Variant discovery, functional characterisation, and clinical translation

Hereditary Hearing Loss & Rare Genetic Disorders

Identifying the genetic cause of hearing loss in patients who have remained undiagnosed after standard clinical workup is a core part of our work at the Radboudumc Expertise Center Hearing & Genes and in the national DOOFNL network. Combining state-of-the-art genotyping with detailed audiological phenotyping frequently reveals variants of uncertain significance or novel disease mechanisms that require functional follow-up.

Main findings

Gene / locus Phenotype Key finding Reference
RIPOR2 / DFNA21 Adult-onset ADSNHL c.1696_1707del in-frame deletion is frequent (≥1% of ADSNHL in the Netherlands) and highly penetrant; establishes DFNA21 as a major cause of adult-onset hearing loss (De Bruijn et al., 2021)
RIPOR2 / DFNA21 Variable adult-onset SNHL Rotterdam Study replication confirms population prevalence; documents phenotypic variability (Velde et al., 2023)
ATP2B2 Rapidly progressive SNHL De novo and inherited loss-of-function variants cause rapidly progressive hearing impairment; first DOOFNL cohort gene discovery with direct implications for CI timing (DOOFNL Consortium et al., 2019)
GAS2 Autosomal recessive SNHL GAS2 required for cochlear supporting cell cytoskeletal architecture; first functional characterisation linking this gene to human hearing (Chen et al., 2021)
COCH / DFNA9 Progressive ADSNHL + vestibular HuGE systematic review and audiometric meta-analysis quantifies variant-specific progression rates; provides data-driven basis for patient counselling (Robijn et al., 2022)
WFS1 / DFNA6/14/38 Low-frequency SNHL Novel p.Pro838Ser variant characterised; genotype–phenotype correlation described; good CI outcomes in mono-allelic carriers (Velde et al., 2023; Fehrmann et al., 2024)
SLC26A4 / DFNB4 SNHL + enlarged vestibular aqueduct Systematic exploration of missing heritability in mono-allelic EVA cases; digenic and modifier mechanisms evaluated (Smits et al., 2022)
ARSG / Usher type IV Syndromic HL + retinitis pigmentosa Novel ARSG variants confirm Usher type IV as clinically and molecularly distinct; detailed audiological profile described (Velde et al., 2022)
USH2A / Usher type 2A Syndromic HL + RP Age-related typical audiograms (ARTA) characterised across a large Dutch cohort; mid-frequency-predominant pattern with relatively stable progression (Wijn et al., 2025)
IKZF2 Non-syndromic SNHL Exome-first variant prioritisation in a large hearing loss cohort identifies IKZF2 as a novel candidate gene; guides future molecular investigation (Velde et al., 2024)

Summary

The RIPOR2 story exemplifies the diagnostic return possible when genotyping and audiological phenotyping are tightly coupled. The c.1696_1707del in-frame deletion, discovered in the DOOFNL cohort and subsequently validated in the Rotterdam Study general population, is now established as the most prevalent genetic cause of adult-onset autosomal dominant sensorineural hearing loss (ADSNHL) in the Netherlands, with penetrance above 90% (De Bruijn et al., 2021; Velde et al., 2023). Similarly, ATP2B2 loss-of-function variants — both de novo and inherited — were identified through cohort-wide sequencing as a cause of rapidly progressive hearing loss, a finding with immediate implications for prognosis and cochlear implantation timing (DOOFNL Consortium et al., 2019).

RIPOR2 Figure. Functionality of mutant RIPOR2 is altered in mouse cochlear outer hair cells.

Functional and mechanistic work complements the clinical variant studies. Cochlear supporting cells were shown to require GAS2 for cytoskeletal integrity, directly linking a cellular structural role to human hereditary hearing loss (Chen et al., 2021). On the phenotyping side, a HuGE systematic review of all reported COCH variants quantified variant-specific audiometric progression rates in DFNA9, providing a rigorous basis for individualised counselling on expected disease trajectory (Robijn et al., 2022).

