Publications by authors named "Ibis Menendez"

15 Publications

  • Page 1 of 1

Novel pathogenic variants underlie SLC26A4-related hearing loss in a multiethnic cohort.

Int J Pediatr Otorhinolaryngol 2017 Oct 8;101:167-171. Epub 2017 Aug 8.

John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, USA; Dr. John T. Macdonald Foundation, Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL, USA; Department of Otorhinolaryngology, University of Miami, Miller School of Medicine, Miami, FL, USA. Electronic address:

Objectives: The genetics of sensorineural hearing loss is characterized by a high degree of heterogeneity. Despite this heterogeneity, DNA variants found within SLC26A4 have been reported to be the second most common contributor after those of GJB2 in many populations.

Methods: Whole exome sequencing and/or Sanger sequencing of SLC26A4 in 117 individuals with sensorineural hearing loss with or without inner ear anomalies but not with goiter from Turkey, Iran, and Mexico were performed.

Results: We identified 27 unique SLC26A4 variants in 31 probands. The variants c.1673A > G (p.N558S), c.1708-1G > A, c.1952C > T (p.P651L), and c.2090-1G > A have not been previously reported. The p.N558S variant was detected in two unrelated Mexican families.

Conclusion: A range of SLC26A4 variants without a common recurrent mutation underlies SLC26A4-related hearing loss in Turkey, Iran, and Mexico.
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http://dx.doi.org/10.1016/j.ijporl.2017.08.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5679420PMC
October 2017

Novel EYA1 variants causing Branchio-oto-renal syndrome.

Int J Pediatr Otorhinolaryngol 2017 Jul 26;98:59-63. Epub 2017 Apr 26.

John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA; Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, USA. Electronic address:

Introduction: Branchio-oto-renal (BOR) syndrome is an autosomal dominant genetic disorder characterized by second branchial arch anomalies, hearing impairment, and renal malformations. Pathogenic mutations have been discovered in several genes such as EYA1, SIX5, and SIX1. However, nearly half of those affected reveal no pathogenic variant by traditional genetic testing.

Methods And Materials: Whole Exome sequencing and/or Sanger sequencing performed in 10 unrelated families from Turkey, Iran, Ecuador, and USA with BOR syndrome in this study.

Results: We identified causative DNA variants in six families including novel c.525delT, c.979T > C, and c.1768delG and a previously reported c.1779A > T variants in EYA1. Two large heterozygous deletions involving EYA1 were detected in additional two families. Whole exome sequencing did not reveal a causative variant in the remaining four families.

Conclusions: A variety of DNA changes including large deletions underlie BOR syndrome in different populations, which can be detected with comprehensive genetic testing.
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http://dx.doi.org/10.1016/j.ijporl.2017.04.037DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5516569PMC
July 2017

Dominant deafness-onychodystrophy syndrome caused by an mutation.

Clin Case Rep 2017 04 8;5(4):376-379. Epub 2017 Feb 8.

John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami Florida USA; Department of Human Genetics Dr. John T. Macdonald Foundation University of Miami Miller School of Medicine Miami Florida USA.

Our report clarifies the role of in patients with deafness and onycho-osteodystrophy and confirms that a recurring c.1516C>T [p.(Arg506*)], variant causes dominant deafness-onychodystrophy (DDOD) syndrome.
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http://dx.doi.org/10.1002/ccr3.761DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5378843PMC
April 2017

Targeted Resequencing of Deafness Genes Reveals a Founder MYO15A Variant in Northeastern Brazil.

Ann Hum Genet 2016 Nov;80(6):327-331

John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA.

Identifying the genetic etiology in a person with hearing loss (HL) is challenging due to the extreme genetic heterogeneity in HL and the population-specific variability. In this study, after excluding GJB2 variants, targeted resequencing of 180 deafness-related genes revealed the causative variants in 11 of 19 (58%) Brazilian probands with autosomal recessive HL. Identified pathogenic variants were in MYO15A (10 families) and CLDN14 (one family). Remarkably, the MYO15A p.(Val1400Met) variant was identified in eight families from the city of Monte Santo in the northeast region of Brazil. Haplotype analysis of this variant was consistent with a single founder. No other cases with this variant were detected among 105 simplex cases from other cities of northeastern Brazil, suggesting that this variant is confined to a geographical region. This study suggests that it is feasible to develop population-specific screening for deafness variants once causative variants are identified in different geographical groups.
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http://dx.doi.org/10.1111/ahg.12177DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5127167PMC
November 2016

Spectrum of DNA variants for non-syndromic deafness in a large cohort from multiple continents.

Hum Genet 2016 08 25;135(8):953-61. Epub 2016 Jun 25.

