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A novel frameshift variant in the TMPRSS3 gene causes nonsyndromic hearing loss in a consanguineous family

BMC Medical Genomics volume 17, Article number: 283 (2024) Cite this article

Abstract

Background

Hearing Loss (HL) is the most common sensorineural condition in humans. Mutations in the TMPRSS3 gene (DNFB8/10 locus) have been linked to autosomal recessive non-syndromic hearing loss (ARNSHL).

Methods

Whole-exome sequencing (WES) was utilized to identify disease-causing variants in a proband from Iran with ARNSHL who presented clinically with sensorineural, bilateral, and prelingual HL. The pathogenicity and novelty of the identified variant were assessed using various databases. A co-segregation study was also performed to confirm the presence of the variant in the proband’s parents. Additionally, the secondary and tertiary structures of the mutant TMPRSS3 protein were predicted using bioinformatics tools. Furthermore, a global mutational spectrum of TMPRSS3 was created and statistically analyzed. The Iranome database was also used to identify other putative mutations in the TMPRSS3 gene in the Iranian population.

Results

We identified a novel homozygous single nucleotide deletion in TMPRSS3 (c.297delA, p.Asp100ThrfsTer52) in the proband. This is the first report of this mutation in a patient with ARNSHL. Sanger sequencing confirmed that this variant co-segregated from the proband’s parents. Bioinformatic tools classified this novel variant as likely pathogenic. Additionally, 49.55% of families with TMPRSS3-related HL patients were shown to have consanguinity, consistent with our study. The Iranome database also revealed the c.268G > A variant as a putative novel mutation in TMPRSS3.

Conclusion

This research expanded the pool of evidence regarding the association between mutations in the TMPRSS3 gene and ARNSHL. The finding confirmed that a single nucleotide deletion caused HL in the proband, suggesting that genetic testing, such as WES, is a robust technique for diagnosing patients with this condition.

Peer Review reports

Introduction

As the most common sensorineural human condition, hereditary hearing loss (HL) occurs in 1 out of every 500 infants [1]. More than half of HL cases result from genetic etiology, with 70% exhibiting Mendelian monogenic inheritance patterns [2, 3]. Various forms of HL arise from alterations in certain genes (also known as pleiotropy), which can significantly impact the severity of the disease. Nevertheless, autosomal recessive non-syndromic hearing loss (ARNSHL) accounts for the majority of cases. To date, more than 150 non-syndromic HL genes have been discovered, with 87 mapped for ARNSHL alone (Hereditary Hearing Loss Homepage). Around 80% of the global burden of HL falls on low and middle-income regions [4], including Iran, where the prevalence of HL is higher than elsewhere (up to three times) largely due to consanguinity [5]. Saadat et al. estimated that the overall rate of consanguineous marriage in Iran is 38.6% [6].

Of the more than 70 loci identified for ARNSHL, mutations in the DNFB10 locus (previously known as DNFB8), which includes the transmembrane serine protease 3 (TMPRSS3) gene (OMIM: 605511), have been shown to contribute mostly to the pre-lingual type of ARNSHL [7]. This gene spans 13 exons, encompassing 24.2 kb in length, and is located on 21q22.3. It encodes a type II transmembrane serine protease enzyme with 454 amino acids, extending over four functional domains: a transmembrane domain (TM), a serine protease domain (SP), an LDL receptor-like domain (LDLR), and a scavenger receptor cysteine-rich domain (SRCR) [8]. The transmembrane domain is postulated to affect the function of amiloride-sensitive Na + channels (also known as the ENaC-Deg family of ion channels) in the epithelium of the endolymph, where its function is to mediate the reabsorption of Na+ [9]. Furthermore, TMPRSS3 is expressed predominantly in the fetal cochlea and is believed to play a pivotal role in the development and maintenance of the inner ear [10].

The high degree of genetic heterogeneity in HL presents challenges for identifying the underlying genetic etiology. According to the ACMG guidelines for the genetic diagnosis of HL [11], it is recommended to employ next-generation sequencing (NGS) approaches, particularly whole-exome sequencing (WES), as efficient methods to recognize disease-causing variants in patients. WES enables the analysis of coding regions, which constitute approximately 2% of the human genome. It is widely accepted that these sequences contain more than 80% of human disease-causing variants [12]. WES is effective in detecting variants associated with specific clinical features by prioritizing genes and sorting identified sequence changes. Compared to whole-genome sequencing (WGS), WES is a less time-consuming and cost-effective way to investigate large-scale amounts of DNA [3, 13, 14].

