Publications by authors named "Rehan S Shaikh"

18 Publications

  • Page 1 of 1

Multi-omic studies on missense PLG variants in families with otitis media.

Sci Rep 2020 09 14;10(1):15035. Epub 2020 Sep 14.

Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.

Otitis media (OM), a very common disease in young children, can result in hearing loss. In order to potentially replicate previously reported associations between OM and PLG, exome and Sanger sequencing, RNA-sequencing of saliva and middle ear samples, 16S rRNA sequencing, molecular modeling, and statistical analyses including transmission disequilibrium tests (TDT) were performed in a multi-ethnic cohort of 718 families and simplex cases with OM. We identified four rare PLG variants c.112A > G (p.Lys38Glu), c.782G > A (p.Arg261His), c.1481C > T (p.Ala494Val) and c.2045 T > A (p.Ile682Asn), and one common variant c.1414G > A (p.Asp472Asn). However TDT analyses for these PLG variants did not demonstrate association with OM in 314 families. Additionally PLG expression is very low or absent in normal or diseased middle ear in mouse and human, and salivary expression and microbial α-diversity were non-significant in c.1414G > A (p.Asp472Asn) carriers. Based on molecular modeling, the novel rare variants particularly c.782G > A (p.Arg261His) and c.2045 T > A (p.Ile682Asn) were predicted to affect protein structure. Exploration of other potential disease mechanisms will help elucidate how PLG contributes to OM susceptibility in humans. Our results underline the importance of following up findings from genome-wide association through replication studies, preferably using multi-omic datasets.
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http://dx.doi.org/10.1038/s41598-020-70498-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7490366PMC
September 2020

Novel Mutations in , , , and Identified in Familial Cases of Prelingual Hearing Loss.

Genes (Basel) 2020 08 22;11(9). Epub 2020 Aug 22.

Department of Molecular Biology, Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad 44000, Pakistan.

We report the underlying genetic causes of prelingual hearing loss (HL) segregating in eight large consanguineous families, ascertained from the Punjab province of Pakistan. Exome sequencing followed by segregation analysis revealed seven potentially pathogenic variants, including four novel alleles c.257G>A, c.6083A>C, c.89A>G, and c.1249A>G of , , , and , respectively. We also identified three previously reported HL-causing variants (c.4528C>T, c.35delG, and c.1219T>C) of , , and segregating in four families. All identified variants were either absent or had very low frequencies in the control databases. Our in silico analyses and 3-dimensional (3D) molecular modeling support the deleterious impact of these variants on the encoded proteins. Variants identified in , , , and were classified as "pathogenic" or "likely pathogenic", while the variants in and fall in the category of "uncertain significance" based on the American College of Medical Genetics and Genomics/Association for Molecular Pathology (ACMG/AMP) variant pathogenicity guidelines. This paper highlights the genetic diversity of hearing disorders in the Pakistani population and reports the identification of four novel mutations in four HL families.
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http://dx.doi.org/10.3390/genes11090978DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7564084PMC
August 2020

Molecular characterization of SLC24A5 variants and evaluation of Nitisinone treatment efficacy in a zebrafish model of OCA6.

Pigment Cell Melanoma Res 2020 07 27;33(4):556-565. Epub 2020 Apr 27.

Department of Otorhinolaryngology Head and Neck Surgery, School of Medicine, University of Maryland, Baltimore, MD, USA.

Skin pigmentation is a highly heterogeneous trait with diverse consequences worldwide. SLC24A5, encoding a potent K -dependent Na /Ca exchanger, is among the known color-coding genes that participate in melanogenesis by maintaining pH in melanosomes. Deficient SLC24A5 activity results in oculocutaneous albinism (OCA) type 6 in humans. In this study, by utilizing a exome sequencing (ES) approach, we identified two new variants [p. (Gly110Arg) and p. (IIe189Ilefs*1)] of SLC24A5 cosegregating with the OCA phenotype, including nystagmus, strabismus, foveal hypoplasia, albinotic fundus, and vision impairment, in three large consanguineous Pakistani families. Both of these variants failed to rescue the pigmentation in zebrafish slc24a5 morphants, confirming the pathogenic effects of the variants. We also phenotypically characterized a commercially available zebrafish mutant line (slc24a5 ) that harbors a nonsense (p.Tyr208*) allele of slc24a5. Similar to morphants, homozygous slc24a5 mutants had significantly reduced melanin content and pigmentation. Next, we used these slc24a5 zebrafish mutants to test the efficacy of nitisinone, a compound known to increase ocular and fur pigmentation in OCA1 (TYR) mutant mice. Treatment of slc24a5 mutant zebrafish embryos with varying doses of nitisinone did not improve melanin production and pigmentation, suggesting that treatment with nitisinone is unlikely to be therapeutic in OCA6 patients.
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http://dx.doi.org/10.1111/pcmr.12879DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7269830PMC
July 2020