Department of Otolaryngology (D-48), University of Miami Miller School of Medicine, 1666 NW 12th Avenue, Miami, FL, 33136, USA.

Hearing loss is the most common sensory deficit in humans with causative variants in over 140 genes. With few exceptions, however, the population-specific distribution for many of the identified variants/genes is unclear. Until recently, the extensive genetic and clinical heterogeneity of deafness precluded comprehensive genetic analysis. Here, using a custom capture panel (MiamiOtoGenes), we undertook a targeted sequencing of 180 genes in a multi-ethnic cohort of 342 GJB2 mutation-negative deaf probands from South Africa, Nigeria, Tunisia, Turkey, Iran, India, Guatemala, and the United States (South Florida). We detected causative DNA variants in 25 % of multiplex and 7 % of simplex families. The detection rate varied between 0 and 57 % based on ethnicity, with Guatemala and Iran at the lower and higher end of the spectrum, respectively. We detected causative variants within 27 genes without predominant recurring pathogenic variants. The most commonly implicated genes include MYO15A, SLC26A4, USH2A, MYO7A, MYO6, and TRIOBP. Overall, our study highlights the importance of family history and generation of databases for multiple ethnically discrete populations to improve our ability to detect and accurately interpret genetic variants for pathogenicity.
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http://dx.doi.org/10.1007/s00439-016-1697-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5497215PMC
August 2016

Comprehensive analysis via exome sequencing uncovers genetic etiology in autosomal recessive nonsyndromic deafness in a large multiethnic cohort.

Genet Med 2016 Apr 30;18(4):364-71. Epub 2015 Jul 30.

Dr. John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, USA.

Purpose: Autosomal recessive nonsyndromic deafness (ARNSD) is characterized by a high degree of genetic heterogeneity, with reported mutations in 58 different genes. This study was designed to detect deafness-causing variants in a multiethnic cohort with ARNSD by using whole-exome sequencing (WES).

Methods: After excluding mutations in the most common gene, GJB2, we performed WES in 160 multiplex families with ARNSD from Turkey, Iran, Mexico, Ecuador, and Puerto Rico to screen for mutations in all known ARNSD genes.

Results: We detected ARNSD-causing variants in 90 (56%) families, 54% of which had not been previously reported. Identified mutations were located in 31 known ARNSD genes. The most common genes with mutations were MYO15A (13%), MYO7A (11%), SLC26A4 (10%), TMPRSS3 (9%), TMC1 (8%), ILDR1 (6%), and CDH23 (4%). Nine mutations were detected in multiple families with shared haplotypes, suggesting founder effects.

Conclusion: We report on a large multiethnic cohort with ARNSD in which comprehensive analysis of all known ARNSD genes identifies causative DNA variants in 56% of the families. In the remaining families, WES allows us to search for causative variants in novel genes, thus improving our ability to explain the underlying etiology in more families.Genet Med 18 4, 364-371.
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http://dx.doi.org/10.1038/gim.2015.89DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4733433PMC
April 2016

Novel domain-specific POU3F4 mutations are associated with X-linked deafness: examples from different populations.

BMC Med Genet 2015 Feb 25;16. Epub 2015 Feb 25.

John P. Hussmann Institute for Human Genomics and John T. Macdonald Foundation, Department of Human Genetics, Miller school of Medicine, University of Miami, 1501 NW 10th Avenue, BRB-610 (M-860), Miami, FL, 33136, USA.

Background: Mutations in the POU3F4 gene cause X-linked deafness type 3 (DFN3), which is characterized by inner ear anomalies.

Methods: Three Turkish, one Ecuadorian, and one Nigerian families were included based on either inner ear anomalies detected in probands or X-linked family histories. Exome sequencing and/or Sanger sequencing were performed in order to identify the causative DNA variants in these families.

Results: Four novel, c.707A>C (p.(Glu236Ala)), c.772delG (p.(Glu258ArgfsX30)), c.902C>T (p.(Pro301Leu)), c.987T>C (p.(Ile308Thr)), and one previously reported mutation c.346delG (p.(Ala116ProfsX26)) in POU3F4, were identified. All mutations identified are predicted to affect the POU-specific or POU homeo domains of the protein and co-segregated with deafness in all families.

Conclusions: Expanding the spectrum of POU3F4 mutations in different populations along with their associated phenotypes provides better understanding of their clinical importance and will be helpful in clinical evaluation and counseling of the affected individuals.
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http://dx.doi.org/10.1186/s12881-015-0149-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4422282PMC
February 2015

An amino acid deletion inSZT2 in a family with non-syndromic intellectual disability.

