Genetic spectrum of autosomal recessive non-syndromic hearing loss in Pakistani families

PLoS ONE

Volumn 9, Issue 6, 2014, Pages

  Shafique, Sobia ^a   Siddiqi, Saima ^b   Schraders, Margit ^c,d,e   Oostrik, Jaap ^c,d,e   Ayub, Humaira ^a   Bilal, Ammad ^f   Ajmal, Muhammad ^a   Seco, Celia Zazo ^c,d,e   Strom, Tim M ^g   Mansoor, Atika ^b   Mazhar, Kehkashan ^b   Shah, Syed Tahir A ^a   Hussain, Alamdar ^a   Azam, Maleeha ^a   Kremer, Hannie ^c,d,e   Qamar, Raheel ^a,h  

^a Department of Electrical Computer Engineering   (Pakistan)

^b INSTITUTE OF BIOMEDICAL AND GENETIC ENGINEERING IBGE   (Pakistan)

^c RADBOUD UNIVERSITY MEDICAL CENTER   (Netherlands)

^d RADBOUD UNIVERSITY MEDICAL CENTER   (Netherlands)

^e RADBOUD UNIVERSITY   (Netherlands)

^f SIMON FRASER UNIVERSITY   (Canada)

^g INSTITUTE OF EPIDEMIOLOGY   (Germany)

^h ISRA UNIVERSITY   (Pakistan)

Author keywords

[No Author keywords available]

Indexed keywords

ADENINE; ARGININE; CONNEXIN 26; CYSTEINE; CYTOSINE; GLUTAMINE; GLYCINE; GUANINE; LEUCINE; PHENYLALANINE; SERINE; THYMINE; TRYPTOPHAN; VALINE; GAP JUNCTION PROTEIN; MEMBRANE PROTEIN; MYO15A PROTEIN, HUMAN; MYOSIN; SERINE PROTEINASE; TMPRSS3 PROTEIN, HUMAN; TUMOR PROTEIN;

ARTICLE; AUTOSOMAL RECESSIVE DISORDER; AUTOSOMAL RECESSIVE NON SYNDROMIC HEARING LOSS; BSND GENE; CLINICAL ARTICLE; COHORT ANALYSIS; CONTROLLED STUDY; ETHNIC GROUP; FAMILY STUDY; FEMALE; FRAMESHIFT MUTATION; GENE; GENE MAPPING; GENE MUTATION; GENETIC SCREENING; GENOTYPE; GJB2 GENE; HEARING IMPAIRMENT; HOMOZYGOSITY; HOMOZYGOTE; HUMAN; HUMAN GENOME; INHERITANCE; INTRONIC MUTATION; MALE; MISSENSE MUTATION; MSRB3 GENE; MUTATIONAL ANALYSIS; MYO15A GENE; NONSENSE MUTATION; NUCLEOTIDE SEQUENCE; PAKISTAN; PAKISTANI; POPULATION GENETICS; RNA SPLICING; SINGLE NUCLEOTIDE POLYMORPHISM; TMC1 GENE; TMPRSS3 GENE; CHEMICAL STRUCTURE; CHEMISTRY; GENETICS; GENOMICS; MOLECULAR GENETICS; PEDIGREE; PROTEIN CONFORMATION; RECESSIVE GENE;

BASE SEQUENCE; CONNEXINS; DNA MUTATIONAL ANALYSIS; FEMALE; GENES, RECESSIVE; GENOMICS; HEARING LOSS; HOMOZYGOTE; HUMANS; MALE; MEMBRANE PROTEINS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MYOSINS; NEOPLASM PROTEINS; PAKISTAN; PEDIGREE; PROTEIN CONFORMATION; SERINE ENDOPEPTIDASES;

EID: 84903398951     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0100146     Document Type: Article

References (53)

