Mutations of GIPC3 cause nonsyndromic hearing loss DFNB72 but not DFNB81 that also maps to chromosome 19p

Abstract

A missense mutation of Gipc3 was previously reported to cause age-related hearing loss in mice. Point mutations of human GIPC3 were found in two small families, but association with hearing loss was not statistically significant. Here, we describe one frameshift and six missense mutations in GIPC3 cosegregating with DFNB72 hearing loss in six large families that support statistically significant evidence for genetic linkage. However, GIPC3 is not the only nonsyndromic hearing impairment gene in this region; no GIPC3 mutations were found in a family cosegregating hearing loss with markers of chromosome 19p. Haplotype analysis excluded GIPC3 from the obligate linkage interval in this family and defined a novel locus spanning 4.08 Mb and 104 genes. This closely linked but distinct nonsyndromic hearing loss locus was designated DFNB81.

Fig. 1

a Representative pure-tone air conduction thresholds from an affected individual from each family segregating HL due to mutations of GIPC3 (DFNB72). Hearing loss ranged from mild to severe in families PKDF1258 and PKDF1048, moderate to severe in PKDF335 and PKDF793, and severe to profound in families DEM4322 and DEM4197. All individuals with reported bone-conduction thresholds had sensorineural HL. Two carriers from families PKDF1048 and PKDF793 have normal hearing sensitivity (data not shown). b Pure-tone air (filled symbol) and bone (open symbol) conduction thresholds from members of family PKDF291 that define the DFNB81 locus. Note that unaffected individual 1 has normal hearing sensitivity, individuals 2, 3, and 5 have severe to profound mixed HL, and individual 4 has a profound sensorineural HL. Asterisks indicate response to vibrotactile sensation; arrows indicate no response at audiometer output limits

Fig. 2

a Pedigrees of families segregating deafness genetically mapped to DFNB72 on chromosome 19p. Squares and circles denote male and female family members, respectively. Filled symbols represent affected individuals. b Pedigree and haplotypes of family members of PKDF291 that genetically excludes GIPC3. Genotypes of individuals for SNP rs8113232 located in exon 2 of GIPC3 are shown. Hearing-impaired individuals are heterozygous for rs8113232. c Telomeric region of chromosome 19p includes three closely linked hearing loss loci DFNB72, DFNB81, and DFNB68. Regions of homozygosity for each family are represented by vertical lines while crosses at the ends of vertical lines indicate meiotic recombinations. Haplotype analysis (data not shown) of family PKDF1258 refined the DFNB72 critical interval between markers D19S209 and D19S894. Gray rectangle highlights the refined DFNB72 interval that includes GIPC3. Note that the linkage region of family PKDF291 does not overlap with the genomic positions of GIPC3 or DFNB68, defining an unreported deafness locus designated DFNB81. Locations of STR markers and GIPC3 are based on human genome reference sequence NCBI Build 36.1 (hg18). Mb megabases

Fig. 3

a Nucleotide sequence chromatograms from selected regions of GIPC3 harboring homozygous mutations segregating in seven DFNB72 families. The mutated nucleotides and predicted altered amino acid residues are highlighted in gray. b GIPC3 amino acid conservation from nine vertebrates. Conserved amino acids are shaded in gray while the amino acids affected due to nucleotide variants identified in our DFNB72 families are highlighted in orange. c Gene structure (black rectangles) and predicted domains of GIPC3 (colored illustration). Thick rectangles, joining lines, and thin rectangles represent exons, introns, and untranslated regions (UTRs), respectively. Locations of seven mutations of GIPC3 detected in DFNB72 families (above) and two previously reported in Charizopoulou et al. (2011) (below) are shown for schematics of the gene and protein. Mutation names are based on the full length GIPC3 transcript (NM_133261.2) and encoded protein (NP_573568.1). GH GIPC homology; PDZ PSD-95, Dlg, and ZO-1