Warning: mkdir(): Permission denied in /home/virtual/lib/view_data.php on line 87 Warning: chmod() expects exactly 2 parameters, 3 given in /home/virtual/lib/view_data.php on line 88 Warning: fopen(/home/virtual/audiology/journal/upload/ip_log/ip_log_2025-02.txt): failed to open stream: No such file or directory in /home/virtual/lib/view_data.php on line 95 Warning: fwrite() expects parameter 1 to be resource, boolean given in /home/virtual/lib/view_data.php on line 96 A 250-kb Microdeletion Identified in Chromosome 16 Is Associated With Non-Syndromic Sensorineural Hearing Loss in a South Indian Consanguineous Family

A 250-kb Microdeletion Identified in Chromosome 16 Is Associated With Non-Syndromic Sensorineural Hearing Loss in a South Indian Consanguineous Family

Article information

J Audiol Otol. 2025;29(1):31-37
Publication date (electronic) : 2025 January 20
doi : https://doi.org/10.7874/jao.2024.00038
1Department of Biochemistry, Aarupadai Veedu Medical College and Hospital, Vinayaka Mission’s Research Foundation (Deemed to be University), Kirumampakkam, Puducherry, India
2Department of Otorhinolaryngology, Aarupadai Veedu Medical College and Hospital, Vinayaka Mission’s Research Foundation (Deemed to be University), Kirumampakkam, Puducherry, India
3Department of Medical Biotechnology, Aarupadai Veedu Medical College and Hospital, Vinayaka Mission’s Research Foundation (Deemed to be University), Kirumampakkam, Puducherry, India
4Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
Address for correspondence Sambandam Ravikumar, PhD Department of Medical Biotechnology, Faculty of Interdisciplinary Studies, Aarupadai Veedu Medical College and Hospital, Vinayaka Mission’s Research Foundation (Deemed to be University), Kirumampakkam, Puducherry 607403, India Tel +91-413-2611245 (217) E-mail ravikumar.sambandam@avmc.edu.in
Received 2024 March 8; Revised 2024 May 2; Accepted 2024 June 15.

Abstract

Background and Objectives

Hereditary hearing loss is the most common genetic disorder in children. Nearly 120 genes associated with auditory impairment have been identified. Although the disease is clinically and genetically complex, the chances of identifying deafness-causing loci increase when studying consanguineous families.

Materials and Methods

Whole-exome sequencing was performed to identify genetic variants underlying sensorineural hearing loss in affected individuals from a family with third-degree consanguineous practices.

Results

A homozygous deletion of 250.285 kb was identified in the 16p12.2 region encompassing three genes, METTL9, IGSF6, and OTOA, and a partial deletion of the NPIPB4 gene co-segregated within the family.

Conclusions

This study highlighted the genetic heterogeneity of hearing loss in consanguineous families. Future research should focus on the OTOA mutational spectrum in South Indian populations with hearing loss.

Introduction

Genetic hearing loss is the most common sensory defect, particularly among children [1]. Approximately 2.7 cases out of every 1,000 newborns are affected by sensorineural hearing loss [2]. In India, the prevalence of hearing loss is 6.3%, according to the World Health Organization (WHO) [3]. There is a high prevalence of consanguinity practice in India, particularly in Southern regions due to ethnic customs and socioeconomic beliefs [4,5]. Due to the high inbreeding co-efficient, offspring of parental consanguinity tend to carry causal variants, making them an ideal population for understanding and studying genetic disorders [6,7]. Based on the etiology, hearing loss (HL) is classified into syndromic forms and non-syndromic forms, affecting the inner ear and causing sensorineural HL [8]. Clinical severity of HL varies from mild to profound, with ages of onset ranging from congenital to adult. Non-syndromic hearing loss (NSHL) can follow autosomal and sexlinked, mitochondrial patterns of inheritance. Nearly 70% of NSHL follows autosomal recessive patterns of inheritance [8,9]. To date, more than 120 genes are associated with NSHL (https://hereditaryhearingloss.org/). Among these, GJB2 is the most common gene associated with autosomal recessive NSHL in different ethnicities. Many studies have implicated those mutations in DFNB loci (autosomal recessive NSHL causing loci), particularly GJB6, CDH23, SLC26A4, and MYO15A, to be highly associated with sensorineural hearing loss [9]. Pathogenic mutations in NSHL genes could be single nucleotide variants, small insertions/deletions (indels), splice site variants, and copy number variations (CNVs). CNVs of STRC and OTOA genes are found to be the most prevalent in NSHL patients [10,11]. Due to the phenotypic complexity and genetic heterogeneity of NSHL, the molecular diagnosis remains difficult. Therefore, investigating the correlation of phenotype-genotype of NSHL is more appropriate in consanguineous populations [10,12]. Whole exome sequencing (WES) enables the identification of single nucleotide variants (SNV), small insertion and deletions (indels), and structural variants including CNV in the coding regions of the genome, making it an ideal approach for investigating the genetic architecture of NSHL [13]. Therefore, in this study, we performed WES for two siblings affected by NSHL and their unaffected parents.