A simple method for preparing ultra-light graphene aerogel for rapid removal of U(VI) from aqueous solution.

Environ Pollut 2019 Aug 9;251:547-554. Epub 2019 May 9.

Key Laboratory of Photovoltaic and Energy Conservation Materials, Institute of Plasma Physics, Chinese Academy of Sciences, P.O. Box 1126, Hefei, 230031, Anhui, PR China; NAAM Research Group, Faculty of Science, King Abdulaziz University, Jeddah, 21589, Saudi Arabia. Electronic address:

In this study, graphene aerogel (GA) was successfully prepared through a simple hydrothermal method. The resulting GA exhibited a porous network structure with a large specific surface area (350.8 m/g), ultra-light mass and easy separation from water. The pH value of the GA was estimated to be 3.5. The adsorption process and the factors that affect adsorption capacity were studied. The adsorption could be conducted in a wide pH range from 2.0 to 7.0. The maximum adsorption capacity of GA towards U(VI) at pH 4.0 and T = 298 K was 238.67 mg/g calculated from the Langmuir model. The GA had greatly rapid adsorption property for the removal of U(VI) at pH 4.0. Kinetic data showed good correlation with pseudo-second-order equation. Fourier transform infrared spectroscopy and X-ray photoelectron spectrometry characterizations showed that GA adsorbed U(VI) through chemical interaction by oxygen-containing and nitrogen-containing groups functional groups. The results show that GA has excellent application potential as an adsorbent material for removing U(VI) from aqueous solution.
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http://dx.doi.org/10.1016/j.envpol.2019.05.011DOI Listing
August 2019

A2ML1 and otitis media: novel variants, differential expression, and relevant pathways.

Hum Mutat 2019 08 21;40(8):1156-1171. Epub 2019 May 21.

Department of Otolaryngology, University of Colorado School of Medicine, Aurora, Colorado.

A genetic basis for otitis media is established, however, the role of rare variants in disease etiology is largely unknown. Previously a duplication variant within A2ML1 was identified as a significant risk factor for otitis media in an indigenous Filipino population and in US children. In this report exome and Sanger sequencing was performed using DNA samples from the indigenous Filipino population, Filipino cochlear implantees, US probands, Finnish, and Pakistani families with otitis media. Sixteen novel, damaging A2ML1 variants identified in otitis media patients were rare or low-frequency in population-matched controls. In the indigenous population, both gingivitis and A2ML1 variants including the known duplication variant and the novel splice variant c.4061 + 1 G>C were independently associated with otitis media. Sequencing of salivary RNA samples from indigenous Filipinos demonstrated lower A2ML1 expression according to the carriage of A2ML1 variants. Sequencing of additional salivary RNA samples from US patients with otitis media revealed differentially expressed genes that are highly correlated with A2ML1 expression levels. In particular, RND3 is upregulated in both A2ML1 variant carriers and high-A2ML1 expressors. These findings support a role for A2ML1 in keratinocyte differentiation within the middle ear as part of otitis media pathology and the potential application of ROCK inhibition in otitis media.
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http://dx.doi.org/10.1002/humu.23769DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6711784PMC
August 2019

Identities and frequencies of variants in causing primary congenital glaucoma in Pakistan.

Mol Vis 2019 22;25:144-154. Epub 2019 Feb 22.

Department of Otorhinolaryngology Head and Neck Surgery, School of Medicine, University of Maryland, Baltimore, MD.

Purpose: Primary congenital glaucoma (PCG) is a clinically and genetically heterogeneous disease. The present study was undertaken to find the genetic causes of PCG segregating in 36 large consanguineous Pakistani families.

