –PCR products generated from the YACs, and PAC end probes. A contig of &gt;50 PAC clones has been assembled between  D11S1310  and  D11S1890,  confirming the order of markers used in haplotyping. Three PAC clones representing nearly two-thirds of the USH1C critical region have been sequenced. PowerBLAST analysis identified six clusters of expressed sequence tags (ESTs), two known genes ( BIR,SUR1 ) mapped previously to this region, and a previously characterized but unmapped gene  NEFA (D N A binding/ EF  hand/ a cidic amino-acid-rich). GRAIL analysis identified 11 CpG islands and 73 exons of excellent quality. These data allowed the construction of a transcription map for the USH1C critical region, consisting of three known genes and six or more novel transcripts. Based on their map location, these loci represent candidate disease loci for USH1C. The NEFA gene was assessed as the  USH1C  locus by the sequencing of an amplified  NEFA  cDNA from an USH1C patient; however, no mutations were detected.  [The sequence data described in this paper have been submitted to GenBank under accession numbers AC000406 – AC000407 .]

Contig Maps and Genomic Sequencing Identify Candidate Genes in the Usher 1C Locus