Subjects and Methods

Patient history and clinical evaluation

The probands (II-1, II-2), an 18-year-old female and a 17-year-old male, who visited ENT outpatient department were siblings affected with sensorineural hearing loss. The probands were born of consanguineous marriage, wherein the parents were first cousins with normal hearing ability. A complete medical history was collected. Clinical examination including otoscopy followed by pure tone audiometry (PTA) was performed for air and bone conduction of the participants. Based on the PTA criteria, the severity of the HL was categorized into moderate (41 to 70 dB), severe (71 to 90 dB), and profound (above 91 dB).

WES and CNV analysis

Genomic DNA was extracted from whole blood using a DNA QIAmp mini kit (Qiagen, Hilden, Germany). Targeted gene enrichment of exonic regions was done by Twist Biosciences Exome Capture Kit (San Francisco, CA, USA). DNA libraries were prepared and sequenced by Illumina HiSeq4500 sequencer Illumina (San Diego, CA, USA) with an average 100×coverage. The reads obtained were aligned to the human reference genome (GRCh38) using a Burrows-Wheeler Aligner (BWA-MEM, v 0.7.10) (Supplementary Fig. 1 in the online-only Data Supplement). Integrative Genomics Viewer (IGV; https://igv.org/) was used to visualize the read alignment and confirm the variant calls. Sentieon DNAseq (San Jose, CA, USA) was used for duplicate removal, base recalibration, and indel re-alignment. Sentieon haplotype caller identified variants in the samples and were deeply annotated by the VariMAT pipeline. Gene annotation of the variants was performed using the VEP program against the Ensembl release 99 (www.ensembl.org) human gene model. In addition to variants and indels, CNVs were also detected based on the read depths of the sequenced data. ExomeDepth tool compared the read distribution of the test sample with the normal reference (EST00000646100.2) to determine the CNV regions. ExomeDepth tool has been shown to detect CNV with a higher sensitivity percentage [14]. Variants identified in both coding and non-coding regions were annotated based on a set of databases like ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/), OMIM (https://www.omim.org/), HGMD (https://www.hgmd.cf.ac.uk/ac/index.php), LOVD (https://www.lovd.nl/), DECIPHER (https://www.deciphergenomics.org/), and SwissVar (https://bio.tools/swissvar). The pathogenicity of the variants was classified based on the guidelines for the interpretation of sequence variants from the American College of Medical Genetics and Genomics (ACMG) and the Association for Molecular Pathology [15]. Common variants were filtered based on allele frequency in 1000 Genome Phase 3, gnomAD (v3.1 & 2.1.1), dbSNP (GCF_000001405.38), 1000 Japanese Genome, TOPMed (Freeze_8), Genome Asia, and Indian population database (MedVarDb v2.1). The functional prediction of clinically relevant variants was evaluated by SIFT, PolyPhen2, and MutationTaster2.

Ethical approval

This study was approved by the Institutional Human Ethical Committee of Aarupadai Veedu Medical College & Hospital (IEC.No: AV/IEC/2020/010), and informed consent was obtained from participants included in the study. This study was performed in line with the principles of the Declaration of Helsinki.

Results

Clinical findings

In the probands, an auditory finding showed type A tympanogram, indicating no middle ear dysfunction by immittance testing. PTA confirmed the affected individuals with moderately severe sensorineural hearing loss (Supplementary Fig. 2 in the online-only Data Supplement). The affected siblings showed no dysmorphic features or clinical deformities. The parents had normal hearing ability (Supplementary Fig. 2 in the online-only Data Supplement).