In this study, we applied WES to elucidate the underlying molecular mechanism of non-syndromic HL in a first-cousin consanguineous family, which resulted in the identification of a novel causative deletion variant. Moreover, a multidimensional in silico study on the variant provided new insights into the nature of the condition and the reported variant’s role.

Materials and methods

Clinical evaluation

The present study included a six-year-old girl born to first-cousin parents. Written informed consent was obtained from the patient’s parents prior to the study. The patient and her parents were interviewed, and a comprehensive medical and family history was obtained to exclude non-hereditary causes of hearing loss, such as ototoxicity, infection, and trauma. A physical examination was conducted to carefully assess for syndromic features and vestibular problems. Additionally, an audiometric evaluation was performed to assess air-conduction thresholds at frequencies ranging from 250 to 8000 Hz. A 1mL sample of peripheral blood was collected in an EDTA-containing tube from the patient. Direct sequencing of the GJB2 gene (OMIM: 121011), the most commonly mutated gene in hearing loss patients, was also performed.

The research was conducted according to the guidelines set forth by the Ethics Committee of Golestan University of Medical Sciences (Ethics Code: IR.GOUMS.REC.1401.227).

DNA extraction

DNA was extracted from 200 µLof the patient’s peripheral blood mononuclear cells using the Kowsar DNA extraction kit (catalog number: K1135). The concentration of the purified DNA samples was quantified using a Nanodrop device.

Direct PCR sequencing for GJB2 gene

Only exon 2 of the two GJB2 exons is considered the coding region, and it was chosen for direct PCR sequencing in this study. The primers for GJB2 exon 2 were obtained from a previous study conducted by Scott et al. [15]. After standard PCR amplification, the products were purified according to the purification kit protocol, and DNA sequencing was performed.

Whole exome sequencing

The patient’s DNA underwent whole exome sequencing (WES) on the Illumina HiSeq 6000 platform. DNA was fragmented, barcoded, and hybridized using the Agilent SureSelect Human All Exon V7 Plus probe set, achieving an average coverage of 100X, with 90–95% of bases covered at least 20X. Sequencing reads were aligned to the human reference genome (GRCh37/hg19) using the Burrows-Wheeler Aligner (BWA) [16]. SAMtools sorted and indexed the BAM files, removing duplicates and low-quality reads (QBase < 20). Variant calling for single nucleotide variants (SNVs) and indels was performed using the Genome Analysis Toolkit (GATK) [17]. Variants, including nonsense, missense, and splicing variations, were filtered based on a minor allele frequency (MAF) threshold of < 0.01, comparing them with databases like 1000 Genomes and gnomAD. The pathogenic potential of selected variants was assessed using bioinformatic tools such as SIFT, CADD, and PolyPhen-2, following guidelines from InterVar, Varsome, and ClinVar. This reduced the initial 70,000 variants to a manageable number of potential disease-causing mutations for further verification, considering inheritance patterns, mutation localization, and published studies, while adhering to ACMG guidelines for pathogenicity evaluation [18].

Co-segregation study to validate the reported mutation

Conventional Sanger sequencing was performed in both forward and reverse directions to confirm the final variant. Additionally, segregation analysis was conducted for family members. To amplify the locus containing the variant, primers were designed using the Primer3 software. Subsequently, standard PCR was performed with an initial denaturation at 94 °C for 3 min, followed by 35 cycles of denaturation at 94 °C for 30 s, annealing at 58.9 °C for 30 s, extension at 72 °C for 1 min, and a final extension at 72 °C for 10 min. The resulting products were then used for sequencing. Afterwards, CodonCode Aligner was used to evaluate the resulting sequence chromatograms.

Computational analysis of TMPRSS3 mutations

Bioinformatic tools including SIFT [19], CADD [20], Mutation Taster [21], and Polyphen-2 [22], and FATHMM [23] were utilized in order to validate the pathogenicity of all TMRPSS3 variant, which were retrieved from The Human Gene Mutation Database (HGMD) database. Also we checked MUpro [24] to predict the effects of the variants on protein stability. We also check each variant’s publication to evaluate patient’s nationality and mode of inheritance.

