Deafness, Autosomal Recessive 16 (DFNB16) via MLPA of STRC

Pathogenic variants in STRC are associated with autosomal recessive nonsyndromic hearing loss characterized by moderate to profound non-progressive hearing loss sloping towards high frequencies, with onset being congenital to the first decade (Verpy et al. 2001. PubMed ID: 11687802; Yokota et al. 2019. PubMed ID: 30867468; Vona et al. 2015. PubMed ID: 26011646). 

Hearing loss (HL) or deafness is the most common sensory deficit in humans, affecting an estimated 5% of the world's population (Azaiez et al. 2018. PubMed ID: 30245029). Molecular genetic testing is possible for many types of hearing loss and plays a prominent role in diagnosis, genetic counseling, evaluating hearing loss stability and potential of undiagnosed related clinical features (Shearer et al. 2017. PubMed ID: 20301607).

Pathogenic variants in STRC are the second most common cause of autosomal recessive nonsyndromic hearing loss after the GJB2 gene, and have been estimated to account for 80% of causative copy number variants (CNVs) in hearing loss cases. Large STRC deletions are the most common pathogenic variant type with an estimated carrier frequency of 2.6-4.7% across populations, with STRC to STRCP1 gene conversion carrier frequency estimated at 2.6% (Shearer et al. 2014. PubMed ID: 24963352; Yokota et al. 2019. PubMed ID: 30867468).

STRC missense, nonsense and splicing variants have also been reported as pathogenic, although technical care must be taken to ensure the variant in question is located in STRC as opposed to the STRCP1 pseudogene (Schrauwen et al. 2013. PubMed ID: 23208854; Miyagawa et al. 2013. PubMed ID: 23967202; Mandelker et al. 2014. PubMed ID: 25157971).

The vast majority of pathogenic STRC variants appear to be inherited. A knockout mouse model exhibited progressive deafness (Verpy et al. 2008. PubMed ID: 18849963), and the gene is generally considered to be loss of function intolerant.

STRC is located on chromosome 15 at band q15.3, is comprised of 29 exons and encodes the 1,775 amino acid stereocilin protein. STRC is expressed in microvilli called stereocilia projecting from sensory 'hair' cells of the inner ear. STRC links the tips of adjacent stereocilia together, forming hair 'bundles' involved in mechanoreception of sound waves as they pass through the cochlea (Verpy et al. 2001. PubMed ID: 11687802; Vona et al. 2015. PubMed ID: 26011646).

STRC is located within a tandem genomic duplication, with the STRC pseudogene STRCP1 residing in the second copy. The high degree of sequence similarity between STRC and STRCP1, with almost identical coding sequence in exons 1-14, complicates the analysis of this region by short read next-gen sequencing and likely predisposes this locus to structural variation.

This test includes analysis of CATSPER2 due to deletion of both STRC and CATSPER2 together being associated with autosomal recessive deafness and male infertility (OMIM #611102). However, CATSPER2 copy number variants in patients with normal STRC copy number will not be reported due to lack of an established disease association without STRC involvement. 

The clinical sensitivity of this test is difficult to estimate given the genetic heterogeneity of hearing loss. The analytical sensitivity of this test is expected to approach 100% for copy number variants that encompass STRC exons 19, 20, 23-25, and 28, and CATSPER2 exons 1, 2, 4, and 7. Copy number variants not involving these exons are not expected to be detected due to technical limitations related to pseudogenes.

MLPA probes are only available for STRC exons 19, 20, 23-25, and 28, and CATSPER2 exons 1, 2, 4, and 7 due to technical limitations related to pseudogenes.

Multiplex Ligation-Dependent Probe Amplification (MLPA) enables the detection of deletion and duplications of single and multiple exons within a given gene (Eijk-Van Os and Schouten. 2011. PubMed ID: 20938835). It is a semi-quantitative technique to determine relative copy number using a multiplex PCR-based reaction. Only hybridized and ligated adjacent probe oligonucleotides of approximately 60 nucleotides in length are amplified using PCR and thus are specific for the sequence of interest. A stuffer sequence attached to the probe ensures a particular length for deciphering the probe target. Therefore, MLPA enables the detection of relatively small deletions and duplications within a single exon of a given gene or deletions and duplications encompassing the entire gene. For additional information please see www.mlpa.com.