Abstract
LHFPL5, the gene for DFNB67, underlies autosomal recessive nonsyndromic hearing impairment. We identified seven Pakistani families that mapped to 6p21.31, which includes the LHFPL5 gene. Sanger sequencing of LHFPL5 using DNA samples from hearing impaired and unaffected members of these seven families identified four variants. Among the identified variants, two were novel: one missense c.452 G > T (p.Gly151Val) and one splice site variant (c.*16 + 1 G > A) were each identified in two families. Two known variants: c.250delC (p.Leu84*) and c.380 A > G (p.Tyr127Cys) were also observed in two families and a single family, respectively. Nucleotides c.452G and c.*16 + 1G and amino-acid residue p.Gly151 are under strong evolutionary conservation. In silico bioinformatics analyses predicted these variants to be damaging. The splice site variant (c.*16 + 1 G > A) is predicted to affect pre-mRNA splicing and a loss of the 5′ donor splice site in the 3′-untranslated region (3′-UTR). Further analysis supports the activation of a cryptic splice site approximately 357-bp downstream, leading to an extended 3′-UTR with additional regulatory motifs. In conclusion, we identified two novel variants in LHFPL5, including a unique 3′-UTR splice site variant that is predicted to impact pre-mRNA splicing and regulation through an extended 3′-UTR.
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References
Morton CC, Nance WE. Newborn hearing screening - a silent revolution. N Engl J Med Boston. 2006;354:2151–64.
Shabbir MI, Ahmed ZM, Khan SY, Riazuddin S, Waryah AM, Khan SN, et al. Mutations of human TMHS cause recessively inherited non-syndromic hearing loss. J Med Genet. 2006;43:634–40.
Bensaïd M, Hmani-Aifa M, Hammami B, Tlili A, Hakim B, Charfeddine I, et al. DFNB66 and DFNB67 loci are non allelic and rarely contribute to autosomal recessive nonsyndromic hearing loss. Eur J Med Genet. 2011;54:e565–9.
Kalay E, Li Y, Uzumcu A, Uyguner O, Collin RW, Caylan R, et al. Mutations in the lipoma HMGIC fusion partner-like 5 (LHFPL5) gene cause autosomal recessive nonsyndromic hearing loss. Hum Mutat Hoboken. 2006;27:633.
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 EJHG Leiden. 2010;18:407–13.
Ammar‐Khodja F, Bonnet C, Dahmani M, Ouhab S, Lefèvre GM, Ibrahim H, et al. Diversity of the causal genes in hearing impaired Algerian individuals identified by whole exome sequencing. Mol Genet Genomic Med. 2015;3:189–96.
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.
Longo-Guess CM, Gagnon LH, Cook SA, Wu J, Zheng QY, Johnson KR. A missense mutation in the previously undescribed gene Tmhs underlies deafness in hurry-scurry (hscy) mice. Proc Natl Acad Sci USA. 2005;102:7894–9.
Abecasis GR, Cherny SS, Cookson WO, Cardon LR. Merlin—rapid analysis of dense genetic maps using sparse gene flow trees. Nat Genet. 2002;30:97–101.
O’Connell JR, Weeks DE. PedCheck: a program for identification of genotype incompatibilities in linkage analysis. Am J Hum Genet. 1998;63:259–66.
Silberstein M, Tzemach A, Dovgolevsky N, Fishelson M, Schuster A, Geiger D.Online system for faster multipoint linkage analysis via parallel execution on thousands of personal computers. Am J Hum Genet. 2006;78:922–35.
Sobel E, Lange K. Descent graphs in pedigree analysis: applications to haplotyping, location scores, and marker-sharing statistics. Am J Hum Genet. 1996;58:1323–37.
Matise TC, Chen F, Chen W, FMDL Vega, Hansen M, He C, et al. A second-generation combined linkage–physical map of the human genome. Genome Res. 2007;17:1783–6.
Rozen S, Skaletsky H. Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol Clifton Nj. 2000;132:365–86.
Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, et al. A method and server for predicting damaging missense mutations. Nat Methods. 2010;7:248–9.
Schwarz JM, Rödelsperger C, Schuelke M, Seelow D. MutationTaster evaluates disease-causing potential of sequence alterations. Nat Methods. 2010;7:575–6.
Kumar P, Henikoff S, Ng PC. Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat Protoc. 2009;4:1073–81.
Chun S, Fay JC. Identification of deleterious mutations within three human genomes. Genome Res. 2009;19:1553–61.
Reva B, Antipin Y, Sander C. Predicting the functional impact of protein mutations: application to cancer genomics. Nucleic Acids Res. 2011;39:e118–e118.
Shihab HA, Gough J, Cooper DN, Stenson PD, Barker GLA, Edwards KJ, et al. Predicting the functional, molecular, and phenotypic consequences of amino acid substitutions using hidden Markov models. Hum Mutat. 2013;34:57–65.
Kircher M, Witten DM, Jain P, O’Roak BJ, Cooper GM, Shendure J. A general framework for estimating the relative pathogenicity of human genetic variants. Nat Genet. 2014;46:310–5.
