Effective research and clinical application in audiology and hearing loss (HL) often require the integration of diverse data. However, the absence of a dedicated database impeded understanding and insight extraction in HL. To address this, the Genetic Deafness Commons (GDC) was developed by consolidating extensive genetic and genomic data from 51 public databases and the Chinese Deafness Genetics Consortium, encompassing 5,983,613 variants across 201 HL genes. This comprehensive dataset detailed the genetic landscape of HL, identifying six novel mutational hotspots within DNA binding domains of transcription factor genes, which were eligible for evidence-based variant pathogenicity classification. Comparative phenotypic analyses highlighted considerable disparities between human and mouse models, with only 130 human HL genes exhibiting hearing abnormality in mice. Moreover, gene expression analyses in the cochleae of mice and rhesus macaques demonstrated a notable correlation (R2 = 0.76). Utilizing gene expression, function, pathway, and phenotype data, a SMOTE-Random Forest model identified 18 candidate HL genes, including TBX2 and ERCC2, newly confirmed as HL genes. The GDC, as a comprehensive and unified repository, significantly advances audiology research and clinical practice by enhancing data accessibility and usability, thereby facilitating deeper insights into hearing disorders. ### Competing Interest Statement The authors have declared no competing interest.

IntroductionWaardenburg syndrome (WS) is a genetic disorder characterized by hearing loss, hypopigmentation, and distinct facial features. Despite > 60% molecular diagnosis rate for WS patients, pathogenic variants within coding regions are predominant, with few non-coding copy number variations (CNVs) reported.MethodsIn this study, we performed whole genome sequencing (WGS) on 59 undiagnosed WS patients and analyzed the CNVs within the promoter and enhancer regions of the SOX10 gene.ResultsWe identified five novel pathogenic deletions ranging from 448 bp to 70 kb upstream of SOX10. Two deletions were in the enhancer region, while three were in the promoter and 5'UTR region. These CNVs manifested as WS type II in eight patients from five unrelated families, demonstrating phenotypic heterogeneity. Furthermore, analysis of CNV1 within the enhancer region suggested a potential mechanism involving Alu-mediated non-allelic homologous recombination (NAHR).ConclusionOur findings extend the mutation spectrum of the SOX10 gene and elucidate the pathogenic role of CNVs in cis-regulatory elements, particularly variations in enhancer and promoter regions, thereby enhancing clinical gene detection and interpretation of non-coding regions.

Background Townes-Brocks syndrome (TBS) is a rare genetic disorder characterised by multiple malformations. Due to its phenotypic heterogeneity and rarity, diagnosis and recognition of TBS can be challenging and there has been a lack of investigation of patients with atypical TBS in large cohorts and delineation of their phenotypic characteristics.Methods We screened SALL1 and DACT1 variants using next-generation sequencing in the China Deafness Genetics Consortium (CDGC) cohort enrolling 20 666 unrelated hearing loss (HL) cases. Comprehensive clinical evaluations were conducted on seven members from a three-generation TBS family. Combining data from previously reported cases, we also provided a landscape of phenotypes and genotypes of patients with TBS.Results We identified five novel and two reported pathogenic/likely pathogenic (P/LP) SALL1 variants from seven families. Audiological features in patients differed in severity and binaural asymmetry. Moreover, previously undocumented malformations in the middle and inner ear were detected in one patient. By comprehensive clinical evaluations, we further provide evidence for the causal relationship between SALL1 variation and certain endocrine abnormalities. Penetrance analysis within familial contexts revealed incomplete penetrance among first-generation patients with TBS and a higher disease burden among their affected offspring.Conclusion This study presents the first insight of genetic screening for patients with TBS in a large HL cohort. We broadened the phenotypic-genotypic spectrum of TBS and our results supported an underestimated prevalence of TBS. Due to the rarity and phenotypic heterogeneity of rare diseases, broader spectrum molecular tests, especially whole genome sequencing, can improve the situation of underdiagnosis and provide effective recommendations for clinical management.