PLoS One 2013 6;8(12):e82810. Epub 2013 Dec 6.

Dr. John T. Macdonald Department of Human Genetics and John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida, United States of America.

Autosomal recessive intellectual disability (ID) is characterized by extensive genetic heterogeneity. Recently, three mutations in SZT2 were reported in two unrelated children with unexplained infantile epileptic encephalopathy with severe ID. Here we report a European American family with three children having non-syndromic mild or moderate ID without seizures. Whole-exome sequencing of three affected siblings revealed a three base pair deletion (c.4202_4204delTTC) located in a 19 mb autozygous region on chromosome 1, leading to an amino acid deletion (p.Phe1401del) in SZT2. All three children were homozygous for the deletion and their parents were heterozygous as expected in autosomal recessive inheritance. SZT2 is highly expressed in neuronal tissues and regulates seizure threshold and neuronal excitation in mice. We conclude that the disruption of SZT2 with some residual function might lead to mild or moderate ID without seizures.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0082810PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3855772PMC
July 2014

Whole-exome sequencing efficiently detects rare mutations in autosomal recessive nonsyndromic hearing loss.

PLoS One 2012 30;7(11):e50628. Epub 2012 Nov 30.

John P. Hussman Institute for Human Genomics and the Dr. John T. Macdonald Department of Human Genetics, University of Miami Miller School of Medicine, Miami, Florida, United States of America.

Identification of the pathogenic mutations underlying autosomal recessive nonsyndromic hearing loss (ARNSHL) is difficult, since causative mutations in 39 different genes have so far been reported. After excluding mutations in the most common ARNSHL gene, GJB2, via Sanger sequencing, we performed whole-exome sequencing (WES) in 30 individuals from 20 unrelated multiplex consanguineous families with ARNSHL. Agilent SureSelect Human All Exon 50 Mb kits and an Illumina Hiseq2000 instrument were used. An average of 93%, 84% and 73% of bases were covered to 1X, 10X and 20X within the ARNSHL-related coding RefSeq exons, respectively. Uncovered regions with WES included those that are not targeted by the exome capture kit and regions with high GC content. Twelve homozygous mutations in known deafness genes, of which eight are novel, were identified in 12 families: MYO15A-p.Q1425X, -p.S1481P, -p.A1551D; LOXHD1-p.R1494X, -p.E955X; GIPC3-p.H170N; ILDR1-p.Q274X; MYO7A-p.G2163S; TECTA-p.Y1737C; TMC1-p.S530X; TMPRSS3-p.F13Lfs*10; TRIOBP-p.R785Sfs*50. Each mutation was within a homozygous run documented via WES. Sanger sequencing confirmed co-segregation of the mutation with deafness in each family. Four rare heterozygous variants, predicted to be pathogenic, in known deafness genes were detected in 12 families where homozygous causative variants were already identified. Six heterozygous variants that had similar characteristics to those abovementioned variants were present in 15 ethnically-matched individuals with normal hearing. Our results show that rare causative mutations in known ARNSHL genes can be reliably identified via WES. The excess of heterozygous variants should be considered during search for causative mutations in ARNSHL genes, especially in small-sized families.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0050628PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3511533PMC
May 2013

Unique spectrum of GJB2 mutations in Mexico.

Int J Pediatr Otorhinolaryngol 2012 Nov 24;76(11):1678-80. Epub 2012 Aug 24.

Departamento de Genetica, Instituto Nacional de Rehabilitacion, Calzada de Mexico Xochimilco No. 289, Colonia Arenal de Guadalupe, Delegacion Tlalpan, Mexico CP 14389, Mexico.

Objective: The aim of this study was to elucidate the involvement of mutations in three relatively common deafness genes in Mexican individuals with non-syndromic hearing loss.

Methods: We sequenced GJB2 for mutations, screened for two deletions involving GJB6, del(GJB6-D13S1830) and del(GJB6-D13S1854), and for the m.1555A>G mutation in the MTRNR1 gene in 76 (71 simplex and 5 multiplex) unrelated Mexican probands with prelingual non-syndromic hearing loss. Samples were obtained from the Department of Genetics at Instituto Nacional de Rehabilitacion in Mexico City.

Results: Eight previously reported pathogenic variants and two polymorphic variants in GJB2 were identified. The two screened GJB6 deletions and the m.1555A>G mutation were not detected. Eight cases (10.6%) were found to have bi-allelic mutations in GJB2 and six (7.9%) were found to have a monoallelic GJB2 mutation. Of the six monoallelic mutations, one (p.R184Q) was a previously reported autosomal dominant variant. The most frequent pathological allele detected in this population was the c.35delG mutation in the GJB2 gene. The p.V27I polymorphic variant was also detected, with an allele frequency of 0.24. All eight probands with GJB2 mutations had symmetric profound deafness, whereas patients without GJB2 mutations had moderate, severe or profound hearing loss.

