DFNB31 — deafness, autosomal recessive 31

The DFNB31 gene, also known as WHRN, provides instructions for making a protein called whirlin. Whirlin acts like a scaffold or a molecular organizer within certain cells, helping to build and maintain important structures. It is particularly important in two areas of the body: the inner ear and the retina (the light-sensitive tissue at the back of the eye). In the inner ear, whirlin helps form the tiny hair-like structures needed for hearing. In the retina, it helps maintain the specialized cells (photoreceptors) that capture light and allow us to see. When there is a mutation (a harmful change) in the DFNB31 gene, the whirlin protein may not work correctly or may not be produced at all. Depending on where the mutation occurs in the gene, it can cause two different conditions. Some mutations cause a condition called Usher syndrome type 2D, which involves both hearing loss from birth and a gradual loss of vision (retinitis pigmentosa) that usually begins in adolescence or early adulthood. Other mutations in this gene cause only hearing loss without affecting vision, a condition known as nonsyndromic hearing loss (DFNB31). Both of these conditions are inherited in an autosomal recessive pattern. This means that a person must inherit two mutated copies of the gene (one from each parent) to develop the condition. Parents who carry only one mutated copy are called carriers; they typically do not have any symptoms of the condition themselves but have a 25% chance with each pregnancy of passing the condition on to their child. Genetic testing can help confirm a diagnosis and provide important information for families.

Gene description: DFNB31 (also known as WHRN) encodes whirlin, a scaffold protein crucial for the development of stereocilia in the inner ear and photoreceptor outer segments.

Patient and family guide: The DFNB31 gene, also known as WHRN, provides instructions for making a protein called whirlin. Whirlin acts like a scaffold or a molecular organizer within certain cells, helping to build and maintain important structures. It is particularly important in two areas of the body: the inner ear and the retina (the light-sensitive tissue at the back of the eye). In the inner ear, whirlin helps form the tiny hair-like structures needed for hearing. In the retina, it helps maintain the specialized cells (photoreceptors) that capture light and allow us to see. When there is a mutation (a harmful change) in the DFNB31 gene, the whirlin protein may not work correctly or may not be produced at all. Depending on where the mutation occurs in the gene, it can cause two different conditions. Some mutations cause a condition called Usher syndrome type 2D, which involves both hearing loss from birth and a gradual loss of vision (retinitis pigmentosa) that usually begins in adolescence or early adulthood. Other mutations in this gene cause only hearing loss without affecting vision, a condition known as nonsyndromic hearing loss (DFNB31). Both of these conditions are inherited in an autosomal recessive pattern. This means that a person must inherit two mutated copies of the gene (one from each parent) to develop the condition. Parents who carry only one mutated copy are called carriers; they typically do not have any symptoms of the condition themselves but have a 25% chance with each pregnancy of passing the condition on to their child. Genetic testing can help confirm a diagnosis and provide important information for families.

Gene function: While primarily known for its role in hearing, DFNB31's protein, whirlin, is also expressed in the retina where it is involved in the organization and maintenance of photoreceptor outer segments. It interacts with other proteins to ensure the proper structure and function of these light-sensing organelles, which are essential for phototransduction and normal vision.

Protein structure: The WHRN gene encodes the protein whirlin, which is characterized by the presence of multiple PDZ (PSD-95/Discs-large/ZO-1) domains. PDZ domains are structural motifs that facilitate protein-protein interactions, allowing whirlin to function as a critical scaffolding protein. The full-length, long isoform of whirlin (approximately 907 amino acids) contains three PDZ domains: two located near the N-terminus and one at the C-terminus, along with a proline-rich region. Alternative splicing of the WHRN gene produces several different isoforms. The most notable are the long isoforms, which contain all three PDZ domains, and the short C-terminal isoforms, which contain only the third PDZ domain and the proline-rich region. These different isoforms allow whirlin to assemble into various functional complexes depending on the tissue. In the retina, the long isoform of whirlin interacts with other proteins like USH2A and ADGRV1 to form the large USH2 multiprotein complex, which is essential for the structural integrity of the photoreceptor connecting cilium.

Molecular function: The WHRN gene encodes whirlin, a crucial scaffolding protein that plays a vital role in the structural organization and function of sensory cells in both the inner ear and the retina. Whirlin contains multiple PDZ domains, which are specialized protein-protein interaction modules that allow it to act as a central hub, organizing multi-protein complexes at specific cellular locations. In the inner ear, whirlin is essential for the proper development, elongation, and maintenance of stereocilia on sensory hair cells. It interacts with other proteins, such as myosin XVa and espin, to regulate actin polymerization and cytoskeletal assembly at the tips of the stereocilia. This structural integrity is critical for the mechanotransduction process, converting sound waves into electrical signals. In the retina, whirlin localizes to the periciliary membrane complex at the base of the photoreceptor connecting cilium. Here, it interacts with other Usher syndrome-associated proteins, including USH2A (usherin) and ADGRV1 (VLGR1), to form the USH2 protein complex. This complex is thought to be involved in the structural maintenance of the connecting cilium and the regulation of intracellular transport between the inner and outer segments of the photoreceptors, a process essential for photoreceptor survival and normal vision.