Recessive genotypes, including compound heterozygotes and homozygotes formed by rare variants that impact gene function, affect both alleles and were linked to numerous diseases and traits. However, the underlying patterns and interconnections of these recessive genotypes in large cohorts have rarely been studied. To address this gap, the Recessive Genotype Network (RGnet) was developed. This network model maps variant and genotype features to visualize and analyze recessive genotype patterns within large cohorts. Additionally, it uses permutation-based analyses to assess the enrichment of these genotypes in relation to specific phenotypes. Demonstrated through its application to the genetic deafness gene SLC26A4 in 22,125 cases affected by hearing loss, RGnet successfully identified pathogenic variants with high connectivity, providing a reliable method for exploring the pathogenic mechanisms underlying recessive disorders or traits. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement This work was supported by the Natural Science Foundation of Sichuan Province, China (Grant No. 2024NSFSC1767), the National Natural Science Foundation of China (Grant No. 82171836) and the 1 3 5 project for disciplines of excellence, West China Hospital, Sichuan University (Grant No. ZYJC20002). ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: Ethics committee/IRB of West China Hospital gave ethical approval for this work I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes All data produced in the present study are available upon reasonable request to the authors

Purpose: The transcription factor TBX2 plays a critical role in inner hair cells development in mice. Yet, the link between TBX2 malfunction and human hearing-related disorders remains unexplored. Methods: Linkage analysis combined with whole genome sequencing was applied to identify the causative gene in two autosomal dominant Chinese families characterized by late-onset progressive sensorineural hearing loss and incomplete penetrance of horizontal oscillatory nystagmus. Functional evaluation of TBX2 variants was performed through protein expression, localization, and transcriptional activity analysis in vitro, phenotypic analysis and mechanism study in knockout mice model in vivo. Results: Multipoint parametric linkage analysis of Family 1 revealed a maximum LOD score of 3.01 on chromosome 17q23.2. Whole genome sequencing identified distinct TBX2 variants, c.977delA (p.Asp326Alafs*42) and c.987delC (p.Ala330Argfs*38) in each family, co-segregating with hearing loss. These variants resulted in premature termination and the generation of a new peptide segment, reducing transcriptional activity. Further, heterozygous Tbx2 knockout mice exhibited late-onset progressive hearing loss, along with ectopic expression of Prestin in IHCs and a gradual decrease in expression from P7 to P42. Conclusion: Our findings indicate that heterozygous TBX2 frameshift variants are the genetic cause of late-onset progressive hearing loss and incomplete penetrance of nystagmus. The heterozygous Tbx2 knockout mouse model mirrored the human hearing loss phenotype, further validating TBX2's role in auditory function. These insights enhance our understanding of TBX2 in the auditory system, providing valuable information for molecular diagnostics and genetic counseling in related hearing disorders. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement This work was supported by the National Natural Science Foundation of China (No. 82030030 & 82202046) and 135 project for the disciplines of excellence-Interdisciplinary innovation project, West China Hospital, Sichuan University (No.ZYJC20002). ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: Informed consent was obtained from all participants. The Institutional Review Board of West China Hospital gave ethical approval for this work. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes All data produced in the present work are contained in the manuscript

A comprehensive understanding of the genetic basis of rare diseases and their regulatory mechanisms is essential for human molecular genetics. However, the genetic mutant spectrum of pathogenic genes within the Chinese population remains underrepresented. Here, we reported previously unreported functional ABHD12 variants in two Chinese families and explored the correlation between genetic polymorphisms and phenotypes linked to PHARC syndrome. Participants with biallelic pathogenic ABHD12 variants were recruited from the Chinese Deafness Genetics Cohort. These participants underwent whole-genome sequencing. Subsequently, a comprehensive literature review was conducted. Two Han Chinese families were identified, one with a compound heterozygous variant and the other with a novel homozygous variant in ABHD12. Among 65 PHARC patients, including 62 from the literature and 3 from this study, approximately 90

ABBREVIATIONS:AO: acridine orange; ATM: ATM serine/threonine kinase; CHEK1: checkpoint kinase 1; CHEK2: checkpoint kinase 2; CI: combination index; DMSO: dimethyl sulfoxide; DSBs: double-strand breaks; GBM: glioblastoma; HR: homologous recombination; H2AX: H2A.X variant histone; IHC: immunohistochemistry; LAPTM4B: lysosomal protein transmembrane 4 beta; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; PARP: poly(ADP-ribose) polymerase; RAD51: RAD51 recombinase; SQSTM1: sequestosome 1; SSBs: single-strand breaks; RNF168: ring finger protein 168; XPO1: exportin 1.

