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In silico analysis missense mutation

Malene Rask Andersen, Muhammad Farooq, Karen Koefoed, Klaus W Kjaer, Ane Simony, Sren Tvorup Christensen, Lars Allan Larsen
STUDY DESIGN: Mutation analysis of a candidate disease gene in a cohort of patients with moderate to severe Adolescent idiopathic scoliosis (AIS). OBJECTIVE: To investigate if damaging mutations in the planar cell polarity gene VANGL1 could be identified in AIS patients. SUMMARY OF BACKGROUND DATA: AIS is a spinal deformity which occurs in 1-3% of the population. The cause of AIS is often unknown, but genetic factors are important in the etiology...
October 17, 2016: Spine
Michael P Heaton, Timothy P L Smith, Jacky K Carnahan, Veronica Basnayake, Jiansheng Qiu, Barry Simpson, Theodore S Kalbfleisch
The availability of whole genome sequence (WGS) data has made it possible to discover protein variants in silico. However, existing bovine WGS databases do not show data in a form conducive to protein variant analysis, and tend to under represent the breadth of genetic diversity in U.S. beef cattle. Thus, our first aim was to use 96 beef sires, sharing minimal pedigree relationships, to create a searchable and publicly viewable set of mapped genomes relevant for 19 popular breeds of U.S. cattle. Our second aim was to identify protein variants encoded by the bovine endothelial PAS domain-containing protein 1 gene ( EPAS1), a gene associated with high-altitude pulmonary hypertension in Angus cattle...
2016: F1000Research
Alana Christina Gast, Julia Metzger, Andrea Tipold, Ottmar Distl
BACKGROUND: Spinocerebellar ataxia also referred to as hereditary ataxia comprises different forms of progressive neurodegenerative diseases. A complex mode of inheritance was most likely in Parson Russell Terriers (PRT) and in Jack Russell Terriers (JRT). Recently, the missense mutation KCNJ10:c.627C > G was shown to be associated with the spinocerebellar ataxia (SCA) in JRT and related Russell group of terriers, whereas the missense mutation CAPN1:c.344G > A was associated with late onset ataxia (LOA) in PRT...
October 10, 2016: BMC Veterinary Research
Samiha S Shaikh, Ya-Chun Chen, Sally-Anne Halsall, Michael S Nahorski, Kiyoyuki Omoto, Gareth T Young, Anne Phelan, Christopher Geoffrey Woods
Hereditary sensory and autonomic neuropathy type IV (HSAN IV) is an autosomal recessive disorder characterized by a complete lack of pain perception and anhidrosis. Here, we studied a cohort of seven patients with HSAN IV and describe a comprehensive functional analysis of seven novel NTRK1 missense mutations, c.1550G>A, c.1565G>A, c.1970T>C, c.2096T>C, c.2254T>A, c.2288G>C, c.2311C>T, corresponding to p.G517E, p.G522E, p.L657P, p.I699T, p.C752S, p.C763S and p.R771C, all of which were predicted pathogenic by in-silico analysis...
September 27, 2016: Human Mutation
Antonio C S Marcolino, William F Porto, Állan S Pires, Octavio L Franco, Sérgio A Alencar
The guanylate cyclase activator 2B, also known as uroguanylin, is part of the guanylin peptide family, which includes peptides such as guanylin and lymphoguanylin. The guanylin peptides could be related to sodium absorption inhibition and water secretion induction and their dysfunction may be related to various pathologies such as chronic renal failure, congestive heart failure and nephrotic syndrome. Besides, uroguanylin point mutations have been associated with essential hypertension. However, currently there are no studies on the impact of missense SNPs on uroguanylin structure...
September 9, 2016: Journal of Theoretical Biology
D Thirumal Kumar, C George Priya Doss
Recent statistics describe breast cancer has the leading cause of death among women across the world with varied causes and reasons. Lifestyle, diet, genetic, and environmental factors introduce their generous contributions towards breast cancer. Among which, genetic factors have lately become one of the most important aspects in understanding the mechanism. Although various genes have already been reported in causing breast cancer, PIK3CA stands second on the list. Mutations observed in this gene has the ability to trigger the different activities of the cell thereby bypassing the regular cellular cycle...