Genetic analysis

The genetic analysis of the family with two siblings affected by autosomal recessive NSHL carrying OTOA deletion is shown in Table 1. The two affected individuals showed homozygous deletion of 250.285 kb in 16p12.2 region [chr16: g.21597256-21847541del], encompassing 3 genes including METTL9, IGSF6, OTOA, and partial deletion of NPIPB4 gene (Figs. 1 and 2). CNV co-segregated between father and mother in the heterozygous state (Fig. 3). As per Franklin (https://franklin.genoox.com/clinical-db/home) and ACMG guidelines, 250 kb microdeletion was classified as a pathogenic variant (PVS1) [15]. Additionally, two compound heterozygous variants c.3815-3816del, c.4910C>G in the TRIOBP gene were detected in the son and the mother. A novel heterozygous variant in the COL4A6 gene was identified in the affected daughter and also in the father. In silico pathogenicity analyses have predicted COL4A6 c.4277C >T, TRIOBP variants c.4910C>G, and c.3815-3816del to be damaging.

Genetic variants identified by whole exome sequencing in family members affected and unaffected by hearing loss

Fig. 1.

Homozygous OTOA CNV identified in proband II-1 (daughter). Integrative Genome Viewer (IGV) shows homozygous OTOA deletion in the proband II. Red and blue rectangles indicate pair-end reads generated by sequencer, which were compared and visualized by IGV. CNV, copy number variation.

Fig. 2.

Homozygous OTOA CNV identified in Proband II-2 (son). Integrative Genome Viewer (IGV) shows homozygous OTOA deletion in the proband II-2. Reference sample was used for comparison. Red and blue rectangles indicate pair-end reads generated by sequencer, which were compared and visualized by IGV. CNV, copy number variation.

Fig. 3.

Heterozygous OTOA CNV identified in parents. IGV shows heterozygous OTOA deletion in both unaffected parents, were compared with reference sample. Red and blue rectangles indicate pair-end reads generated by sequencer, which were compared and visualized by IGV. CNV, copy number variation.

Discussion

This study reports, for the first time, a 250 kb microdeletion in Chr16 resulting in the whole deletion of 3 genes METTL9, IGSF6, OTOA, and partial deletion of NPIPB4 gene in NSHL subjects of South Indian origin. Microdeletions occur recurrently in a critical region of Chr16p12.2 via non-allelic homologous recombination owing to the presence of three breakpoints (BP), leading to segmental duplications/deletions [11]. BP1 and BP2 flank the three genes: METTL9, IGSF6, and OTOA; while BP2 and BP3 span about 520 kb and comprise 7 genes: PDZD9, C16orf52, VWA3A, POLR3E, UQCRC2, EEF2K, and CDR2 [16]. The 16p12.2 region is designated as a “hot spot” for genomic deletion [17]. The frequency of OTOA-associated HL is high in Middle-Eastern countries such as Iran, Israel, and Qatar [12]. Previous studies reporting OTOA CNVcausing NSHL are shown in Table 2. An extensive study by Sugiyama, et al. [12] identified OTOA-associated HL from sporadic 2,262 Japanese autosomal recessive HL patients and prevalence was found to be 0.3% (7/2,262). Among seven probands, two cases were found to have a homozygous deletion in OTOA gene, four cases carry heterozygous OTOA deletions in trans to SNVs, and one case with homozygous SNV (c.647T>C). This study also identified the audiometric characteristics of the affected individuals to be of mid-frequency [12]. The frequency of 16p12.2 OTOA deletion in the heterozygous state was identified to be about 1% in the Palestinian population [18]. To date, two studies have reported an association between OTOA gene deletion and HL in nonconsanguineous families [19,20]. Segregation analysis revealed compound heterozygous OTOA deleterious variant p. Trp741* in an Italian family wherein two siblings were affected by NSHL [20]. The molecular diagnosis of 131 patients affected with autosomal recessive NSHL in the Western European population emphasized that screening of OTOA CNV in the comprehensive analysis of NSHL [21]. However, no point mutation or CNV of OTOA has been reported in the Indian HL subjects.