Conclusions: This study shows that GJB2 mutations are an important cause of prelingual deafness in the Mexican population.
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http://dx.doi.org/10.1016/j.ijporl.2012.08.005DOI Listing
November 2012

Pathogenic validation of unique germline intronic variants of RB1 in retinoblastoma patients using minigenes.

Hum Mutat 2007 Dec;28(12):1245

OncoLab, Departamento de Biología Molecular y Celular del Cáncer, Instituto de Investigaciones Biomédicas A. Sols, CSIC-UAM, C/ Arturo Duperier 4, 28029 Madrid, Spain.

Precise identification of the pathogenic character of germline mutations in the retinoblastoma gene (RB1) is fundamental to provide genetic counselling to patients at risk of developing retinoblastoma. In contrast to bona fide oncogenic RB1 mutations like nonsense or frameshift mutations, and those affecting invariant dinucleotides at splice sites, intronic variants affecting less conserved splice motifs require additional analysis to ascertain whether splicing is altered. Although the frequency of these variations is low, their impact on genetic counselling is high, since they are usually associated with low penetrance phenotypes and unaffected carriers. In this work, we used minigene assays to study infrequent germline intronic variations for which functional data were not available. Using this approach, the aberrant splicing and the resulting oncogenic nature of three intronic RB1 mutations was established (c.501-15T>G, c.719-9C>G, c.2326-8T>A). Conversely, the intronic variant c.1961-12T>C was categorized by minigene assay as a very infrequent neutral polymorphism. To our knowledge this is the first report describing the use of minigene constructs to study the oncogenic character of intronic RB1 variants detected during mutational screening and show the utility of this approach to ascertain the oncogenic nature of unique RB1 intronic variants for which no previous functional and clinical data are available. Minigene assay can be especially useful when lymphocyte RNA is not available for study, or when aberrant mRNA can not be detected as a consequence of nonsense mediated decay. Since RB1 minigene are time-consuming assays, owing to the genomic organization of the RB1 gene, it should be welcome the design of new expression vectors that make this type of studies more straightforward.
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http://dx.doi.org/10.1002/humu.9512DOI Listing
December 2007

[Molecular diagnosis of retinoblastoma: molecular epidemiology and genetic counseling].

Med Clin (Barc) 2006 Mar;126(11):401-5

OncoLab, Departamento de Biología Molecular y Celular del Cáncer, Instituto de Investigaciones Biomédicas (IIB) Alberto Sols, CSIC-UAM, Madrid, Spain.

Background And Objective: Retinoblastoma, a prototype of hereditary cancer, is the most common intraocular tumor in children and a potential cause of blindness from therapeutic eye ablation, second tumors in germ line mutation carriers, and even death when untreated. The molecular scanning of RB1 in search of germ line mutations in 213 retinoblastoma patients from Spain, Cuba, Colombia and Serbia, has led to the detection of 106 mutations whose knowledge is important for genetic counselling and characterization of phenotypic-genotypic relations.

Patients And Method: Mutational study (PCR-sequentiation and microsatellites analysis) in patients with retinoblastoma, from Spain, Cuba, Colombia and Serbia.

Results: 45% of mutations, including most of the frame shift (FS), missense (MS) and splicing (SP), were new, while all nonsense mutations (NS) corresponded to hypermutable sites in RB1. Germ line mutations were found in 22% of unilateral sporadic patients. The incidence of SP plus MS mutations in this group of patients was greater (p = 0.018) than in bilateral patients. The frequency of SP mutations was higher (p = 0.0003) in Spain and France than in Germany and United Kingdom, while the incidence of NS mutations was lower (p = 0.0006). SP mutations were associated with the low penetrance phenotype and were also overrepresented (p = 0.018) in patients with delayed retinoblastoma onset.

Conclusions: Mutational scanning of unilateral patients is important for genetic counselling and may help decipher the molecular mechanisms leading to low penetrance or expressivity. The functional characterization of mutations associated with low-penetrance or expressivity phenotypes and the molecular classification of tumors using multiple expression profiling is important for a better understanding of the retinoblastoma pathogenesis.
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http://dx.doi.org/10.1157/13086125DOI Listing
March 2006

Identification of 26 new constitutional RB1 gene mutations in Spanish, Colombian, and Cuban retinoblastoma patients.