Methods: Ophthalmic examination including fundoscopy, or slit-lamp microscopy was performed to clinically characterize the PCG phenotype. Genomic nucleotide sequences of the and genes were analyzed with either Sanger or whole exome sequencing. In silico prediction programs were used to assess the pathogenicity of identified alleles. ClustalW alignments were performed to determine evolutionary conservation, and three-dimensional (3D) modeling was performed using HOPE and Phyre2 software.

Results: Among the known loci, mutations in and are the common causes of PCG. Therefore, we analyzed the genomic nucleotide sequences of and , and detected probable pathogenic variants cosegregating with PCG in 14 families. These included the three novel (c.542T>A, c.1436A>G, and c.1325delC) and five known (c.868dupC, c.1168C>T, c.1169G>A, c.1209InsTCATGCCACC, and c.1310C>T) variants in . Two of the novel variants are missense substitutions [p.(Leu181Gln), p.(Gln479Arg)], which replaced evolutionary conserved amino acids, and are predicted to be pathogenic by various in silico programs, while the third variant (c.1325delC) is predicted to cause reading frameshift and premature truncation of the protein. A single mutation, p.(Arg390His), causes PCG in six (~43%) of the 14 mutations harboring families, and thus, is the most common variant in this cohort. Surprisingly, we did not find any pathogenic variants in the families, which further supports the genetic heterogeneity of PCG in the Pakistani population.

Conclusions: In conclusion, results of the present study enhance our understanding of the genetic basis of PCG, support the notion of a genetic modifier of , and contribute to the development of genetic testing protocols and genetic counseling for PCG in Pakistani families.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6386514PMC
June 2019

FUT2 Variants Confer Susceptibility to Familial Otitis Media.

Am J Hum Genet 2018 11 25;103(5):679-690. Epub 2018 Oct 25.

Department of Otorhinolaryngology, Head and Neck Surgery, School of Medicine, University of Maryland, Baltimore, MD 21201, USA.

Non-secretor status due to homozygosity for the common FUT2 variant c.461G>A (p.Trp154) is associated with either risk for autoimmune diseases or protection against viral diarrhea and HIV. We determined the role of FUT2 in otitis media susceptibility by obtaining DNA samples from 609 multi-ethnic families and simplex case subjects with otitis media. Exome and Sanger sequencing, linkage analysis, and Fisher exact and transmission disequilibrium tests (TDT) were performed. The common FUT2 c.604C>T (p.Arg202) variant co-segregates with otitis media in a Filipino pedigree (LOD = 4.0). Additionally, a rare variant, c.412C>T (p.Arg138Cys), is associated with recurrent/chronic otitis media in European-American children (p = 1.2 × 10) and US trios (TDT p = 0.01). The c.461G>A (p.Trp154) variant was also over-transmitted in US trios (TDT p = 0.01) and was associated with shifts in middle ear microbiota composition (PERMANOVA p < 10) and increased biodiversity. When all missense and nonsense variants identified in multi-ethnic US trios with CADD > 20 were combined, FUT2 variants were over-transmitted in trios (TDT p = 0.001). Fut2 is transiently upregulated in mouse middle ear after inoculation with non-typeable Haemophilus influenzae. Four FUT2 variants-namely p.Ala104Val, p.Arg138Cys, p.Trp154, and p.Arg202-reduced A antigen in mutant-transfected COS-7 cells, while the nonsense variants also reduced FUT2 protein levels. Common and rare FUT2 variants confer susceptibility to otitis media, likely by modifying the middle ear microbiome through regulation of A antigen levels in epithelial cells. Our families demonstrate marked intra-familial genetic heterogeneity, suggesting that multiple combinations of common and rare variants plus environmental factors influence the individual otitis media phenotype as a complex trait.
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http://dx.doi.org/10.1016/j.ajhg.2018.09.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6217759PMC
November 2018

Molecular detection of Ehrlichia canis in dogs from three districts in Punjab (Pakistan).

Vet Med Sci 2018 05 7;4(2):126-132. Epub 2018 Feb 7.

Institute of Pure and Applied Biology, Zoology Division, Bahauddin Zakariya University, Multan, Pakistan.