Previous studies reporting OTOA variants associated with sensorineural hearing loss

OTOA encodes OTOAncorin, a glycosyl phosphatidylinositol protein with a molecular weight of 120 kDa essential for the anchoring of tectorial membrane (TM) with the apical surface of hair cells in the cochlear duct [22]. OTOA links the tectorial membrane with the spiral limbus of the cochlear wall required for creating an endo cochlear potential by shearing [22,23]. Mutations in the OTOA gene affect the anchoring of TM with inner hair cells as well as the detachment of TM, from the cochlear wall [23]. Zwaenepoel, et al. [23] first reported the mutation of OTOA underlying prelingual onset of severe to profound hearing loss (DFNB22 loci).

In the present study, probands carrying OTOA CNV show similarities with a phenotypic spectrum of “distal 16p12.2 microdeletion.” Distal 16p12.2 microdeletions are extremely rare compared to recurrent 520 kb 16p12.2 deletions, which occur often [16]. The prevalence of distal 16p12.2 deletion as shown in gnomAD (DEL_CHR16_2A34FF15) is 0.00040%. The common characteristics of 520 kb 16p12.2 microdeletion include developmental problems such as autism, delayed speech, intellectual disability, hypotonia, short stature, microcephaly along with dysmorphic facial pattern, congenital cardiac defects, and epilepsy, as well as psychiatric illnesses such as schizophrenia [11,24]. However, phenotypic features of 16p12.2 microdeletion vary between individuals [25]. The clinical phenotypes of distal 16p12.2 microdeletion include autism, dyslexia, intellectual disability, delayed speech and development, along with hearing impairment due to OTOA gene deletion [16]. Phenotypes associated with the chromosomal rearrangements vary even among affected members of the same family, and sometimes, individuals with the deletion have no physical or developmental abnormalities [11]. In this study, probands showed no clinical deformities other than NSHL following the autosomal recessive pattern of inheritance. The probands in this study showed different audiograms. In an earlier study, Sugiyama, et al. [12] found OTOA-associated HL in 7 out of 2,262 Japanese sporadic autosomal recessive HL patients. This study summarized audiometric characteristics of these seven probands ranging from moderate to severe HL with audiometric configuration of mid-frequency. Among 7 patients, three adult probands had progressive HL. A proband in the study, seven years of age, showed an asymmetric pattern of SNHL. Similar to the study, proband II-2 also had asymmetrical hearing loss (moderately severe HL in the right ear and mild HL in the left ear) in our study. These changes are due to environmental or genetic factors including aging. The genotype-phenotype correlation of CNVs is complex and unclear due to the incomplete penetrance and variable expressivity leading to differences in the severity of genetic disorders necessitating crucial measures for diagnosis and treatment [26].

Additionally, COL4A6 novel heterozygous variant was identified in the probands affected with NSHL in this study. COL4A6 gene found in the Chr X encodes collagen type IV alpha-6 chain protein expressed in the basement membrane of the inner ear and plays a crucial part in the development of cochlea. Mutations in the gene associated with X-linked hearing loss (DFX4) [8,27]. A novel variant c.4277C>T identified in COL4A6 gene segregated with carrier mother and affected son in this study.

A novel compound heterozygous variation, two-base pair deletion in exon 7 (chr22: g.37726371-37726372del) and p. Thr1637Ser in exon 9 of TRIOBP gene located in Chr22 possess, was identified in this study. Multiple isoforms of TRIOBP have been discovered. It encodes a protein called TRIO and F actin-binding protein BP, primarily modulating the assembly of the actin cytoskeleton in the inner ear. Mice deficient in TRIOBP result in thin actin rootlets affecting the mechanism of hearing [1,2,28]. Mutations found in the study phenotypically correlated by segregation analysis are shown in Fig. 4. The current study highlights the genetic complexity of non-syndromic hearing loss in a South Indian family.

Fig. 4.

Pedigree of the family studied showing heterozygous parents and affected children for OTOA deletion. Pedigree chart of the affected family shows probands II-1 and II-2 born to consanguineous parents, affected with non-syndromic hearing loss due to complete OTOA gene deletion in homozygous state. The parents of the affected siblings and carriers of OTOA gene deletion exhibited with normal hearing.

In conclusion, CNVs also contribute to NSHL and their identification must be included in genetic screening for hearing loss. The results of the study provide insights into the genetic basis of hearing disorders highlighting the future investigation to elucidate the underlying mechanism and therapeutic strategies. Future studies elucidating the mutational spectrum of OTOA genes causing hearing loss are warranted.