目的 鉴定1例重度感音神经性耳聋患者的遗传病因,明确检出突变的致病性,以及患者人工耳蜗康复效果,为该家庭再生育提供遗传指导.方法 采集广西壮族自治区一个耳聋小家系样本3例,包括1例重度感音神经性耳聋患儿和其正常听力父母.对该家系成员进行病史调查、体格及听力学检查,采集外周静脉血.进行全基因组测序和生物信息学分析鉴定致病基因,评估人工耳蜗术后听觉与言语康复效果.结果 ESPN基因c.1916-1G>A纯合突变是该家系的致聋原因,人工耳蜗术后听觉与言语康复效果良好.结论 研究发现了ESPN基因一个新的突变,是该耳聋家系的致病原因.回访发现人工耳蜗术后患儿言语康复效果好.该研究丰富了遗传性聋的突变谱,并对人工耳蜗植入的术前评估具有指导意义.

目的 对一个遗传性非综合征型耳聋家系的临床特征进行分析并鉴定其致聋基因突变,同时在大规模耳聋人群队列中对鉴定出的致病性突变致中国人群耳聋的特征进行分析.方法 完善家系成员的问卷调查、听力学检查、体格检査等临床检查,同时采集血液样本,通过耳聋相关基因的大规模平行测序(MPS)和生物信息学分析进行致病基因鉴定.总结及分析鉴定出的致病性突变在中国耳聋基因研究战略联盟(CDGC)耳聋数据库中的检出情况.结果 在一个早发性极重度感音神经性耳聋家系中鉴定出MYO15A基因NM_016239.4:c.8182C>G(p.Arg2728Gly)/c.9861C>T(p.Gly3287=)复合杂合突变,为该家系耳聋患者的致聋原因.其中MYO15A基因c.9861C>T(p.Gly3287=)同义突变通过改变剪接导致基因功能缺陷,其在中国广西壮族人群中次要等位基因频率为0.2％(3/1438),在其他人群及公共数据库中均未检出.结论 研究确定了MYO15A基因c.9861C>T(p.Gly3287=)在中国非综合征型耳聋患者中的致病性,该突变在中国广西壮族自治区富集明显.通过研究强调了在致病基因鉴定时,高频与同义突变并非过滤的绝对指标,尤其是在某些地区富集格外明显的突变,应格外注意.

Background The American College of Medical Genetics and Genomics (ACMG)/Association for Molecular Pathology (AMP) guidelines recommend using variant enrichment among cases as "strong" evidence for pathogenicity per the PS4 criterion. However, quantitative support for PS4 thresholds from real-world Mendelian case–control cohorts is lacking. Methods To address this gap, we evaluated and established PS4 thresholds using data from the Chinese Deafness Genetics Consortium. A total of 9,050 variants from 13,845 patients with hearing loss (HL) and 6,570 ancestry-matched controls were analyzed. Positive likelihood ratio and local positive likelihood ratio values were calculated to determine the thresholds corresponding to each strength of evidence across three variant subsets. Results In subset 1, consisting of variants present in both cases and controls with an allele frequency (AF) in cases ≥ 0.0005, an odds ratio (OR) ≥ 6 achieved strong evidence, while OR ≥ 3 represented moderate evidence. For subset 2, which encompassed variants present in both cases and controls with a case AF < 0.0005, and subset 3, comprising variants found only in cases and absent from controls, we defined the PS4_Supporting threshold (OR > 2.27 or allele count ≥ 3) and the PS4_Moderate threshold (allele count ≥ 6), respectively. Reanalysis applying the adjusted PS4 criteria changed the classification of 15 variants and enabled diagnosis of an additional four patients. Conclusions Our study quantified evidence strength thresholds for variant enrichment in genetic HL cases, highlighting the importance of defining disease/gene-specific thresholds to improve the precision and accuracy of clinical genetic testing.