Canine monocytic ehrlichiosis is a tick-borne disease caused by an intracellular alpha-proteobacterium, Ehrlichia canis, which replicates within mononuclear cells in the host. This study was designed to use a polymerase chain reaction (PCR) protocol for the molecular detection of E. canis by the amplification of a portion of its 16S rRNA gene, as well as the effects of this alpha-proteobacterium on the haematological parameters of the sampled dogs and the risk factors associated with E. canis infection. A total of 151 blood samples were collected from dogs of various breeds at three sampling sites (Lahore, Rawalpindi/Islamabad and Multan) in Punjab, Pakistan. Data regarding the epidemiological factors (including age, gender, breed, body temperature, deworming, vaccination, mucous membrane status, hydration status, the presence of haematuria and tick infestation) were collected through a questionnaire at the time of sample collection. A 400 bp DNA fragment of the 16S rRNA gene of E. canis was amplified from 42 dog blood samples (28% of the total), [Lahore (N = 24), Rawalpindi/Islamabad (N = 13) and Multan (N = 05)] through PCR. Data analysis revealed that the character of the animals (age, sex and breed) had no significant association (P > 0.05) with the presence of E. canis. Various haematological parameters were also compared, and the results revealed that all of the parameters remained unaffected, except significantly lower white blood cell counts (P = 0.004) in E. canis-positive blood samples, as compared with the control group. We concluded that this is the first molecular confirmation of canine infection by E. canis using PCR. Moreover, no specific epidemiological parameter was found associated with the prevalence of E. canis in dogs.
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http://dx.doi.org/10.1002/vms3.94DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5979635PMC
May 2018

Molecular outcomes, clinical consequences, and genetic diagnosis of Oculocutaneous Albinism in Pakistani population.

Sci Rep 2017 03 7;7:44185. Epub 2017 Mar 7.

Department of Otorhinolaryngology Head and Neck Surgery, School of Medicine, University of Maryland, Baltimore, MD, USA.

Nonsyndromic oculocutaneous Albinism (nsOCA) is clinically characterized by the loss of pigmentation in the skin, hair, and iris. OCA is amongst the most common causes of vision impairment in children. To date, pathogenic variants in six genes have been identified in individuals with nsOCA. Here, we determined the identities, frequencies, and clinical consequences of OCA alleles in 94 previously unreported Pakistani families. Combination of Sanger and Exome sequencing revealed 38 alleles, including 22 novel variants, segregating with nsOCA phenotype in 80 families. Variants of TYR and OCA2 genes were the most common cause of nsOCA, occurring in 43 and 30 families, respectively. Twenty-two novel variants include nine missense, four splice site, two non-sense, one insertion and six gross deletions. In vitro studies revealed retention of OCA proteins harboring novel missense alleles in the endoplasmic reticulum (ER) of transfected cells. Exon-trapping assays with constructs containing splice site alleles revealed errors in splicing. As eight alleles account for approximately 56% (95% CI: 46.52-65.24%) of nsOCA cases, primarily enrolled from Punjab province of Pakistan, hierarchical strategies for variant detection would be feasible and cost-efficient genetic tests for OCA in families with similar origin. Thus, we developed Tetra-primer ARMS assays for rapid, reliable, reproducible and economical screening of most of these common alleles.
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http://dx.doi.org/10.1038/srep44185DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5339803PMC
March 2017

Identification and clinical characterization of Hermansky-Pudlak syndrome alleles in the Pakistani population.

Pigment Cell Melanoma Res 2016 Mar 18;29(2):231-5. Epub 2015 Dec 18.

Department of Otorhinolaryngology Head and Neck Surgery, School of Medicine, University of Maryland, Baltimore, MD, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5062593PMC
http://dx.doi.org/10.1111/pcmr.12438DOI Listing
March 2016

Identification and functional characterization of natural human melanocortin 1 receptor mutant alleles in Pakistani population.

Pigment Cell Melanoma Res 2015 Nov 22;28(6):730-5. Epub 2015 Sep 22.

Department of Otorhinolaryngology Head and Neck Surgery, School of Medicine, University of Maryland, Baltimore, MD, USA.