Conservation study of TMPRSS3 protein sequence

To conduct an evolutionary conservation study for the TMPRSS3 protein amino acid sequence, the Clustal Omega [25], and ConSurf [26] web servers were used. The aim was to evaluate the protein sequence and determine whether it is conserved across different species. TMPRSS3 protein sequences from various species, including zebrafish (Danio rerio), red junglefowl (Gallus gallus), wild Bactrian camel (Camelus ferus), house mouse (Mus musculus), brown rat (Rattus norvegicus), rhesus macaque (Macaca mulatta), humans (Homo sapiens), chimpanzee (Pan troglodytes), domestic cattle (Bos taurus), and dog (Canis lupus familiaris), were extracted from NCBI and submitted in the proper format for Clustal Omega to align the sequences. The TMPRSS3 protein sequence was also presented to the ConSurf web server, which is a bioinformatic tool that investigates the phylogenetic relationships between homologous sequences to predict the functional and structural regions. ConSurf assigns a conservation score ranging from 1 (indicating a variable residue) to 9 (indicating a conserved residue) for each residue, and it also predicts exposed and buried residues with high scores as ‘functional’ and ‘structural’, respectively. The results of these analyses would provide valuable insights to understand the properties and the potential effects of a given mutation on the TMPRSS3 protein.

Predicting secondary and tertiary structure

We performed a secondary structure analysis using the PSIPRED software for the TMPRSS3 protein. PSIPRED is a neural network tool that calculates the probability for a given residue to be present in different elements of a sequence (including helix, strand, and coil), and it accumulates all probabilities to predict the entire secondary structure. Additionally, the I-TASSER server was used to model the 3D structure of TMPRSS3. I-TASSER uses the Protein Data Bank (PDB) to retrieve sequences that are homologous to different regions of the input sequence, assembles them into a whole 3D structure, and applies molecular simulations and modeling techniques to fine-tune the model based on energy and stability. The final result of the I-TASSER analysis was visualized using the UCSF Chimera [27] softwere.

Protein–protein interaction study using STRING and networkX python package

According to the Pathcards database, a superpathway named “sensory perception of sound” contains 4 signaling pathways: (a) sensory processing of sound by outer hair cells of the cochlea, (b) sensory processing of sound by inner hair cells of the cochlea, (c) sensory perception of sound, and (d) acetylcholine inhibits contraction of outer hair cells. A total of 76 genes are involved in this superpathway. We studied the interaction network of TMPRSS3 along with the proteins in this superpathway to clarify its role. For this purpose, we obtained the raw data from the STRING database [28] and visualized them using the NetworkX Python package (https://github.com/networkx) [29]. The STRING database uses a combination of gene fusion, co-expression, functional, and experimental evidence to predict protein-protein interactions.

Prediction of putative pathogenic mutations in TMPRSS3 using iranome database

Potentially deleterious variants in the TMPRSS3 gene have been predicted using the Iranome Genomic Database [30]. The Iranome database comprises over 1.5 million variants obtained by analyzing the WES data of 800 healthy Iranian subjects from 8 major Iranian ethnicities, including Persians, Azeris, Lurs, Kurds, Turkmen, Arabs, and Persian Gulf Islanders. Notably, 300,000 of those variants were novel [31]. The pathogenicity of each variant was evaluated using prediction tools, including SIFT, PolyPhen-2, Mutation Taster, Mutation Assessor, FATHMM, and FATHMM MKL. We predicted the pathogenic variants in the TMPRSS3 gene using the Iranome database. For this purpose, we obtained all the missense variants available in Iranome with the query ‘TMPRSS3’. Then, we determined the pathogenicity predictions, the number of heterozygotes, and the populations with the highest and lowest allele frequencies for each variant. The criteria to ascertain putative pathogenic mutations with the highest probability of occurrence within the Iranian population are as follows: (a) elimination of variants with fewer than 10 instances of heterozygotes, (b) removal of variants with a CADD score below 20, and (c) exclusion of variants predicted as pathogenic by fewer than 3 out of 6 web server predictors.