September 1, 2016: Journal of Biomolecular Structure & Dynamics
Gyorgy Mate Milley, Edina Timea Varga, Zoltan Grosz, Benjamin Bereznai, Zsuzsanna Aranyi, Judit Boczan, Peter Dioszeghy, Bernadette Kálmán, Aniko Gal, Maria Judit Molnar
Pathogenic variants of the gap junction beta 1 (GJB1) gene are responsible for the Charcot-Marie-Tooth neuropathy X type 1 (CMTX1). In this study, we report the mutation frequency of GJB1 in 210 Hungarian CMT patients and the phenotype comparison between male and female CMTX1 patients. Altogether, 13 missense substitutions were found in the GJB1 gene. Among them, 10 have been previously described as pathogenic variants (p.Arg15Trp, p.Val63Ile, p.Leu89Val, p.Ala96Gly, p.Arg107Trp, p.Arg142Gln, p.Arg164Trp, p...
October 2016: Neuromuscular Disorders: NMD
A Ribani, F Bertolini, G Schiavo, E Scotti, V J Utzeri, S Dall'Olio, P Trevisi, P Bosi, L Fontanesi
Taste perception in animals affects feed intake and may influence production traits. In particular, bitter is sensed by receptors encoded by the family of TAS2R genes. In this research, using a DNA pool-seq approach coupled with next generation semiconductor based target resequencing, we analysed nine porcine TAS2R genes (TAS2R1, TAS2R3, TAS2R4, TAS2R7, TAS2R9, TAS2R10, TAS2R16, TAS2R38 and TAS2R39) to identify variability and, at the same time, estimate single nucleotide polymorphism (SNP) allele frequencies in several populations and testing differences in an association analysis...
July 20, 2016: Animal Genetics
Lin Li, Xueya Zhou, Xi Wang, Jing Wang, Wei Zhang, Binbin Wang, Yunxia Cao, Kehkooi Kee
STUDY QUESTION: Does a heterozygous mutation in AMHR2, identified in whole-exome sequencings (WES) of patients with primary ovarian insufficiency (POI), cause a defect in anti-Müllerian hormone (AMH) signaling? SUMMARY ANSWER: The I209N mutation at the adenosine triphosphate binding domain of AMHR2 exerts dominant negative defects in the AMH signaling pathway. WHAT IS KNOWN ALREADY: Previous studies have demonstrated the associations of several sequence variants in AMH or AMHR2 with POI, but no functional assay has been performed to verify whether there was any defect on AMH signaling...
September 2016: Molecular Human Reproduction
Santasree Banerjee, Qian Wu, Yuyi Ying, Yanni Li, Matsuyuki Shirota, Dante Neculai, Chen Li
The K1 and K10 associated genodermatoses are characterized by clinical symptoms of mild to severe redness, blistering and hypertrophy of the skin. In this paper, we set out to computationally investigate the structural and functional effects of missense mutations on the 2B domain of K1/K10 heterodimer and its consequences in disease phenotype. We modeled the structure of the K1/K10 heterodimer based on crystal structures for the human homolog K5/K14 heterodimer, and identified that the missense mutations exert their effects on stability and assembly competence of the heterodimer by altering physico-chemical properties, interatomic interactions, and inter-residue atomic contacts...
July 13, 2016: Oncotarget
E Edison, B A Konkle, A C Goodeve
Molecular genetic analysis of inherited bleeding disorders has been practised for over 30 years. Technological changes have enabled advances, from analyses using extragenic linked markers to next-generation DNA sequencing and microarray analysis. Two approaches for genetic analysis are described, each suiting their environment. The Christian Medical Centre in Vellore, India, uses conformation-sensitive gel electrophoresis mutation screening of multiplexed PCR products to identify candidate mutations, followed by Sanger sequencing confirmation of variants identified...