Syndromic forms of hereditary hearing loss have received particular attention. Novel ARSG variants confirmed Usher syndrome type IV as a clinically and molecularly distinct entity, and longitudinal audiometric profiling of a large Dutch USH2A cohort produced the first age-related typical audiograms (ARTA) for this syndrome — a mid-frequency-predominant, relatively stable pattern that diverges from canonical non-syndromic trajectories (Velde et al., 2022; Wijn et al., 2025). Mono-allelic SLC26A4 cases with enlarged vestibular aqueducts were also systematically analysed, revealing the complexity of missing heritability in this group and guiding further molecular investigation (Smits et al., 2022).

Beyond known genes, the group has applied exome-first variant prioritisation to previously unsolved hearing loss, identifying IKZF2 as a novel candidate gene and characterising variants in WFS1 that extend the DFNA6/14/38 phenotypic spectrum, including demonstration of good cochlear implantation outcomes in mono-allelic carriers (Velde et al., 2024; Velde et al., 2023; Fehrmann et al., 2024). Together, this body of work spans the full translational arc — from gene discovery to functional validation to audiological characterisation to clinical counselling — directly informing the diagnostic yield and management of patients seen at the Radboudumc Expertise Center Hearing & Genes and within ERN-CRANIO.

Key references

Journal Articles

  1. Wijn, D. H., Fehrmann, M. L. A., Robijn, S. M. M., Velde, H. M., Smits, J. J., van Wijk, E., Beynon, A. J., Cals, F. L. J., Hoyng, C. B., Yzer, S., Lanting, C. P., & Pennings, R. J. E. (2025). From Sound to Stability: Lessons Learned From the CRUSH Study on Hearing Loss Progression and Vestibular Phenotype in Usher Syndrome Type 2A. Otology & Neurotology, 10.1097/MAO.0000000000004851. https://doi.org/10.1097/MAO.0000000000004851
  2. Fehrmann, M. L. A., Lanting, C. P., Haer-Wigman, L., Mylanus, E. A. M., Huinck, W. J., & Pennings, R. J. E. (2024). Good Cochlear Implantation Outcomes in Subjects with Mono-Allelic WFS1- Associated Sensorineural Hearing Loss – a Case Series. International Journal of Audiology, 1–9. https://doi.org/10.1080/14992027.2024.2411579
  3. Velde, H. M., Vaseghi-Shanjani, M., Smits, J. J., Ramakrishnan, G., Oostrik, J., Wesdorp, M., Astuti, G., Yntema, H. G., Hoefsloot, L., Lanting, C. P., Huynen, M. A., Lehman, A., Turvey, S. E., DOOFNL Consortium, Aten, E., Van Den Boogaard, M. J., Cals, F. L. J., Van Dooren, M. F., Ebbens, F. A., … Kremer, H. (2024). Exome Variant Prioritization in a Large Cohort of Hearing-Impaired Individuals Indicates IKZF2 to Be Associated with Non-Syndromic Hearing Loss and Guides Future Research of Unsolved Cases. Human Genetics, 143(11), 1379–1399. https://doi.org/10.1007/s00439-024-02706-w
  4. Velde, H. M., Huizenga, X. J. J., Yntema, H. G., Haer-Wigman, L., Beynon, A. J., Oostrik, J., Pegge, S. A. H., Kremer, H., Lanting, C. P., & Pennings, R. J. E. (2023). Genotype and Phenotype Analyses of a Novel WFS1 Variant (c.2512C>T p.(Pro838Ser)) Associated with DFNA6/14/38. Genes, 14(2), 457. https://doi.org/10.3390/genes14020457