Expression pattern: The WHRN gene exhibits a distinct and highly specific expression pattern, primarily localized to the inner ear and the retina, which correlates with its clinical manifestations. In the inner ear, whirlin is expressed in the sensory hair cells of the cochlea and the vestibular system. It is specifically localized to the stereocilia, the mechanosensing organelles of these cells, where it is concentrated at the tips during development and later at the ankle links. In the retina, whirlin is expressed in the photoreceptor cells (both rods and cones). It localizes specifically to the periciliary membrane complex (PMC) at the base of the connecting cilium, a crucial region for the transport of proteins between the inner and outer segments of the photoreceptors. The gene produces multiple transcript variants through alternative splicing, resulting in different protein isoforms (long and short). The long isoforms are predominantly expressed in both the retina and the inner ear, while the short isoforms have a more restricted expression pattern, primarily in the inner ear.

Mutation spectrum: The mutation spectrum of the WHRN gene includes a variety of pathogenic variants, such as missense, nonsense, frameshift, and splice-site mutations, as well as large deletions. These mutations are distributed across the gene, but their location often correlates with the resulting phenotype. Mutations causing Usher syndrome type 2D are typically found in the N-terminal and central regions of the gene, affecting the long isoform of the protein. In contrast, mutations causing nonsyndromic hearing loss (DFNB31) are frequently located in the C-terminal region. While WHRN mutations are a relatively rare cause of Usher syndrome (accounting for a small percentage of USH2 cases), numerous pathogenic variants have been identified and cataloged in databases like ClinVar and HGMD. There are no widely recognized major founder mutations for WHRN, and the variants are generally private or found in specific isolated populations.

Pathogenic variants: 1. p.Arg776Cys (c.2326C>T): A missense mutation located in the C-terminal region, associated with autosomal recessive nonsyndromic hearing loss (DFNB31). 2. p.Gln407Ter (c.1219C>T): A nonsense mutation resulting in a premature stop codon, leading to a truncated protein. This variant is associated with Usher syndrome type 2D. 3. c.1802_1803del (p.Leu601ArgfsTer23): A frameshift mutation caused by a two-base pair deletion, leading to a premature stop codon. This variant has been identified in patients with Usher syndrome type 2D. 4. c.2383G>A (p.Gly795Arg): A missense mutation affecting a conserved residue, reported in cases of nonsyndromic hearing loss. 5. c.436_444del (p.Val146_Gln148del): An in-frame deletion variant that has been associated with Usher syndrome type 2D, highlighting the importance of the deleted region for the function of the long isoform.

Clinical significance: Mutations in the DFNB31 (WHRN) gene manifest clinically in two primary ways: Usher syndrome type 2D (USH2D) and autosomal recessive nonsyndromic hearing loss 31 (DFNB31). Usher syndrome type 2D is characterized by congenital, bilateral sensorineural hearing loss that is typically mild to moderate in the low frequencies and severe to profound in the higher frequencies. Unlike Usher syndrome type 1, vestibular function is generally normal in USH2D. The retinal manifestation of USH2D is retinitis pigmentosa (RP), which typically presents with nyctalopia (night blindness) starting around adolescence or early adulthood. As the disease progresses, patients experience a gradual loss of peripheral vision, leading to "tunnel vision." In the later stages of the disease, central vision and color vision may also be affected, eventually leading to severe visual impairment or legal blindness. The severity and age of onset of the retinal degeneration can vary among individuals. When mutations in WHRN cause nonsyndromic hearing loss (DFNB31), patients present with prelingual, bilateral sensorineural hearing loss without any associated visual or vestibular symptoms. The hearing loss can range from moderate to profound. The specific clinical manifestation (syndromic vs. nonsyndromic) is largely determined by the location and nature of the mutation within the gene and its effect on the different whirlin isoforms.

Inheritance: Autosomal Recessive

Chromosomal location: 9q32

Genotype-phenotype correlations: There is a strong genotype-phenotype correlation associated with mutations in the WHRN gene, largely dependent on how the mutations affect the different protein isoforms. The WHRN gene produces a long isoform containing three PDZ domains and a short C-terminal isoform containing only the third PDZ domain. Mutations that affect the N-terminal region of the gene, thereby disrupting the long isoform but leaving the short C-terminal isoform intact, are typically associated with Usher syndrome type 2D (USH2D). This indicates that the long isoform is essential for both retinal and auditory function. Conversely, mutations located in the C-terminal region that affect both the long and short isoforms, or specifically disrupt the short isoform, tend to manifest as autosomal recessive nonsyndromic hearing loss (DFNB31) without retinal involvement. This suggests that the short isoform plays a critical, specific role in the inner ear that is not required in the retina.

