Usher Syndrome Panel

Usher syndrome is a clinically heterogeneous genetic disorder that is characterized by progressive retinitis pigmentosa (RP), sensorineural hearing impairment, and in some cases, vestibular abnormalities. Features of RP include night blindness progressing to constriction of the peripheral visual field with eventual loss of central vision, abnormal fundus with bone-spicule deposits/attenuated retinal vessels, and abnormal electroretinographic (ERG) findings (Daiger et al. 2007). Vestibular abnormalities often result in development delay in sitting and walking. Three clinical subtypes of Usher syndrome are currently recognized based on the age of onset, severity of symptoms, and vestibular involvement, although there is considerable variability within a subtype thus resulting in overlapping symptoms between subtypes. Usher syndrome type 1 (USH1) is the most common type and is distinguished by severe to profound congenital hearing loss, RP beginning in childhood, and abnormal vestibular function (Ahmed et al. 2013). Usher syndrome type 2 (USH2) involves moderate to severe hearing impairment, late-onset RP, and normal vestibular function. Usher syndrome type 3 (USH3) is characterized by progressive hearing loss and variable age of onset for retinal degeneration. The prevalence of Usher syndrome in the United States is 1 in 6,000 (Kimberling et al. 2010).

Sequence variants in one of 12 genes cause Usher syndrome, a clinically heterogeneous autosomal recessive disorder (Bolz and Roux 2011; Khateb et al. 2018. PubMed ID: 29300381). USH1 is caused by pathogenic sequence variants in the following genes: cadherin-related family, member 23 (CDH23), which encodes for a 3,354-amino acid calcium ion-dependent transmembrane adhesion protein that contains ankyrin repeats; calcium- and integrin-binding protein 2 (CIB2), which encodes a calcium-binding actin-based protein that mediates intracellular calcium signaling; myosin VIIA (MYO7A), which encodes unconventional myosins with structurally conserved heads that move along actin filaments; protocadherin 15 (PCDH15), which encodes a 1,955-amino acid calcium ion-binding protein that contains 11 cadherin repeats and two domains that are proline-rich; Usher syndrome type 1C (USH1C), which encodes a 652-amino acid PDZ domain-containing protein called harmonin that is predominantly expressed in the sensory hair cells of the inner ear; and Usher syndrome type 1G (USH1G), which encodes a scaffold protein containing ankyrin repeats and a sterile alpha motif (SAM) called sans that is expressed in the cochlea (Ahmed et al. 2001; Riazuddin et al. 2012; Blanco-Sanchez et al. 2014).

USH2 is caused by causative sequence variants in the following genes: deafness, autosomal recessive 31 (WHRN), which encodes a PDZ domain-containing protein called whirlin that contains actin polymerization and the growth of stereocilia in the inner ear; G protein-coupled receptor 98 (GPR98), which encodes a 326-amino acid protein that is involved in neurotransmission and in the formation of synaptic contacts; PDZ domain-containing 7 (PDZD7), which encodes a binding protein that is expressed in the mechanosensory hair cells of the inner ear; and Usher syndrome type 2a (USH2A), which encodes a 1,551-amino acid protein that acts as a component of the basal lamina and extracellular matrices of the ears and eyes (Yang et al. 2010; Garcia-Garcia et al. 2013; Zou et al. 2014).

USH3 is caused by pathogenic sequence variants the clarin 1 (CLRN1) gene, which encodes a 232-amino acid transmembrane protein that is expressed in the inner and outer hair cells of the organ of Corti and the spiral ganglion cells; it possesses mechanotransduction channel activity and assists in the proper localization of synaptic components (Ogun and Zallocchi 2014).

The mutational spectrum of the 12 genes implicated in Usher syndrome mainly include missense, nonsense, and splicing sequence variants, as well as some small deletions, duplications, and insertions. The most common sequence variants that have been reported as pathogenic for Usher syndrome occur in the following genes: USH2A, MYO7A, CDH23, GPR98, and PCDH15. On the other hand, only a few pathogenic sequence variants have been reported for the USH1C, CLRN1, USH1G, WHRN, CIB2, and PDZD7 genes (Stenson et al. 2003).

Pathogenic variants in ARSG have been associated with autosomal recessive Usher syndrome type 4, with later onset than other forms of Usher syndrome in the fourth decade or later (Khateb et al. 2018. PubMed ID: 29300381; Abad-Morales et al. 2020. PubMed ID: 32455177; Fowler et al. 2021. PubMed ID: 33629623; Peter et al. 2021. PubMed ID: 33300174; Velde et al. 2022. PubMed ID: 35226187).

Pathogenic variants in the genes in this NextGen panel may be responsible for 11.3% to 91% of Usher syndrome cases, depending on the combination of genes utilized in the NextGen assay and the specific population being screened. A German study that performed sequencing of 9 genes showed that all 42 Usher syndrome patients (100%) harbored causative sequence variants (Krawitz et al. 2014). In a French study that involved sequencing of 9 genes, 49 out of 54 (91%) Usher syndrome patients showed pathogenic sequence variants (Bonnet et al. 2011). On the other hand, a Spanish study that conducted sequencing of 10 genes reported that 22 out of 32 (69%) Usher syndrome patients tested positive for causative pathogenic sequence variants (Aparisi et al. 2014). A US-based study that performed sequencing of 5 genes showed that 15 out of 133 (11.3%) hard-of-hearing or deaf pediatric patients harbored pathogenic sequence variants (Kimberling et al. 2010).

Large-scale copy number variants may be responsible for around 6% of Usher syndrome alleles. The most frequent CNVs have been detected in the USH2A, MYO7A, CDH23, GPR98, and PCDH15 genes (Stenson et al. 2003).

This test is performed using Next-Gen sequencing with additional Sanger sequencing as necessary.

This panel typically provides 99.9% coverage of all coding exons of the genes plus 10 bases of flanking noncoding DNA in all available transcripts along with other non-coding regions in which pathogenic variants have been identified at PreventionGenetics or reported elsewhere. We define coverage as ≥20X NGS reads or Sanger sequencing. PGnome panels typically provide slightly increased coverage over the PGxome equivalent. PGnome sequencing panels have the added benefit of additional analysis and reporting of deep intronic regions (where applicable).

Dependent on the sequencing backbone selected for this testing, discounted reflex testing to any other similar backbone-based test is available (i.e., PGxome panel to whole PGxome; PGnome panel to whole PGnome).