1. Mustapha M, Salem N, Delague V, Chouery E, Ghassibeh M, et al. (2001) Autosomal recessive non-syndromic hearing loss in the Lebanese population: prevalence of the 30delG mutation and report of two novel mutations in the connexin 26 (GJB2) gene. J Med Genet 38: E36.
2. Van Camp G, Coucke PJ, Kunst H, Schatteman I, Van Velzen D, et al. (1997) Linkage analysis of progressive hearing loss in five extended families maps the DFNA2 gene to a 1.25-Mb region on chromosome 1p. Genomics 41: 70-74. (Pubitemid 27152823)
3. Morton NE (1991) Genetic epidemiology of hearing impairment. Ann N Y Acad Sci 630: 16-31.
4. Bayazit YA, Yilmaz M (2006) An overview of hereditary hearing loss. ORL J Otorhinolaryngol Relat Spec 68: 57-63.
5. Elahi MM, Elahi F, Elahi A, Elahi SB (1998) Paediatric hearing loss in rural Pakistan. J Otolaryngol 27: 348-353.
6. Hilgert N, Smith RJ, Van Camp G (2009) Forty-six genes causing nonsyndromic hearing impairment: which ones should be analyzed in DNA diagnostics? Mutat Res 681: 189-196.
7. Zelante L, Gasparini P, Estivill X, Melchionda S, D'Agruma L, et al. (1997) Connexin26 mutations associated with the most common form of non-syndromic neurosensory autosomal recessive deafness (DFNB1) in Mediterraneans. Hum Mol Genet 6: 1605-1609. (Pubitemid 27397040)
8. Estivill X, Fortina P, Surrey S, Rabionet R, Melchionda S, et al. (1998) Connexin-26 mutations in sporadic and inherited sensorineural deafness. Lancet 351: 394-398. (Pubitemid 28064162)
9. Kelley PM, Harris DJ, Comer BC, Askew JW, Fowler T, et al. (1998) Novel mutations in the connexin 26 gene (GJB2) that cause autosomal recessive (DFNB1) hearing loss. Am J Hum Genet 62: 792-799. (Pubitemid 28194320)
10. Bashir R, Fatima A, Naz S (2012) Prioritized sequencing of the second exon of MYO15A reveals a new mutation segregating in a Pakistani family with moderate to severe hearing loss. Eur J Med Genet 55: 99-102.
11. Sambrook J, Russell DW (2006) The condensed protocols from Molecular cloning: a laboratory manual. Cold Spring Harbor, N.Y.: Cold Spring Harbor Laboratory Press v, 800 p.p.
12. de Heer AM, Collin RWJ, Huygen PL, Schraders M, Oostrik J, et al. (2011) Progressive sensorineural hearing loss and normal vestibular function in a Dutch DFNB7/11 family with a novel mutation in TMC1. Audiol Neurootol 16: 93-105.
13. Schraders M, Lee K, Oostrik J, Huygen PL, Ali G, et al. (2010) Homozygosity mapping reveals mutations of GRXCR1 as a cause of autosomal-recessive nonsyndromic hearing impairment. Am J Hum Genet 86: 138-147.
14. Rozen S, Skaletsky H (2000) Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol 132: 365-386.
15. Seelow D, Schuelke M, Hildebrandt F, Nurnberg P (2009) HomozygosityMapper - an interactive approach to homozygosity mapping. Nucleic Acids Res 37: W593-599.
16. Hoffmann K, Lindner TH (2005) easyLINKAGE-Plus - automated linkage analyses using large-scale SNP data. Bioinformatics 21: 3565-3567. (Pubitemid 41236002)
17. Sim NL, Kumar P, Hu J, Henikoff S, Schneider G, et al. (2012) SIFT web server: predicting effects of amino acid substitutions on proteins. Nucleic Acids Res 40: W452-457.
18. Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, et al. (2010) A method and server for predicting damaging missense mutations. Nat Methods 7: 248-249.
19. Brunak S, Engelbrecht J, Knudsen S (1991) Prediction of human mRNA donor and acceptor sites from the DNA sequence. J Mol Biol 220: 49-65. (Pubitemid 121004542)
20. Petersen TN, Brunak S, von Heijne G, Nielsen H (2011) SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat Methods 8: 785-786.