Melanocortin 1 receptor (MC1R), a Gs protein-coupled receptor of the melanocyte's plasma membrane, is a major determinant of skin pigmentation and phototype. Upon activation by α-melanocyte stimulating hormone, MC1R triggers the cAMP cascade to stimulate eumelanogenesis. We used whole-exome sequencing to identify causative alleles in Pakistani families with skin and hair hypopigmentation. Six MC1R mutations segregated with the phenotype in seven families, including a p.Val174del in-frame deletion and a p.Tyr298* nonsense mutation, that were analyzed for function in heterologous HEK293 cells. p.Tyr298* MC1R showed no agonist-induced signaling to the cAMP or ERK pathways, nor detectable agonist binding. Conversely, signaling was comparable for p.Val174del and wild-type in HEK cells overexpressing the proteins, but binding analysis suggested impaired cell surface expression. Flow cytometry and confocal imaging studies revealed reduced plasma membrane expression of p.Val174del and p.Tyr298*. Therefore, p.Tyr298* was a total loss-of-function (LOF) allele, while p.Val174del displayed a partial LOF attribute.
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http://dx.doi.org/10.1111/pcmr.12400DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4609612PMC
November 2015

Homozygous missense variant in the human CNGA3 channel causes cone-rod dystrophy.

Eur J Hum Genet 2015 Apr 23;23(4):473-80. Epub 2014 Jul 23.

1] Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University, Multan, Pakistan [2] Department of Otorhinolaryngology Head and Neck Surgery, School of Medicine, University of Maryland, Baltimore, MD, USA.

We assessed a large consanguineous Pakistani family (PKAB157) segregating early onset low vision problems. Funduscopic and electroretinographic evaluation of affected individuals revealed juvenile cone-rod dystrophy (CRD) with maculopathy. Other clinical symptoms included loss of color discrimination, photophobia and nystagmus. Whole-exome sequencing, segregation and haplotype analyses demonstrated that a transition variant (c.955T>C; p.(Cys319Arg)) in CNGA3 co-segregated with the CRD phenotype in family PKAB157. The ability of CNGA3 channel to influx calcium in response to agonist, when expressed either alone or together with the wild-type CNGB3 subunit in HEK293 cells, was completely abolished due to p.Cys319Arg variant. Western blotting and immunolocalization studies suggest that a decreased channel density in the HEK293 cell membrane due to impaired folding and/or trafficking of the CNGA3 protein is the main pathogenic effect of the p.Cys319Arg variant. Mutant alleles of the human cone photoreceptor cyclic nucleotide-gated channel (CNGA3) are frequently associated with achromatopsia. In rare cases, variants in CNGA3 are also associated with cone dystrophy, Leber's congenital amaurosis and oligo cone trichromacy. The identification of predicted p.(Cys319Arg) missense variant in CNGA3 expands the repertoire of the known genetic causes of CRD and phenotypic spectrum of CNGA3 alleles.
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http://dx.doi.org/10.1038/ejhg.2014.136DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4666578PMC
April 2015

Association of XRCC1, XRCC3, and XPD genetic polymorphism with an increased risk of hepatocellular carcinoma because of the hepatitis B and C virus.

Eur J Gastroenterol Hepatol 2013 Feb;25(2):166-79

Institute of Molecular Biology & Biotechnology, Bahauddin Zakariya University, Multan, Pakistan.

Objective: The south-east Asian and sub-Saharan African populations are the most susceptible to hepatocellular carcinoma (HCC). We aimed to establish whether XRCC1, XRCC3, and XPD are associated with liver cancer in Pakistan and to examine the interaction of hepatitis B virus (HBV) or hepatitis C virus (HCV) with repaired genes in the occurrence of liver cancer.

Materials And Methods: We enrolled 74 healthy individuals, 75 had either HBV or HCV, and 50 were HCC patients. The characteristic information of all the study participants were collected through a standard interviewer-administered questionnaire. The PCR-RFLP was used to identify the genotype of the patients.

Results: The results of our study indicated that the patients infected with HBV or HCV had a four or three-fold greater risk of developing liver cancer. Patients older than 55 years of age had a significantly higher risk of developing cancer compared with younger patients. The homozygous wild types Arg/Arg for 280 and Thr/Thr for 241 were more frequent in the controls than in the cases. The allelic frequency of mutant 280His and 399Gln was more pronounced among HCC cases than the controls or the HBV-infected patients.