Results

Clinical features

The patient in this study was a six-year-old girl with non-syndromic hearing loss (HL) born to a first-cousin consanguineous marriage. The family has an Iranian Baloch origin and resides in Gonbad-e Kavus city in Iran. Pedigree analysis of this family (Fig. 1) shows two younger healthy offspring and no positive history of HL in the last three generations. Medical evaluation reveals no environmental factors associated with HL. The audiograms demonstrate bilateral, severe-to-profound HL at all tested frequencies, indicating a sensorineural, bilateral, and pre-lingual type of HL.

Fig. 1
figure 1

Illustration of the first cousin consanguineous pedigree of an Iranian family with a girl suffering from hearing loss as a result of a novel mutation in TMPRSS3. (a) Homozygous (mutant) and heterozygous (carrier) variant identified in affected proband and her unaffected parents, respectively. (b)

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Genetic findings

Analysis of the GJB2 exon 2 coding region using direct PCR sequencing revealed no pathogenic variants. Although GJB2 mutations are the most frequent cause of hereditary hearing loss, this negative result necessitated further investigation via WES to identify the disease-causing variant in this patient. The application of WES led to the identification of a variant that was consistent with criteria for additional studies. WES revealed a novel homozygous deletion of a single nucleotide, c.297delA (p.Asp100ThrfsTer52, NM_001256317) in the TMPRSS3 gene (Fig. 1b), which is associated with deafness, autosomal recessive 8/10 (DFNB8/10; 601072) disorder. p.Asp100ThrfsTer52 indicates that at position 100, aspartic acid (Asp) is replaced by threonine (Thr), and the frameshift causes the translation to continue until an early stop codon (Ter) is generated 52 amino acids downstream from the new reading frame. This is expected to result in a truncated protein (compared to the 454 residues in the intact TMPRSS3) that is likely non-functional. According to the American College of Medical Genetics (ACMG) guidelines for variant classification, c.297delA is classified as a likely pathogenic variant. Evidence, including PVS1 (null variant in a gene where LOF is a known mechanism of disease) and PM2 (absence in population databases), is presented to support this classification. Additionally, the CADD (Combined Annotation Dependent Depletion) score for this variant is 20.7. The CADD score is a measure of the deleteriousness of genetic variants, and a score of 20.7 indicates that c.297delA has a higher predicted deleteriousness than approximately 99.9% of all possible human genetic variants.

Trio-based co-segregation study

Blood samples from the proband and her parents were subjected to Sanger sequencing. The results showed that the c.297delA variant co-segregated with hearing loss (Fig. 2).

Fig. 2
figure 2

Genomic location of the c.297delA mutation in the TMPRSS3 gene, from chromosomal to the nucleotide level

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TMPRSS3 mutational spectrum

A total of 113 mutations were retrieved from the HGMD database, including 82 missense/nonsense mutations, 8 splice site mutations, 8 small deletions, 6 small insertions, 3 gross deletions, 3 complex rearrangements, 2 regulatory mutations, and 1 small indel. Supplementary Material 1 lists the variants, pathogenicity and stability predictions, origin of patients, and mode of inheritance. Based on the results, 56 families (49.55%) were identified to have consanguineous marriages. The most frequent inheritance pattern observed in the TMPRSS3 mutation spectrum was autosomal recessive, accounting for 53.98% (n = 61) of cases. Autosomal dominant inheritance was observed in 10.62% (n = 12) of cases, while sporadic cases accounted for 7.96% (n = 9). Complex inheritance patterns were detected in only 1.77% (n = 2) of cases. The inheritance pattern was not reported in 28.32% of the studies (n = 32). Additionally, the majority of reported TMPRSS3-related hearing-impaired patients originated from Pakistan (12.39%, n = 14), followed by China and Japan, both with a prevalence of 9.73% (n = 11) each. Other countries with a notable number of reported cases included Turkey (8.85%, n = 10), Poland (7.08%, n = 8), and Taiwan (5.3%, n = 6).

Clustal Omega and consurf web server results

A conservational analysis of the TMPRSS3 protein sequence was performed using the Clustal Omega and Consurf web servers. The Consurf results showed that the aspartic acid residue at position 100, which is the site of the mutation, had a normalized conservation score of 0.708 (color score of 4 on a scale of 1 - variable to 9 - highly conserved). No functional or structural role was assigned to this residue. Additionally, 14 other amino acid residues were observed at this position across different species (Supplementary Material 2). The 3D structural model of TMPRSS3, colored according to the Consurf results, is shown in Fig. 3a.