The UniProt Consortium. Reorganizing the protein space at the universal protein resource (UniProt). Nucleic Acids Res. 2012;40:D71–5.
Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, et al. Clustal W and Clustal X version 2.0. Bioinformatics. 2007;23:2947–8.
Krogh A, Larsson B, von Heijne G, Sonnhammer EL. Predicting transmembrane protein topology with a hidden markov model: application to complete genomes11. Edited by F. Cohen. J Mol Biol. 2001;305:567–80.
Reese MG, Eeckman FH, Kulp D, Haussler D. Improved splice site detection in Genie. J Comput Biol J Comput Mol Cell Biol. 1997;4:311–23.
Desmet F-O, Hamroun D, Lalande M, Collod-Béroud G, Claustres M, Béroud C. Human splicing finder: an online bioinformatics tool to predict splicing signals. Nucleic Acids Res. 2009;37:e67.
Brunak S, Engelbrecht J, Knudsen S. Prediction of human mRNA donor and acceptor sites from the DNA sequence. J Mol Biol. 1991;220:49–65.
Lorenz R, Bernhart SH, Höner zu Siederdissen C, Tafer H, Flamm C, Stadler PF, et al. ViennaRNA package 2.0. Algorithms Mol Biol. 2011;6:26.
Grillo G, Turi A, Licciulli F, Mignone F, Liuni S, Banfi S, et al. UTRdb and UTRsite (RELEASE 2010): a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs. Nucleic Acids Res. 2010;38:D75–80.
Kertesz M, Iovino N, Unnerstall U, Gaul U, Segal E. The role of site accessibility in microRNA target recognition. Nat Genet. 2007;39:1278–84.
Jian X, Boerwinkle E, Liu X. In silico prediction of splice-altering single nucleotide variants in the human genome. Nucleic Acids Res. 2014;42:13534–44.
Jin C, Jiang J, Wang W, Yao K. Identification of a MIP mutation that activates a cryptic acceptor splice site in the 3′ untranslated region. Mol Vis. 2010;16:2253–8.
Mencía Á, Modamio-Høybjør S, Redshaw N, Morín M, Mayo-Merino F, Olavarrieta L, et al. Mutations in the seed region of human miR-96 are responsible for nonsyndromic progressive hearing loss. Nat Genet. 2009;41:609–13.
Soldà G, Robusto M, Primignani P, Castorina P, Benzoni E, Cesarani A, et al. A novel mutation within the MIR96 gene causes non-syndromic inherited hearing loss in an Italian family by altering pre-miRNA processing. Hum Mol Genet. 2012;21:577–85.
Lewis MA, Quint E, Glazier AM, Fuchs H, De Angelis MH, Langford C, et al. An ENU-induced mutation of miR-96 associated with progressive hearing loss in mice. Nat Genet. 2009;41:614–8.
Rudnicki A, Avraham KB. microRNAs: the art of silencing in the ear. EMBO Mol Med. 2012;4:849–59.
Yoo H, Yoo JK, Lee J, Lee DR, Ko JJ, Oh SH, et al. The hsa-miR-5787 represses cellular growth by targeting eukaryotic translation initiation factor 5 (eIF5) in fibroblasts. Biochem Biophys Res Commun. 2011;415:567–72.
Bejarano F, Bortolamiol-Becet D, Dai Q, Sun K, Saj A, Chou Y-T, et al. A genome-wide transgenic resource for conditional expression of Drosophila microRNAs. Development. 2012;139:2821–31.
Terrinoni A, Serra V, Bruno E, Strasser A, Valente E, Flores ER, et al. Role of p63 and the Notch pathway in cochlea development and sensorineural deafness. Proc Natl Acad Sci USA. 2013;110:7300–5.
Acknowledgements
We thank the family members who participated in the study. This work was funded by the Higher Education Commission, Islamabad, Pakistan and by the National Institutes of Health (NIH) – National Institute of Deafness and other Communication Disorders (DC03594 and DC011651). Genotyping services were provided by CIDR through a fully funded federal contract from the NIH to the Johns Hopkins University, contract number N01-HG-65403.
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The following URLs were accessed for data in this article: Hereditary Hearing Loss Homepage, http://hereditaryhearingloss.org; UCSC Genome Browser, http://genome.ucsc.edu; Online Mendelian Inheritance in Man (OMIM), http://www.omim.org; 1000 genomes, http://www.1000genomes.org; http://gnomad.broadinstitute.org; https://bravo.sph.umich.edu/freeze3a/hg19; dbSNP, https://www.ncbi.nlm.nih.gov/SNP
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Liaqat, K., Chiu, I., Lee, K. et al. Novel missense and 3′-UTR splice site variants in LHFPL5 cause autosomal recessive nonsyndromic hearing impairment. J Hum Genet 63, 1099–1107 (2018). https://doi.org/10.1038/s10038-018-0502-3
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DOI: https://doi.org/10.1038/s10038-018-0502-3