Conclusion: The frequency of the XPD gene in the controls was in Hardy-Weinberg equilibrium, indicating that the gene played a protective role in the Pakistani population. XRCC1 or XRCC3 was associated with liver cancer in the Pakistani population; however, the XPD gene played a vital role in the repair of DNA damage.
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http://dx.doi.org/10.1097/MEG.0b013e328359a775DOI Listing
February 2013

Molecular genetic studies and delineation of the oculocutaneous albinism phenotype in the Pakistani population.

Orphanet J Rare Dis 2012 Jun 26;7:44. Epub 2012 Jun 26.

Division of Pediatric Ophthalmology, Cincinnati Children's Hospital Research Foundation, Cincinnati, OH 45229, USA.

Background: Oculocutaneous albinism (OCA) is caused by a group of genetically heterogeneous inherited defects that result in the loss of pigmentation in the eyes, skin and hair. Mutations in the TYR, OCA2, TYRP1 and SLC45A2 genes have been shown to cause isolated OCA. No comprehensive analysis has been conducted to study the spectrum of OCA alleles prevailing in Pakistani albino populations.

Methods: We enrolled 40 large Pakistani families and screened them for OCA genes and a candidate gene, SLC24A5. Protein function effects were evaluated using in silico prediction algorithms and ex vivo studies in human melanocytes. The effects of splice-site mutations were determined using an exon-trapping assay.

Results: Screening of the TYR gene revealed four known (p.Arg299His, p.Pro406Leu, p.Gly419Arg, p.Arg278*) and three novel mutations (p.Pro21Leu, p.Cys35Arg, p.Tyr411His) in ten families. Ex vivo studies revealed the retention of an EGFP-tagged mutant (p.Pro21Leu, p.Cys35Arg or p.Tyr411His) tyrosinase in the endoplasmic reticulum (ER) at 37°C, but a significant fraction of p.Cys35Arg and p.Tyr411His left the ER in cells grown at a permissive temperature (31°C). Three novel (p.Asp486Tyr, p.Leu527Arg, c.1045-15 T > G) and two known mutations (p.Pro743Leu, p.Ala787Thr) of OCA2 were found in fourteen families. Exon-trapping assays with a construct containing a novel c.1045-15 T > G mutation revealed an error in splicing. No mutation in TYRP1, SLC45A2, and SLC24A5 was found in the remaining 16 families. Clinical evaluation of the families segregating either TYR or OCA2 mutations showed nystagmus, photophobia, and loss of pigmentation in the skin or hair follicles. Most of the affected individuals had grayish-blue colored eyes.

Conclusions: Our results show that ten and fourteen families harbored mutations in the TYR and OCA2 genes, respectively. Our findings, along with the results of previous studies, indicate that the p.Cys35Arg, p.Arg278* and p.Gly419Arg alleles of TYR and the p.Asp486Tyr and c.1045-15 T > G alleles of OCA2 are the most common causes of OCA in Pakistani families. To the best of our knowledge, this study represents the first documentation of OCA2 alleles in the Pakistani population. A significant proportion of our cohort did not have mutations in known OCA genes. Overall, our study contributes to the development of genetic testing protocols and genetic counseling for OCA in Pakistani families.
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http://dx.doi.org/10.1186/1750-1172-7-44DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3537634PMC
June 2012

Loss-of-function mutations of ILDR1 cause autosomal-recessive hearing impairment DFNB42.

Am J Hum Genet 2011 Feb 20;88(2):127-37. Epub 2011 Jan 20.

Institute of Human Genetics, University of Cologne, Cologne, Germany.

