Targeted next-generation sequencing identifies a homozygous nonsense mutation in ABHD12, the gene underlying PHARC, in a family clinically diagnosed with Usher syndrome type 3

Abstract

Background: Usher syndrome (USH) is an autosomal recessive genetically heterogeneous disorder with congenital sensorineural hearing impairment and retinitis pigmentosa (RP). We have identified a consanguineous Lebanese family with two affected members displaying progressive hearing loss, RP and cataracts, therefore clinically diagnosed as USH type 3 (USH3). Our study was aimed at the identification of the causative mutation in this USH3-like family.

Methods: Candidate loci were identified using genomewide SNP-array-based homozygosity mapping followed by targeted enrichment and next-generation sequencing.

Results: Using a capture array targeting the three identified homozygosity-by-descent regions on chromosomes 1q43-q44, 20p13-p12.2 and 20p11.23-q12, we identified a homozygous nonsense mutation, p.Arg65X, in ABHD12 segregating with the phenotype.

Conclusion: Mutations of ABHD12, an enzyme hydrolyzing an endocannabinoid lipid transmitter, cause PHARC (polyneuropathy, hearing loss, ataxia, retinitis pigmentosa, and early-onset cataract). After the identification of the ABHD12 mutation in this family, one patient underwent neurological examination which revealed ataxia, but no polyneuropathy. ABHD12 is not known to be related to the USH protein interactome. The phenotype of our patient represents a variant of PHARC, an entity that should be taken into account as differential diagnosis for USH3. Our study demonstrates the potential of comprehensive genetic analysis for improving the clinical diagnosis.

Figure 1

PHARC family described herein and conducted genetic investigations. A Pedigree of the family described herein. B Graphical view of the LOD score calculation of genomewide SNP mapping. Regions showing homozygosity by descent were identified on chromosomes 1 and 20 (two regions) and are indicated by arrows. C Schematic representation of the mapped sequencing reads (reverse strand) visualized with the Integrative Genomics Viewer (IGV) for patient II:1. The c.193C > T mutation in exon 2 of ABHD12 was present in all 87 reads covering this region of the gene (arrow). D Sanger sequencing confirmed the homozygous mutation in both patients (upper panel). It was found in heterozygous state in both parents (I:1 and I:2) and in II:2 (lower panel). II:3 was not a carrier.