Supplementary Materials

The online-only Data Supplement is available with this article at https://doi.org/10.7874/jao.2024.00038.

Supplementary Fig. 1.

Reference region of 16p12.2 used for CNV comparison in the study.

jao-2024-00038-Supplementary-Fig-1.pdf

Supplementary Fig. 2.

Pure tone audiograms of the probands (II1& II2) and parents (I1-father & I2-mother). A: Proband II1. B: Proband II2. C: Father I1. D: Mother I2.

jao-2024-00038-Supplementary-Fig-2.pdf

Notes

Conflicts of Interest

The authors have no financial conflicts of interest.

Author Contributions

Conceptualization: Jayakumar Swetha, Sambandam Ravikumar. Data curation: Arulmozhi Sakthignanavel, Aarthi Manoharan, Priyadharshini Arunagiri. Formal analysis: Jayakumar Swetha, Priyadharshini Arunagiri. Funding acquisition: Arulmozhi Sakthignanavel, Sambandam Ravikumar. Investigation: Arulmozhi Sakthignanavel, Aarthi Manoharan, Priyadharshini Arunagiri. Methodology: Arulmozhi Sakthignanavel, Chandramohan Govindasamy. Project administration: Jayakumar Swetha, Priyadharshini Arunagiri. Software: Chandramohan Govindasamy, Jayakumar Rangarajalu. Supervision: Sambandam Ravikumar, Chandramohan Govindasamy. Visualization: Jayakumar Swetha, Jayakumar Rangarajalu. Writing—original draft: Jayakumar Swetha, Aarthi Manoharan. Writing—review & editing: Aarthi Manoharan, Jayakumar Rangarajalu, Sambandam Ravikumar. Approval of final manuscript: all authors.

Funding Statement

The research leading to these results received funding from Indian Council of Medical Research under Adhoc Research Project No.5/4-5/06/ENT/2020-NCD-I entitled “Genetic Screening to identify the association between consanguineous marriage with deafness in Puducherry and Tamil Nadu.”

Acknowledgements

The author would like to thank the participants in the study. We thankfully acknowledge the School of Rehabilitation and Behavioural Sciences, AVMC Puducherry for audiometric analysis.