By using homozygosity mapping in a consanguineous Pakistani family, we detected linkage of nonsyndromic hearing loss to a 7.6 Mb region on chromosome 3q13.31-q21.1 within the previously reported DFNB42 locus. Subsequent candidate gene sequencing identified a homozygous nonsense mutation (c.1135G>T [p.Glu379X]) in ILDR1 as the cause of hearing impairment. By analyzing additional consanguineous families with homozygosity at this locus, we detected ILDR1 mutations in the affected individuals of 10 more families from Pakistan and Iran. The identified ILDR1 variants include missense, nonsense, frameshift, and splice-site mutations as well as a start codon mutation in the family that originally defined the DFNB42 locus. ILDR1 encodes the evolutionarily conserved immunoglobulin-like domain containing receptor 1, a putative transmembrane receptor of unknown function. In situ hybridization detected expression of Ildr1, the murine ortholog, early in development in the vestibule and in hair cells and supporting cells of the cochlea. Expression in hair cell- and supporting cell-containing neurosensory organs is conserved in the zebrafish, in which the ildr1 ortholog is prominently expressed in the developing ear and neuromasts of the lateral line. These data identify loss-of-function mutations of ILDR1, a gene with a conserved expression pattern pointing to a conserved function in hearing in vertebrates, as underlying nonsyndromic prelingual sensorineural hearing impairment.
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http://dx.doi.org/10.1016/j.ajhg.2010.12.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3035704PMC
February 2011

Mutation spectrum of MYO7A and evaluation of a novel nonsyndromic deafness DFNB2 allele with residual function.

Hum Mutat 2008 Apr;29(4):502-11

Section on Human Genetics, Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Rockville, Maryland 20850, USA.

Recessive mutations of MYO7A, encoding unconventional myosin VIIA, can cause either a deaf-blindness syndrome (type 1 Usher syndrome; USH1B) or nonsyndromic deafness (DFNB2). In our study, deafness segregating as a recessive trait in 24 consanguineous families showed linkage to markers for the DFNB2/USH1B locus on chromosome 11q13.5. A total of 23 of these families segregate USH1 due to 17 homozygous mutant MYO7A alleles, of which 14 are novel. One family segregated nonsyndromic hearing loss DFNB2 due to a novel three-nucleotide deletion in an exon of MYO7A (p.E1716del) encoding a region of the tail domain. We hypothesized that DFNB2 alleles of MYO7A have residual myosin VIIA. To address this question we investigated the effects of several mutant alleles by making green fluorescent protein (GFP) tagged cDNA expression constructs containing engineered mutations of mouse Myo7a at codons equivalent to pathogenic USH1B and DFNB2 alleles of human MYO7A. We show that in transfected mouse hair cells an USH1B mutant GFP-myosin VIIa does not localize properly to inner ear hair cell stereocilia. However, a GFP-myosin VIIa protein engineered to have an equivalent DFNB2 mutation to p.E1716del localizes correctly in transfected mouse hair cells. This finding is consistent with the hypothesis that p.E1716del causes a less severe phenotype (DFNB2) than the USH1B-associated alleles because the resulting protein retains some degree of normal function.
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http://dx.doi.org/10.1002/humu.20677DOI Listing
April 2008

A new locus for nonsyndromic deafness DFNB49 maps to chromosome 5q12.3-q14.1.

Hum Genet 2005 Jan 6;116(1-2):17-22. Epub 2004 Nov 6.

National Centre of Excellence in Molecular Biology, University of the Punjab, 87-West Canal Bank Road, Thokar Niaz Baig, Lahore 53700, Pakistan.

Cosegregation of markers on chromosome 5q12.3-q14.1 with profound congenital deafness in two Pakistani families (PKDF041 and PKDF141) defines a new recessive deafness locus, DFNB49. A maximum two-point lod score of 4.44 and 5.94 at recombination fraction theta=0 was obtained for markers D5S2055 and D5S424 in families PKDF041 and PKDF141, respectively. Haplotype analysis revealed an 11 cM linkage region flanked by markers D5S647 (74.07 cM) and D5S1501 (85.25 cM). Candidate deafness genes in this region include SLC30A5, OCLN, GTF2H2, and BTF3, encoding solute carrier family 30 (zinc transporter) member 5, occludin, RNA polymerase II transcription initiation factor, and basic transcription factor 3, respectively. Sequence analysis of the coding exons of SLC30A5 in DNA samples from two affected individuals of families PKDF041 and PKDF141 revealed no mutation. The mapping of DFNB49 further confirms the heterogeneity underlying autosomal recessive forms of nonsyndromic deafness.
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http://dx.doi.org/10.1007/s00439-004-1205-8DOI Listing
January 2005