Fig. 3
figure 3

Evolutionary conservation analysis of p.Asp100ThrfsTer52 mutation in TMPRSS3 using Consurf (a), and Clustal Omega (b)

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The multiple sequence alignment study using Clustal Omega revealed that at the aligned position of the identified variant (Asp100 in Homo sapiens), the amino acids found in other species were glutamine in Mus musculus, glutamic acid in Gallus gallus, histidine in Danio rerio, and aspartic acid in seven other species, as illustrated in Fig. 3b.

Secondary and 3D structures

The secondary structure of TMPRSS3 was predicted using PSIPRED, which showed that the mutation site (Asp100) is located in a coil domain of the protein with a high degree of prediction confidence (Fig. 4a). Figure 4b and c present the tertiary structures of the mutant (with the p.Asp100ThrfsTer52 variant) and the wild-type TMPRSS3 protein, respectively, alongside schematic diagrams.

Fig. 4
figure 4

Prediction of secondary structure of TMPRSS3 protein sequence using PSIPRED software. a Three-dimensional structure of wild-type b and c.297delA-mutant c form of TMPRSS3 protein. On the right, schematic diagram of protein sequence is shown. (Conf: confidence of prediction, Cart: 3-state assignment cartoon, Pred: 3-state prediction, AA: target sequence

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Protein interaction network

According to the STRING database, the first-shell interactors of TMPRSS3 are USH1C, SLC26A4, CDH23, C3orf14, MYO15A, TMC1, LOXHD1, OTOF, DNFB59, and GJB2 (Fig. 5a). Furthermore, an investigation of the superpathway of sensory processing of sound using the STRING database resulted in the graph shown in Fig. 5b. This undirected weighted graph represents the protein-protein interactions, with the nodes corresponding to proteins and the edges representing their interactions. The nodes related to OTOF, USH1C, MYO7A, TMC1, MYO15A, ESPN, and DNFB31 have the biggest impact on the protein-protein interaction network of the sensory processing of sound superpathway. The graph also revealed that TMPRSS3 interacts with all these proteins, which is consistent with the findings presented in Fig. 5a.

Fig. 5
figure 5

First shell (colored) and second shell (white) interactors of TMPSS3 protein predicted by protein–protein interaction analysis by STRING database (a). Interaction network of proteins involved in superpathway of sensory processing of sound (b). To create this graph NetworkX package used a measure called betweenness centrality, which basically means that size of each node is an indication of its weight within the network. Also, the color range from dark blue to white number of edges connected to the node as known as the node’s degree. Plus, an edge with more width and a darker color represents higher interaction scores between a pair of proteins

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Mutations spectrum in TMPRSS3 using Iranome database

The Iranome database revealed a total of 12 missense variants for the TMPRSS3 gene. These variants were analyzed in terms of their allele frequencies across various Iranian populations, pathogenicity predictions, and the number of heterozygotes. The detailed findings, including the highest and lowest allele frequencies, are presented in Table 1.

Table 1 Missense variants in TMPRSS3 gene within the study sample if Iranome project
Full size table

Discussion

Numerous genetic studies have been conducted on TMPRSS3-related hearing impairment. Figure 6 illustrates all the mutations discovered in the TMPRSS3 gene, represented in both the c. and p. notations. TMPRSS3 has 13 exons and encodes a 454-amino-acid protein belonging to the serine protease family. The protein contains a transmembrane domain (TM, residues 48–69), an LDLRA domain (71–109), a scavenger receptor cysteine-rich domain (SRCR, 110–205), and a trypsin-like serine protease domain (SP, 217–444) [32].

Fig. 6
figure 6

A visual representation of the global mutation spectrum of TMPRSS3 variants (derived from the HGMB database)

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The auditory phenotypes associated with TMPRSS3 are influenced by different combinations of the two mutant forms of the TMPRSS3 gene, indicating a hierarchical relationship between the variations. Specifically, individuals with two severe pathogenic alleles experience more profound, prelingual-onset hearing loss (HL), while those with one severe and one milder pathogenic allele develop milder, postlingual-onset HL [8, 33]. The majority of TMPRSS3 variants impact the proteolytic cleavage and activation of ENaC [9, 34, 35]. However, there is a suggestion that TMPRSS3 might have another, unidentified substrate besides ENaC [36]. The unique proteolytic activities exhibited by different TMPRSS3 mutant proteins are associated with the level of residual hearing and the progression of HL. For instance, the structural instability of the mutant TMPRSS3 resulting from the c.743 C > T variant is connected to its proteolytic activity [37], suggesting that information about the protein structure can help connect genomic analyses with cell-based assessments of protease activity.