References

1. Young A, Ng M. Genetic hearing loss. In: StatPearls [Internet]. Treasure Island: StatPearls Publishing;2023 [cited 2024 March 1]. Available from: https://www.ncbi.nlm.nih.gov/books/NBK580517.
2. Vona B, Nanda I, Hofrichter MA, Shehata-Dieler W, Haaf T. Non-syndromic hearing loss gene identification: a brief history and glimpse into the future. Mol Cell Probes 2015;29:260–70.
3. World Health Organazation. World Hearing Day 2023: ear and hearing care for all! Let’s make it a reality. New Delhi: Office of the WHO Representative to India;2023 [cited 2024 November 11]. Available from: https://doi.org/10.1016/S2665-9913(20)30446-X.
4. Sharma SK, Kalam MA, Ghosh S, Roy S. Prevalence and determinants of consanguineous marriage and its types in India: evidence from the national family health survey, 2015-2016. J Biosoc Sci 2021;53:566–76.
5. Kumar D. Genetic disorders of the Indian subcontinent. 1st ed. New York: Springer Science & Business Media;2004.
6. Richard EM, Santos-Cortez RLP, Faridi R, Rehman AU, Lee K, Shahzad M, et al. Global genetic insight contributed by consanguineous Pakistani families segregating hearing loss. Hum Mutat 2019;40:53–72.
7. Bhinder MA, Sadia H, Mahmood N, Qasim M, Hussain Z, Rashid MM, et al. Consanguinity: a blessing or menace at population level? Ann Hum Genet 2019;83:214–9.
8. Shearer AE, Hildebrand MS, Schaefer AM, Smith RJH. Genetic hearing loss overview. In: Adam MP, Feldman J, Mirzaa GM, et al., editors. GeneReviews® [Internet]. Seattle: University of Washington, Seattle;1999 [cited 2024 March 1]. Available from: https://www.ncbi.nlm.nih.gov/books/NBK1434.
9. Vanniya S P, Chandru J, Pavithra A, Jeffrey JM, Kalaimathi M, Ramakrishnan R, et al. Recurrence of reported CDH23 mutations causing DFNB12 in a special cohort of South Indian hearing impaired assortative mating families – an evaluation. Ann Hum Genet 2018;82:119–26.
10. Ramzan M, Bashir R, Salman M, Mujtaba G, Sobreira N, Witmer PD, et al. Spectrum of genetic variants in moderate to severe sporadic hearing loss in Pakistan. Sci Rep 2020;10:11902.
11. Shearer AE, Kolbe DL, Azaiez H, Sloan CM, Frees KL, Weaver AE, et al. Copy number variants are a common cause of non-syndromic hearing loss. Genome Med 2014;6:37.
12. Sugiyama K, Moteki H, Kitajiri SI, Kitano T, Nishio SY, Yamaguchi T, et al. Mid-frequency hearing loss is characteristic clinical feature of OTOA-associated hearing loss. Genes (Basel) 2019;10:715.
13. Bademci G, Diaz-Horta O, Guo S, Duman D, Van Booven D, Foster J 2nd, et al. Identification of copy number variants through whole-exome sequencing in autosomal recessive nonsyndromic hearing loss. Genet Test Mol Biomarkers 2014;18:658–61.
14. Rajagopalan R, Murrell JR, Luo M, Conlin LK. A highly sensitive and specific workflow for detecting rare copy-number variants from exome sequencing data. Genome Med 2020;12:14.
15. Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, et al. Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet Med 2015;17:405–24.
16. Tassano E, Ronchetto P, Calcagno A, Fiorio P, Gimelli G, Capra V, et al. ‘Distal 16p12.2 microdeletion’ in a patient with autosomal recessive deafness-22. J Genet 2019;98:56.
17. Shahin H, Walsh T, Rayyan AA, Lee MK, Higgins J, Dickel D, et al. Five novel loci for inherited hearing loss mapped by SNP-based homozygosity profiles in Palestinian families. Eur J Hum Genet 2010;18:407–13.
18. Fontana P, Morgutti M, Pecile V, Lenarduzzi S, Cappellani S, Falco M, et al. A novel OTOA mutation in an Italian family with hearing loss. Gene Rep 2017;9:111–4.
19. He L, Pang X, Liu H, Chai Y, Wu H, Yang T. Targeted next-generation sequencing and parental genotyping in sporadic Chinese Han deaf patients. Clin Genet 2018;93:899–904.
20. Ortore RP, Leone MP, Palumbo O, Petracca A, Trecca EMC, D’Ecclesia A, et al. Compound heterozygosity for OTOA truncating variant and genomic rearrangement cause autosomal recessive sensorineural hearing loss in an Italian family. Audiol Res 2021;11:443–51.
21. Sommen M, Schrauwen I, Vandeweyer G, Boeckx N, Corneveaux JJ, van den Ende J, et al. DNA diagnostics of hereditary hearing loss: a targeted resequencing approach combined with a mutation classification system. Hum Mutat 2016;37:812–9.
22. Kim BJ, Kim DK, Han JH, Oh J, Kim AR, Lee C, et al. Clarification of glycosylphosphatidylinositol anchorage of OTOANCORIN and human OTOA variants associated with deafness. Hum Mutat 2019;40:525–31.
23. Zwaenepoel I, Mustapha M, Leibovici M, Verpy E, Goodyear R, Liu XZ, et al. Otoancorin, an inner ear protein restricted to the interface between the apical surface of sensory epithelia and their overlying acellular gels, is defective in autosomal recessive deafness DFNB22. Proc Natl Acad Sci U S A 2002;99:6240–5.
24. Chung WK, Roberts TP, Sherr EH, Snyder LG, Spiro JE. 16p11.2 deletion syndrome. Curr Opin Genet Dev 2021;68:49–56.
25. Girirajan S, Campbell CD, Eichler EE. Human copy number variation and complex genetic disease. Annu Rev Genet 2011;45:203–26.
26. Veltman JA, Brunner HG. Understanding variable expressivity in microdeletion syndromes. Nat Genet 2010;42:192–3.
27. Rost S, Bach E, Neuner C, Nanda I, Dysek S, Bittner RE, et al. Novel form of X-linked nonsyndromic hearing loss with cochlear malformation caused by a mutation in the type IV collagen gene COL4A6. Eur J Hum Genet 2014;22:208–15.
28. Zhou B, Yu L, Wang Y, Shang W, Xie Y, Wang X, et al. A novel mutation in TRIOBP gene leading to congenital deafness in a Chinese family. BMC Med Genet 2020;21:121.
29. Sloan-Heggen CM, Babanejad M, Beheshtian M, Simpson AC, Booth KT, Ardalani F, et al. Characterising the spectrum of autosomal recessive hereditary hearing loss in Iran. J Med Genet 2015;52:823–9.
30. Alkowari MK, Vozzi D, Bhagat S, Krishnamoorthy N, Morgan A, Hayder Y, et al. Targeted sequencing identifies novel variants involved in autosomal recessive hereditary hearing loss in Qatari families. Mutat Res 2017;800-802:29–36.