21. Venselaar H, Te Beek TA, Kuipers RK, Hekkelman ML, Vriend G (2010) Protein structure analysis of mutations causing inheritable diseases. An e-Science approach with life scientist friendly interfaces. BMC Bioinformatics 11: 548.
22. Gamundi MJ, Hernan I, Muntanyola M, Maseras M, Lopez-Romero P, et al. (2008) Transcriptional expression of cis-acting and trans-acting splicing mutations cause autosomal dominant retinitis pigmentosa. Hum Mutat 29: 869-878. (Pubitemid 351794138)
23. Santos RL, Wajid M, Khan MN, McArthur N, Pham TL, et al. (2005) Novel sequence variants in the TMC1 gene in Pakistani families with autosomal recessive hearing impairment. Hum Mutat 26: 396.
24. Searle C, Mavrogiannis LA, Bennett CP, Charlton RS (2012) The common TMC1 mutation c.100C>T (p.Arg34X) is not a significant cause of deafness in British Asians. Genet Test Mol Biomarkers 16: 453-455.
25. Schultz JM, Khan SN, Ahmed ZM, Riazuddin S, Waryah AM, et al. (2009) Noncoding mutations of HGF are associated with nonsyndromic hearing loss, DFNB39. Am J Hum Genet 85: 25-39.
26. Reardon W, O'Mahoney CF, Trembath R, Jan H, Phelps PD (2000) Enlarged vestibular aqueduct: a radiological marker of pendred syndrome, and mutation of the PDS gene. QJM 93: 99-104. (Pubitemid 30098772)
27. Naz S, Giguere CM, Kohrman DC, Mitchem KL, Riazuddin S, et al. (2002) Mutations in a novel gene, TMIE, are associated with hearing loss linked to the DFNB6 locus. Am J Hum Genet 71: 632-636. (Pubitemid 34970134)
28. Batissoco AC, Auricchio MT, Kimura L, Tabith-Junior A, Mingroni-Netto RC (2009) A novel missense mutation p.L76P in the GJB2 gene causing nonsyndromic recessive deafness in a Brazilian family. Braz J Med Biol Res 42: 168-171.
29. Minarik G, Ferak V, Ferakova E, Ficek A, Polakova H, et al. (2003) High frequency of GJB2 mutation W24X among Slovak Romany (Gypsy) patients with non-syndromic hearing loss (NSHL). Gen Physiol Biophys 22: 549-556. (Pubitemid 38324672)
30. Padma G, Ramchander PV, Nandur UV, Padma T (2009) GJB2 and GJB6 gene mutations found in Indian probands with congenital hearing impairment. J Genet 88: 267-272.
31. Bukhari I, Mujtaba G, Naz S (2013) Contribution of GJB2 mutations to hearing loss in the Hazara Division of Pakistan. Biochem Genet 51: 524-529.
32. Matos TD, Simoes-Teixeira H, Caria H, Rosa H, O'Neill A, et al. (2010) The controversial p.Arg127His mutation in GJB2: report on three Portuguese hearing loss family cases. Genet Test Mol Biomarkers 14: 141-144.
33. Santos RL, Wajid M, Pham TL, Hussan J, Ali G, et al. (2005) Low prevalence of Connexin 26 (GJB2) variants in Pakistani families with autosomal recessive non-syndromic hearing impairment. Clin Genet 67: 61-68.
34. Mani RS, Ganapathy A, Jalvi R, Srikumari Srisailapathy CR, Malhotra V, et al. (2009) Functional consequences of novel connexin 26 mutations associated with hereditary hearing loss. Eur J Hum Genet 17: 502-509.
35. Qamar R, Ayub Q, Mohyuddin A, Helgason A, Mazhar K, et al. (2002) Y-chromosomal DNA variation in Pakistan. Am J Hum Genet 70: 1107-1124. (Pubitemid 34450564)
36. Snoeckx RL, Huygen PL, Feldmann D, Marlin S, Denoyelle F, et al. (2005) GJB2 mutations and degree of hearing loss: a multicenter study. Am J Hum Genet 77: 945-957. (Pubitemid 41698516)
37. Weng Z, Rickles RJ, Feng S, Richard S, Shaw AS, et al. (1995) Structure-function analysis of SH3 domains: SH3 binding specificity altered by single amino acid substitutions. Mol Cell Biol 15: 5627-5634.