The variant identified in this study, c.297delA, is expected to first lead to an amino acid substitution at position 100, from aspartic acid to threonine, within the LDLR domain of the TMPRSS3 protein. The LDLR domain is characterized by its cysteine-rich repeats that aid in correct protein folding [38]. Secondly, the variant causes a frameshift, introducing a premature stop codon, resulting in the truncation of the protein at the SRCR domain and the deletion of the SP domain. While the SRCR domain has been suggested to be involved in protein-protein interactions and stabilizing the structure [8], the SP domain performs TMPRSS3’s catalytic activity, which is classified as a trypsin-like serine protease and is crucially dependent on a conserved triad of histidine (His), aspartate (Asp), and serine (Ser) residues. Therefore, the removal of both the SRCR and SP domains will likely render the protein non-functional. Moreover, Nonsense-mediated mRNA decay (NMD) is a cellular surveillance pathway that degrades mRNA transcripts containing premature stop codons, typically those occurring more than 50–55 nucleotides upstream of the last exon-exon junction. Since the stop codon (Ter) introduced by the frameshift occurs significantly downstream of the normal termination point, the mRNA is expected to be targeted for degradation by the NMD pathway. This helps prevent the synthesis of potentially harmful truncated proteins.

Bioinformatic predictions suggested the pathogenic nature of the variant, potentially resulting from structure destabilization and/or a lack of catalytic activity.

According to the HGMD database, the TMPRSS3 gene has been found to exhibit 113 different mutations. We investigated the spectrum of these mutations based on various factors, including the rate of consanguineous marriages within the families. The family in our study had a consanguineous marriage rate of 49.55% among those with TMPRSS3-related hearing loss (HL), which is higher than the 36.8% rate of consanguineous marriages observed in the Iranian population overall. Furthermore, an autosomal recessive inheritance pattern was observed in the family pedigree of our patient, which is the most common pattern seen in families with TMPRSS3 mutation spectrum (53.98%, n = 61). The epidemiological insights from our study indicate that TMPRSS3 mutations are not limited to any specific geographical region and can affect individuals from diverse ethnicities. Our patient has an Iranian descent, which accounts for 1.77% of the reported TMPRSS3-related HL cases (n = 2). Frameshift mutations frequently lead to premature stop codons and truncated proteins, resulting in the loss of essential functional domains.For instance, as observed with the *c.297delA* mutation, which impacts the LDLR and SRCR domains, frameshift mutations in *TMPRSS3* can lead to substantial functional loss, with varying degrees of hearing loss severity depending on the mutation’s specific impact on the protein structure. This study also expands the *TMPRSS3* mutation database by adding new mutations such as *c.297delA*, contributing to the ongoing refinement of mutation-disease correlations. This addition enhances genetic counseling practices and diagnostic accuracy. Data of this nature are invaluable for future diagnostic and therapeutic developments.

There have been two other Iranian hearing-impaired patients reported with a TMPRSS3 variant so far. In 2016, Yan et al. employed a custom capture panel to conduct targeted sequencing of 180 genes in a multi-ethnic cohort of 342 deaf probands. Among the subset of 21 Iranian patients included in their study, a total of 12 positive results were obtained. Notably, they detected a pathogenic variant c.46 C > T in the TMPRSS3 gene in one patient, resulting in a premature stop codon at position 16 at the protein level (p.16R*) [39].

In a study conducted by Najmabadi et al. in 2015, a cohort of 302 Iranian families diagnosed with non-syndromic hearing loss (NSHL) and testing negative for the GJB2 gene underwent analysis using a targeted genomic enrichment panel. The investigation showed a homozygous duplication spanning 4 exons (7 to 10) within the TMPRSS3 gene, which potentially leads to a frameshift resulting in premature truncation [40].