Numerous computational prediction tools have been introduced to estimate the functional impact of variants in the human genome based on evolutionary constraints and biochemical metrics. However, their implementation in diagnostic settings to classify variants faced challenges with accuracy and validity. Most existing tools are pan-genome and pan-diseases, which neglected gene- and disease-specific properties and limited the accessibility of curated data. As a proof-of-concept, we developed a disease-specific prediction tool named Deafness Variant deleteriousness Prediction tool (DVPred) that focused on the 157 genes reportedly causing genetic hearing loss (HL). DVPred applied the gradient boosting decision tree (GBDT) algorithm to the dataset consisting of expert-curated pathogenic and benign variants from a large in-house HL patient cohort and public databases. With the incorporation of variant-level and gene-level features, DVPred outperformed the existing universal tools. It boasts an area under the curve (AUC) of 0.98, and showed consistent performance (AUC = 0.985) in an independent assessment dataset. We further demonstrated that multiple gene-level metrics, including low complexity genomic regions and substitution intolerance scores, were the top features of the model. A comprehensive analysis of missense variants showed a gene-specific ratio of predicted deleterious and neutral variants, implying varied tolerance or intolerance to variation in different genes. DVPred explored the utility of disease-specific strategy in improving the deafness variant prediction tool. It can improve the prioritization of pathogenic variants among massive variants identified by high-throughput sequencing on HL genes. It also shed light on the development of variant prediction tools for other genetic disorders.

Abstract Background Biotinidase deficiency (OMIM 253260) is an autosomal recessively inherited disorder affecting about 1/60,000 people worldwide. The absence or deficiency of biotinidase impairs free biotin recycling and affects biotin‐dependent carboxylase functions. Methods A Chinese patient with spontaneous recurrent epilepsy, an eczema‐like rash, hair loss, hypotonia, and hearing loss began at three months of age. Her biotinidase activity was 1.0 nmol/ml/min, 9.5% of the mean control activity, which confirmed profound biotinidase deficiency. Results Compound heterozygous for c.250‐1G > C and c.878dupT variants in the BTD gene were identified in this patient. These two variants were novel and absent in the population matched controls and any databases. Conclusions This study expanded the mutation spectrum of alterations of the BTD gene. Our patient also emphasized the critical role of biotinidase activity measurement combined with mutation analysis in early diagnosis of biotinidase deficiency.

目的 分析两个HDR综合征家系的临床特征及致病基因鉴定.方法 对两家系成员进行病史、临床信息采集,应用高通量测序和生物信息学分析进行致病基因鉴定.结果 在2个家系中仅表现为感音神经性耳聋的先证者的GATA3基因发现两个新发位点,分别为c.186dup(p.Tyr63Leufs*240)和c.835_836dup(p.Gly280Argfs*15),根据美国医学遗传学与基因组学学会遗传性听力损失判读指南显示,这两突变分别为先证者的致病变异.结论 GATA3基因为这两先证者的致病基因,c.186dup(p.Tyr63Leufs*240)和c.835_836dup(p.Gly280Argfs*15)进一步完善了GATA3基因的突变谱.对仅表现感音神经性耳聋的患者,应重视部分表型不完全外显的综合征型耳聋.

BACKGROUND:Genetic variants in TMPRSS3 have been causally linked to autosomal recessive nonsyndromic hearing loss (HL) at the DFNB8 and DFNB10 loci. These variants include both single nucleotide and copy number variations (CNVs). In this study, we aim to identify the genetic cause in three Chinese subjects with prelingual profound sensorineural HL. METHODS:We applied targeted genomic enrichment and massively parallel sequencing to screen 110 genes associated with nonsyndromic HL in the three affected subjects. CNVplex® analysis and polymerase chain reaction (PCR) were performed for CNV detection. RESULTS:We identified biallelic variations in TMPRSS3 including a novel complex genomic rearrangement and a novel missense mutation, c.551T>C. We have mapped the breakpoints of the genomic rearrangement and showed that it consisted of two deletions and an inversion encompassing exon 3 to exon 9 of TMPRSS3. CONCLUSION:Our study expanded the mutational spectrum of TMPRSS3 to include complex genomic rearrangements. It showcased the importance of an integrative approach to investigate CNVs and their contribution to HL.