GPRASP2, a novel causative gene mutated in an X-linked recessive syndromic hearing loss.

BACKGROUND: A substantial amount of nuclear genes have been identified to be implicated in genetic hearing loss, while X-linked hearing loss is genetically heterogeneous and relatively infrequent. OBJECTIVE: To identify the causative gene mutation in a five-generation Chinese family with an X-linked recessive syndromic hearing loss (SHL). METHODS: Targeted X-chromosome exome sequencing was conducted, and cosegregation analysis was performed in the members of the affected family. The in silico and expression studies were also performed. RESULTS: A 2-bp missense mutation (c.1717_1718GC>AA, p.A573N) in the G protein-coupled receptor associated sorting protein 2 (GPRASP2) gene was identified in four hemizygous male patients and two heterozygous female carriers, which was cosegregated with the clinical phenotypes in this family. In silico analysis supported that this gene mutation is functionally deleterious, and it was detected that homologous Gprasp2 was highly expressed in multiple structures of the mouse cochlea, which suggested that GPRASP2 might be the genetic cause for the described disease phenotypes. CONCLUSIONS: This study presented a novel X-linked SHL combined with unique and unrecognised clinical features, and a missense variation of GPRASP2 was first identified to be implicated in X-linked SHL.

[Phenotype predictions of the pathogenic nonsynonymous single nucleotide polymorphisms in deafness-causing gene COCH].

The COCH (Coagulation factor C homology) gene, located in human chromosome 14q12-q13, is the first gene identified to cause vestibular dysfunction. COCH encodes cochlin, which contains an N-terminal LCCL (Limulus factor C, cochlin, and late gestation lung protein Lgl1) domain and a C-temimal vWFA (Von Willebrand factor type A) domain. Recently, functional research of COCH mutations and cochlin have come under the spotlight in the field of hereditary deafness. Approximately 16 mutations in COCH have been confirmed to date, among which 13 non-synonymous single nucleotide polymorphisms (nsSNPs) are the most common form of genetic variations. Nonetheless, there is poor knowledge on the relationship between the genotype and the phenotype of the other nsSNPs in COCH. Here we analyzed deleterious nsSNPs from all SNPs in the COCH gene in the vWFA domain based on different computational methods and identified eight potential pathogenic nsSNPs (I176T, R180Q, G265E, V269L, I368N, I372T, R416C and Y424D) after combining literatures with 3D structures. Meanwhile, the protein structures of six reported pathogenic nsSNPs (P51S, G87W, I109N, I109T, W117R and F121S) in the LCCL domain have been constructed, and we identified aberrant structural changes in loops and chains. The prediction of pathogenic mutations for COCH nsSNPs will provide a blueprint for screening pathogenic mutations, and it will be beneficial to the functional research of COCH and cochlin in this field.

Targeted genomic capture and massively parallel sequencing to identify novel variants causing Chinese hereditary hearing loss.

BACKGROUND: Hereditary hearing loss is genetically heterogeneous, and hundreds of mutations in than 60 genes are involved in this disease. Therefore, it is difficult to identify the causative gene mutations involved. In this study, we combined targeted genomic capture and massively parallel sequencing (MPS) to address this issue. METHODS: Using targeted genomic capture and MPS, 104 genes and three microRNA regions were selected and simultaneously sequenced in 23 unrelated probands of Chinese families with nonsyndromic hearing loss. The results were validated by Sanger sequencing for all available members of the probands' families. To analyze the possible pathogenic functional effects of the variants, three types of prediction programs (Mutation Taster, PROVEAN and SIFT) were used. A total of 195 healthy Chinese Han individuals were compared as controls to verify the novel causative mutations. RESULTS: Of the 23 probands, six had mutations in DFNA genes [WFS1 (n = 2), COCH, ACTG1, TMC1, and POU4F3] known to cause autosomal dominant nonsyndromic hearing loss. These included one novel in-frame indel mutation, three novel missense mutations and two reported missense mutations. Furthermore, one proband from a family with recessive DFNB carried two monoallelic mutations in the GJB2 and USH2A genes. All of these mutations co-segregated with the hearing loss phenotype in 36 affected individuals from 7 families and were predicted to be pathogenic. CONCLUSIONS: Mutations in uncommon deafness genes contribute to a portion of nonsyndromic deafness cases. In the future, critical gene mutations may be accurately and quickly identified in families with hereditary hearing loss by targeted genomic capture and MPS.

Phenotype Prediction of Pathogenic Nonsynonymous Single Nucleotide Polymorphisms in WFS1.

Wolfram syndrome (WS) is a rare, progressive, neurodegenerative disorder that has an autosomal recessive pattern of inheritance. The gene for WS, wolfram syndrome 1 gene (WFS1), is located on human chromosome 4p16.1 and encodes a transmembrane protein. To date, approximately 230 mutations in WFS1 have been confirmed, in which nonsynonymous single nucleotide polymorphisms (nsSNPs) are the most common forms of genetic variation. Nonetheless, there is poor knowledge on the relationship between SNP genotype and phenotype in other nsSNPs of the WFS1 gene. Here, we analysed 395 nsSNPs associated with the WFS1 gene using different computational methods and identified 20 nsSNPs to be potentially pathogenic. Furthermore, to identify the amino acid distributions and significances of pathogenic nsSNPs in the protein of WFS1, its transmembrane domain was constructed by the TMHMM server, which suggested that mutations outside of the TMhelix could have more effects on protein function. The predicted pathogenic mutations for the nsSNPs of the WFS1 gene provide an excellent guide for screening pathogenic mutations.

Probing the Effect of Two Heterozygous Mutations in Codon 723 of SLC26A4 on Deafness Phenotype Based on Molecular Dynamics Simulations.

A Chinese family was identified with clinical features of enlarged vestibular aqueduct syndrome (EVAS). The mutational analysis showed that the proband (III-2) had EVAS with bilateral sensorineural hearing loss and carried a rare compound heterozygous mutation of SLC26A4 (IVS7-2A>G, c.2167C>G), which was inherited from the same mutant alleles of IVS7-2A>G heterozygous father and c.2167C>G heterozygous mother. Compared with another confirmed pathogenic biallelic mutation in SLC26A4 (IVS7-2A>G, c.2168A>G), these two biallelic mutations shared one common mutant allele and the same codon of the other mutant allele, but led to different changes of amino acid (p.H723D, p.H723R) and both resulted in the deafness phenotype. Structure-modeling indicated that these two mutant alleles changed the shape of pendrin protein encoded by SLC26A4 with increasing randomness in conformation, and might impair pendrin's ability as an anion transporter. The molecular dynamics simulations also revealed that the stability of mutant pendrins was reduced with increased flexibility of backbone atoms, which was consistent with the structure-modeling results. These evidences indicated that codon 723 was a hot-spot region in SLC26A4 with a significant impact on the structure and function of pendrin, and acted as one of the genetic factors responsible for the development of hearing loss.