Article information Continued

Fig. 1.

Homozygous OTOA CNV identified in proband II-1 (daughter). Integrative Genome Viewer (IGV) shows homozygous OTOA deletion in the proband II. Red and blue rectangles indicate pair-end reads generated by sequencer, which were compared and visualized by IGV. CNV, copy number variation.

Fig. 2.

Homozygous OTOA CNV identified in Proband II-2 (son). Integrative Genome Viewer (IGV) shows homozygous OTOA deletion in the proband II-2. Reference sample was used for comparison. Red and blue rectangles indicate pair-end reads generated by sequencer, which were compared and visualized by IGV. CNV, copy number variation.

Fig. 3.

Heterozygous OTOA CNV identified in parents. IGV shows heterozygous OTOA deletion in both unaffected parents, were compared with reference sample. Red and blue rectangles indicate pair-end reads generated by sequencer, which were compared and visualized by IGV. CNV, copy number variation.

Fig. 4.

Pedigree of the family studied showing heterozygous parents and affected children for OTOA deletion. Pedigree chart of the affected family shows probands II-1 and II-2 born to consanguineous parents, affected with non-syndromic hearing loss due to complete OTOA gene deletion in homozygous state. The parents of the affected siblings and carriers of OTOA gene deletion exhibited with normal hearing.

Table 1.

Genetic variants identified by whole exome sequencing in family members affected and unaffected by hearing loss

Variants identified in this study Type of variants ACMG classification I-1 (father) I-2 (mother) II-1 (daughter) II-2 (son)
Chr16: g. (21597256-21847541) del CNV (250.285 kb microdeletion) Pathogenic Heterozygous Heterozygous Homozygous Homozygous
COL4A6 c.4277C>T (p. Pro1426Le) Missense VUS Heterozygous - Heterozygous -
TRIOBP c.3815-3816del (p. Val1272AlafsTer108) Frameshift Pathogenic - Heterozygous - Heterozygous
TRIOBP c.4910C>G (p. Thr1637Ser) Missense VUS - Heterozygous - Heterozygous

CNV, copy number variation; VUS, variant with unknown significance; ACMG, American College of Medical Genetics and Genomics

Table 2.

Previous studies reporting OTOA variants associated with sensorineural hearing loss

Study Ethnicity (n*) HL Phenotype OTOA variants
CNV SNV
Sugiyama, et al. [12] Japanese (7/2,262) Mild to moderate HL Homozygous OTOA deletion c.235C>T
Heterozygous OTOA deletion c.442C>T
c.469C>T
c.1705A>G
c.647T>C
Bademci, et al. [13] Turkish (3/103) Mild to moderate HL Homozygous OTOA deletion -
Shahin, et al. [17] Palestinian population (4/238) Prelingual NSHL Homozygous OTOA deletion -
Fontana, et al. [18] Italian family (3/6) Prelingual severe NSHL Heterozygous OTOA deletion c.1865T>A
He, et al. [19] Chinese (1/44) Moderate to profound HL Heterozygous OTOA deletion c.878A>G
Sloan-Heggen, et al. [29] Iran (3/302) Mild to moderate HL Homozygous OTOA deletion -
Alkowari, et al. [30] Qatar (3/80) Moderate HL Homozygous OTOA deletion -
*

HL patients with OTOA mutations/total of HL patients studied;

compound heterozygotes for OTOA deletion and SNVs.

HL, hearing loss; CNV, copy number variation; SNV, single nucleotide variants; NSHL, non-syndromic hearing loss