Hum Mutat 2005 Jan;25(1):99

Oncogenetic Laboratory (OncoLab), Instituto de Investigaciones Biomédicas Alberto Sols, CSIC-UAM, 28029 Madrid, Spain.

Constitutional mutations in the RB1 gene predispose to retinoblastoma development. Hence genetic screening of retinoblastoma patients and relatives is important for genetic counseling purposes. In addition, RB1 gene mutation studies may help decipher the molecular mechanisms leading to tumors with different degrees of penetrance or expressivity. In the course of genetically screening of 107 hereditary and non-hereditary retinoblastoma patients (11 familiar bilateral, 4 familiar unilateral, 49 sporadic bilateral and 43 sporadic unilateral) and kindred from Spain, Colombia and Cuba, using direct PCR sequencing, we observed 45 distinct mutations and four RB1 deletions in 53 patients (9 familiar bilateral, 2 familiar unilateral, 31 sporadic bilateral and 11 sporadic unilateral). Most of these mutations (26/45, 57%) have not been reported before. In 32 patients, the predisposing mutations correspond to nonsense (mainly CpG transitions) and small insertions or deletions whose expected outcome is a truncated Rb protein that lacks the functional pockets and tail. Five single aminoacid replacements and seventeen mutations affecting splicing sites were also observed in retinoblastoma patients. Two of these sixteen mutations are of unclear pathogenic nature.
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http://dx.doi.org/10.1002/humu.9299DOI Listing
January 2005

Two independent RB1-inactivating mutations in peripheral blood DNA of a hereditary retinoblastoma patient.

Genes Chromosomes Cancer 2004 Jul;40(3):271-5

OncoLab, Unidad de Biología Molecular y Celular del Cáncer, Instituto de Investigaciones Biomédicas Alberto Sols, CSIC-UAM, Madrid, Spain.

We report the presence of a hemizygous inactivating germ-line RB1 mutation (a recurrent g.78250C-->T transition, resulting in a stop codon in exon 17) in peripheral blood DNA from a patient with hereditary bilateral retinoblastoma. Hemizygosity was established by sequencing that showed no traces of the wild-type C nucleotide and by quantitative real-time PCR, which showed loss of one copy of exon 17. Genotyping of the RB1 locus with several polymorphic markers delineated a maximal deletion region between g.76875 and g.99426, including exons 15-17 and a large piece (21 kb) of intron 17. The heterozygosity for the mutation found in skin fibroblasts proves that the intragenic RB1 deletion probably took place in the definitive hematopoietic lineage of the patient. The presence of a null Rb-/- genotype in the hematopoietic cell lineage suggests that the white blood cells of the proband could be useful in the investigation of the role of complementary RBI family proteins in the control of the cell cycle.
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http://dx.doi.org/10.1002/gcc.20042DOI Listing
July 2004

A deletion involving the connexin 30 gene in nonsyndromic hearing impairment.

N Engl J Med 2002 Jan;346(4):243-9

Unidad de Genética Molecular, Hospital Ramón y Cajal, Madrid, Spain.

Background: Inherited hearing impairment affects about 1 in 2000 newborns. Up to 50 percent of all patients with autosomal recessive nonsyndromic prelingual deafness in different populations have mutations in the gene encoding the gap-junction protein connexin 26 (GJB2) at locus DFNB1 on chromosome 13q12. However, a large fraction (10 to 42 percent) of patients with GJB2 mutations have only one mutant allele; the accompanying mutation has not been identified. DFNB1-linked familial cases with no mutation in GJB2 have also been reported.

Methods: We evaluated 33 unrelated probands with nonsyndromic prelingual deafness who had only one GJB2 mutant allele. Nine subjects had evidence of linkage to DFNB1. We used haplotype analysis for markers on 13q12 to search for mutations other than the one involving GJB2.

Results: We identified a 342-kb deletion in the gene encoding connexin 30 (GJB6), a protein that is reported to be expressed with connexin 26 in the inner ear. The deletion extended distally to GJB2, which remained intact. The break-point junction of the deletion was isolated and sequenced, and a specific diagnostic test was developed for this common mutation. Twenty-two of the 33 subjects were heterozygous for both the GJB6 and GJB2 mutations, including all 9 with evidence of linkage to DFNB1. Two subjects were homozygous for the GJB6 mutation.

Conclusions: A 342-kb deletion in GJB6 is the second most frequent mutation causing prelingual deafness in the Spanish population. Our data suggest that mutations in the complex locus DFNB1, which contains two genes (GJB2 and GJB6), can result in a monogenic or a digenic pattern of inheritance of prelingual deafness.
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http://dx.doi.org/10.1056/NEJMoa012052DOI Listing
January 2002