  5. Velde, H. M., Homans, N. C., Goedegebure, A., Lanting, C. P., Pennings, R. J. E., & Kremer, H. (2023). Analysis of Rotterdam Study Cohorts Confirms a Previously Identified RIPOR2 In-Frame Deletion as a Prevalent Genetic Factor in Phenotypically Variable Adult-Onset Hearing Loss (DFNA21) in the Netherlands. Journal of Medical Genetics, 60(11), 1061–1066. https://doi.org/10.1136/jmg-2023-109146
  6. Robijn, S. M. M., Smits, J. J., Sezer, K., Huygen, P. L. M., Beynon, A. J., Van Wijk, E., Kremer, H., De Vrieze, E., Lanting, C. P., & Pennings, R. J. E. (2022). Genotype-Phenotype Correlations of Pathogenic COCH Variants in DFNA9: A HuGE Systematic Review and Audiometric Meta-Analysis. Biomolecules, 12(2), 220. https://doi.org/10.3390/biom12020220
  7. Smits, J. J., de Bruijn, S. E., Lanting, C. P., Oostrik, J., O’Gorman, L., Mantere, T., DOOFNL Consortium, Cremers, F. P. M., Roosing, S., Yntema, H. G., de Vrieze, E., Derks, R., Hoischen, A., Pegge, S. A. H., Neveling, K., Pennings, R. J. E., & Kremer, H. (2022). Exploring the Missing Heritability in Subjects with Hearing Loss, Enlarged Vestibular Aqueducts, and a Single or No Pathogenic SLC26A4 Variant. Human Genetics, 141(3-4), 465–484. https://doi.org/10.1007/s00439-021-02336-6
  8. Velde, H. M., Reurink, J., Held, S., Li, C. H. Z., Yzer, S., Oostrik, J., Weeda, J., Haer-Wigman, L., Yntema, H. G., Roosing, S., Pauleikhoff, L., Lange, C., Whelan, L., Dockery, A., Zhu, J., Keegan, D. J., Farrar, G. J., Kremer, H., Lanting, C. P., … Pennings, R. J. E. (2022). Usher Syndrome Type IV: Clinically and Molecularly Confirmed by Novel ARSG Variants. Human Genetics, 141(11), 1723–1738. https://doi.org/10.1007/s00439-022-02441-0
  9. De Bruijn, S. E., Smits, J. J., Liu, C., Lanting, C. P., Beynon, A. J., Blankevoort, J., Oostrik, J., Koole, W., De Vrieze, E., Cremers, C. W. R. J., Cremers, F. P. M., Roosing, S., Yntema, H. G., Kunst, H. P. M., Zhao, B., Pennings, R. J. E., & Kremer, H. (2021). A RIPOR2 In-Frame Deletion Is a Frequent and Highly Penetrant Cause of Adult-Onset Hearing Loss. Journal of Medical Genetics, 58(2), 96–104. https://doi.org/10.1136/jmedgenet-2020-106863
  10. Chen, T., Rohacek, A. M., Caporizzo, M., Nankali, A., Smits, J. J., Oostrik, J., Lanting, C. P., Kücük, E., Gilissen, C., van de Kamp, J. M., Pennings, R. J. E., Rakowiecki, S. M., Kaestner, K. H., Ohlemiller, K. K., Oghalai, J. S., Kremer, H., Prosser, B. L., & Epstein, D. J. (2021). Cochlear Supporting Cells Require GAS2 for Cytoskeletal Architecture and Hearing. Developmental Cell, 56(10), 1526–1540.e7. https://doi.org/10.1016/j.devcel.2021.04.017
  11. DOOFNL Consortium, Smits, J. J., Oostrik, J., Beynon, A. J., Kant, S. G., De Koning Gans, P. A. M., Rotteveel, L. J. C., Klein Wassink-Ruiter, J. S., Free, R. H., Maas, S. M., Van De Kamp, J., Merkus, P., Koole, W., Feenstra, I., Admiraal, R. J. C., Lanting, C. P., Schraders, M., Yntema, H. G., Pennings, R. J. E., & Kremer, H. (2019). De Novo and Inherited Loss-of-Function Variants of ATP2B2 Are Associated with Rapidly Progressive Hearing Impairment. Human Genetics, 138(1), 61–72. https://doi.org/10.1007/s00439-018-1965-1
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