38. Belyantseva IA, Boger ET, Friedman TB (2003) Myosin XVa localizes to the tips of inner ear sensory cell stereocilia and is essential for staircase formation of the hair bundle. Proc Natl Acad Sci U S A 100: 13958-13963. (Pubitemid 37499173)
39. Anderson DW, Probst FJ, Belyantseva IA, Fridell RA, Beyer L, et al. (2000) The motor and tail regions of myosin XV are critical for normal structure and function of auditory and vestibular hair cells. Hum Mol Genet 9: 1729-1738. (Pubitemid 30608606)
40. Kitajiri SI, McNamara R, Makishima T, Husnain T, Zafar AU, et al. (2007) Identities, frequencies and origins of TMC1 mutations causing DFNB7/B11 deafness in Pakistan. Clin Genet 72: 546-550. (Pubitemid 350131061)
41. Sirmaci A, Duman D, Ozturkmen-Akay H, Erbek S, Incesulu A, et al. (2009) Mutations in TMC1 contribute significantly to nonsyndromic autosomal recessive sensorineural hearing loss: a report of five novel mutations. Int J Pediatr Otorhinolaryngol 73: 699-705.
42. Ben Said M, Hmani-Aifa M, Amar I, Baig SM, Mustapha M, et al. (2010) High frequency of the p.R34X mutation in the TMC1 gene associated with nonsyndromic hearing loss is due to founder effects. Genet Test Mol Biomarkers 14: 307-311.
43. Hilgert N, Alasti F, Dieltjens N, Pawlik B, Wollnik B, et al. (2008) Mutation analysis of TMC1 identifies four new mutations and suggests an additional deafness gene at loci DFNA36 and DFNB7/11. Clin Genet 74: 223-232.
44. Estevez R, Boettger T, Stein V, Birkenhager R, Otto E, et al. (2001) Barttin is a Cl- channel beta-subunit crucial for renal Cl- reabsorption and inner ear K+ secretion. Nature 414: 558-561. (Pubitemid 33131540)
45. Hayama A, Rai T, Sasaki S, Uchida S (2003) Molecular mechanisms of Bartter syndrome caused by mutations in the BSND gene. Histochem Cell Biol 119: 485-493. (Pubitemid 36918586)
46. Janssen AG, Scholl U, Domeyer C, Nothmann D, Leinenweber A, et al. (2009) Disease-causing dysfunctions of barttin in Bartter syndrome type IV. J Am Soc Nephrol 20: 145-153.
47. Kramer BK, Bergler T, Stoelcker B, Waldegger S (2008) Mechanisms of Disease: the kidney-specific chloride channels ClCKA and ClCKB, the Barttin subunit, and their clinical relevance. Nat Clin Pract Nephrol 4: 38-46. (Pubitemid 350308225)
48. Rickheit G, Maier H, Strenzke N, Andreescu CE, De Zeeuw CI, et al. (2008) Endocochlear potential depends on Cl- channels: mechanism underlying deafness in Bartter syndrome IV. EMBO J 27: 2907-2917.
49. Waldegger S, Jeck N, Barth P, Peters M, Vitzthum H, et al. (2002) Barttin increases surface expression and changes current properties of ClC-K channels. Pflugers Arch 444: 411-418. (Pubitemid 35447416)
50. Fasquelle L, Scott HS, Lenoir M, Wang J, Rebillard G, et al. (2011) Tmprss3, a transmembrane serine protease deficient in human DFNB8/10 deafness, is critical for cochlear hair cell survival at the onset of hearing. J Biol Chem 286: 17383-17397.
51. Weegerink NJ, Schraders M, Oostrik J, Huygen PL, Strom TM, et al. (2011) Genotype-phenotype correlation in DFNB8/10 families with TMPRSS3 mutations. J Assoc Res Otolaryngol 12: 753-766.
52. Elbracht M, Senderek J, Eggermann T, Thurmer C, Park J, et al. (2007) Autosomal recessive postlingual hearing loss (DFNB8): compound heterozygosity for two novel TMPRSS3 mutations in German siblings. J Med Genet 44: e81.
53. Ahmed ZM, Yousaf R, Lee BC, Khan SN, Lee S, et al. (2011) Functional null mutations of MSRB3 encoding methionine sulfoxide reductase are associated with human deafness DFNB74. Am J Hum Genet 88: 19-29.