It is important to note that our study had certain limitations. First, we did not conduct functional studies to evaluate the clinical features of mutant animal models with the c.297delA variant in the TMPRSS3 gene, which could have provided more robust evidence for the pathogenicity of the identified mutation. Second, we did not evaluate the level of TMPRSS3 protein expression using techniques such as western blot analysis, which could have been helpful in determining whether the mutation resulted in the production of truncated protein or complete loss of function.

Conclusions

In conclusion, this study investigated the clinical and genomic aspects of a patient from a consanguineous Iranian family with autosomal recessive non-syndromic hearing loss (ARNSHL). Using whole-exome sequencing, we identified a single nucleotide causative variant (c.297delA) in the TMPRSS3 gene, which is the first report of this mutation globally and the third report of a hearing-impaired patient with a TMPRSS3 mutation in Iran. Further studies are necessary to fully understand the genetic bases of TMPRSS3-related hearing loss.

Data availability

The datasets generated and/or analyzed during the current study are available in the ClinVar repository, ClinVar accession number: SCV004244375.1.

Abbreviations

HL:

Hearing Loss

ARNSHL:

Autosomal recessive non-syndromic hearing loss

WES:

Whole-exome sequencing

TMPRSS3 :

Transmembrane serine protease 3

TM:

Transmembrane domain

SP:

Serine protease domain

LDLR:

LDL receptor-like domain

SRCR:

Scavenger receptor cysteine-rich domain

NGS:

Next-generation sequencing

BWA:

Burrows-Wheeler Aligner

SNVs:

Single nucleotide variants

GATK:

Genome Analysis Tool Kit

MAF:

Minor allele frequency

CADD:

Combined Annotation Dependent Depletion

ACMG:

America College of Medical Genetics

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Acknowledgements

We are grateful to the patient and her family members, and everyone who participated. We also thank Human Genetic department of Golestan University of Medical Sciences for their support.

Funding

This study was financially supported by Golestan University of Medical Sciences under grant number 112526.

Author information

Authors and Affiliations

  1. Department of Medical Genetics, School of Advanced Technologies in Medicine, Golestan University of Medical Sciences, Gorgan, Iran

    Nahid Rezaie, Nader Mansour Samaei, Morteza Oladnabi & Teymoor Khosravi

  2. Student Research Committee, Golestan University of Medical Sciences, Gorgan, Iran

    Nahid Rezaie

  3. Mashhad Branch, Mashhad University of Medical Sciences, Islamic Azad University, Mashhad, Iran

    Saeedeh Sadat Ghazanfari

  4. Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran

    Seyede Mahsa Mousavikia & Abdolazim Sarli

  5. Gorgan Congenital Malformations Research Center, Golestan University of Medical Sciences, Gorgan, Iran

    Nader Mansour Samaei & Morteza Oladnabi

  6. Department of Cytogenetics, Genome Genetics Laboratory, Gorgan, Golestan, Iran

    Nader Mansour Samaei

Authors
  1. Nahid Rezaie
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  2. Saeedeh Sadat Ghazanfari
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Contributions

N.R., N.MS. and M.O. participated in the design of the study, analyzed the data, revising the article and final approval of the version to be published. S.S.G. contributed to the preparation of the figures and Tables. S.M.M, A.S. and T.K contributed to interpretation of data, and revising it critically for important intellectual content. All of the authors read and approved the final manuscript.

Corresponding authors

Correspondence to Nader Mansour Samaei or Morteza Oladnabi.

Ethics declarations

Ethics approval and consent to participate

Our research was conducted according to the guidelines set forth by the Ethics Committee of Golestan University of Medical Sciences (Ethics Code: IR.GOUMS.REC.1401.227). Informed consent to participate in the study was acquired after providing the patient’s parents with written information and obtaining their informed agreement.

Consent for publication

We confirm that the parents of the patients signed written informed consent for publication of their own and their child’s genetic data, and clinical details.

Competing interests

The authors declare no competing interests.

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Rezaie, N., Ghazanfari, S.S., Mousavikia, S.M. et al. A novel frameshift variant in the TMPRSS3 gene causes nonsyndromic hearing loss in a consanguineous family. BMC Med Genomics 17, 283 (2024). https://doiorg.publicaciones.saludcastillayleon.es/10.1186/s12920-024-02055-7

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  • DOI: https://doiorg.publicaciones.saludcastillayleon.es/10.1186/s12920-024-02055-7

Keywords

BMC Medical Genomics

ISSN: 1755-8794

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