Research and therapeutic approaches: Currently, there are no approved, curative therapies specifically targeting WHRN-related inherited retinal diseases or hearing loss. Management is primarily supportive. For the hearing loss component, patients often benefit from hearing aids or cochlear implants, which can significantly improve auditory function and communication skills, especially when intervened early. For the visual component (retinitis pigmentosa), management focuses on maximizing remaining vision through low vision aids, orientation and mobility training, and regular ophthalmological monitoring. Research into targeted therapies is ongoing, primarily in the pre-clinical stages. Gene therapy is a major area of investigation. Studies in animal models, such as the whirler mouse, have demonstrated that delivering a functional copy of the WHRN gene using viral vectors (like AAV) can restore the formation of the USH2 protein complex in photoreceptors and improve auditory and vestibular function. However, these approaches are still in the experimental phase and have not yet progressed to human clinical trials. Other potential future strategies could include antisense oligonucleotides (ASOs) for specific splice-site mutations or read-through therapies for nonsense mutations, though these remain largely theoretical for WHRN at this time.

Diagnostic testing: Diagnosis of WHRN-related conditions typically involves a combination of clinical evaluation and molecular genetic testing. Clinical assessments include comprehensive audiological testing (such as pure tone audiometry and otoacoustic emissions) and detailed ophthalmological examinations (including electroretinography (ERG), optical coherence tomography (OCT), and visual field testing) to evaluate hearing and retinal function. Molecular genetic testing is required to confirm the diagnosis. This is most commonly achieved through targeted multi-gene panels that include WHRN and other genes associated with Usher syndrome and inherited retinal diseases. If panel testing is inconclusive, comprehensive genomic testing such as whole exome sequencing (WES) or whole genome sequencing (WGS) may be employed. Genetic counseling is highly recommended for affected individuals and their families to discuss the inheritance pattern (autosomal recessive), recurrence risks, and the implications of the genetic findings for prognosis and family planning.

Animal models: The most prominent animal model for studying WHRN/DFNB31 is the whirler mouse (Whrn^wi), which has a spontaneous mutation in the Whrn gene. These mice exhibit profound deafness and vestibular dysfunction, characterized by short, disorganized stereocilia in the inner ear hair cells. Studies in whirler mice have been instrumental in demonstrating that whirlin is essential for the elongation and maintenance of stereocilia. In addition to the whirler mouse, knockout models specifically targeting different isoforms of whirlin have been developed to study its role in the retina. These models have shown that whirlin localizes to the periciliary membrane complex at the photoreceptor connecting cilium. While retinal degeneration in some of these mouse models is relatively mild or slow-progressing compared to the severe hearing loss, they have provided crucial insights into how whirlin interacts with other Usher syndrome proteins (like USH2A and ADGRV1) to form the USH2 protein complex, which is vital for the structural integrity and function of photoreceptors.

Population genetics: Mutations in the WHRN gene are a rare cause of both Usher syndrome and nonsyndromic hearing loss globally. The carrier frequency in the general population is very low. However, specific pathogenic variants may be more prevalent in certain isolated or consanguineous populations due to founder effects or genetic drift. For example, certain WHRN mutations have been identified in specific families or localized populations, such as in parts of the Middle East or isolated European communities, where consanguinity increases the likelihood of autosomal recessive conditions. Overall, WHRN mutations account for only a small fraction (typically less than 5%) of all Usher syndrome type II cases.

Selected references: 1. Mburu P, et al. Defects in whirlin, a PDZ domain molecule involved in stereocilia elongation, cause deafness in the whirler mouse and families with DFNB31. Nat Genet. 2003;34(4):421-428. PMID: 12833159 2. Ebermann I, et al. A novel gene for Usher syndrome type 2: mutations in the long isoform of whirlin are associated with retinitis pigmentosa and sensorineural hearing loss. Hum Genet. 2007;121(2):203-211. PMID: 17171570 3. Zou J, et al. Whirlin Replacement Restores the Formation of the USH2 Protein Complex in Whirlin Knockout Photoreceptors. Invest Ophthalmol Vis Sci. 2011;52(5):2343-2351. PMID: 21220549 4. Mathur PD, et al. Usher syndrome and non-syndromic deafness: Functions of different whirlin isoforms in the cochlea, vestibular organs, and retina. Hear Res. 2019;375:14-24. PMID: 30831381 5. Tlili A, et al. Identification of a novel frameshift mutation in the DFNB31/WHRN gene in a Tunisian consanguineous family with hereditary non-syndromic recessive hearing loss. Hum Mutat. 2005;25(5):503. PMID: 15841483