July 2016: Haemophilia: the Official Journal of the World Federation of Hemophilia
Marta Cardoso, Paula Paulo, Sofia Maia, Manuel R Teixeira
Truncating activating mutations in the last exon of PPM1D have been described in patients with breast, ovarian, colorectal and non-small cell lung cancer, but recent data indicate that they may be associated with previous chemotherapy. In this study we evaluated the prevalence of PPM1D mutations in white blood cells (WBC) of 462 patients with early-onset and/or familial/hereditary prostate cancer (PrCa) by sequencing the coding region of exon 6. Two truncating mutations were found in two patients (0.4%), both treated with androgen-ablation therapy but no chemotherapy prior to blood collection...
July 12, 2016: Genes, Chromosomes & Cancer
Maddalena Gigante, Luisa Santangelo, Sterpeta Diella, Gianluca Caridi, Lucia Argentiero, Maria Michela D''Alessandro, Marida Martino, Emma Diletta Stea, Gianluigi Ardissino, Vincenza Carbone, Silvana Pepe, Domenico Scrutinio, Silvio Maringhini, Gian Marco Ghiggeri, Giuseppe Grandaliano, Mario Giordano, Loreto Gesualdo
BACKGROUND/AIMS: Loss-of-function mutations in the CYP24A1 gene, which encodes the vitamin D-24 hydroxylase, have been recognized as a cause of elevated 1,25-dihydroxyvitamin D concentrations, hypercalcemia, hypercalciuria, nephrocalcinosis and nephrolithiasis in infants and adults. As only a case report describing 2 adult patients has been reported in Italian population, we report here the mutation analysis of CYP24A1 gene in an Italian cohort of 12 pediatric and adult patients with idiopathic infantile hypercalcemia (IIH)...
2016: Nephron
Benjamin R Lin, Ricardo F Frausto, Rosalind C Vo, Stephan Y Chiu, Judy L Chen, Anthony J Aldave
Purpose. To report the identification of the first de novo UBIAD1 missense mutation in an individual with Schnyder corneal dystrophy (SCD). Methods. A slit lamp examination was performed on a 47-year-old woman without a family history of corneal disorders. The proband's parents, two sisters, and son were also examined and genomic DNA from all six individuals was collected. The exons and exon-intron boundaries of UBIAD1 were screened using Sanger sequencing. Identified mutations were screened for in 200 control chromosomes...
2016: Journal of Ophthalmology
Anne Thomas, Arijit Biswas, Johannes Dodt, Helen Philippou, Emma Hethershaw, Hans Juergen Ensikat, Vytautas Ivaskevicius, Johannes Oldenburg
Inherited defects of coagulation Factor XIII (FXIII) can be categorized into severe and mild forms based on their genotype and phenotype. Heterozygous mutations occurring in F13A1 and F13B genes causing mild FXIII deficiency have been reported only in the last few years primarily because the mild FXIII deficiency patients are often asymptomatic unless exposed to some kind of a physical trauma. However, unlike mutations causing severe FXIII deficiency, many of these mutations have not been comprehensively characterized based on expression studies...
October 2016: Human Mutation
Benjamin R Lin, Derek J Le, Yabin Chen, Qiwei Wang, D Doug Chung, Ricardo F Frausto, Christopher Croasdale, Richard W Yee, Fielding J Hejtmancik, Anthony J Aldave
PURPOSE: To report identification of a COL17A1 mutation in a family with a corneal dystrophy previously mapped to chromosome 10q23-q24. METHODS: Whole-exome sequencing was performed on DNA samples from five affected family members and two unrelated, unaffected individuals. Identified variants were filtered for those that were: located in the linked interval on chromosome 10q23-q24; novel or rare (minor allele frequency ≤0.01); heterozygous; present in all affected individuals and not in controls; and present in genes that encode proteins expressed in human corneal epithelial cells (reads per kilobase per million ≥1)...
2016: PloS One
Marc Bennedbæk, Maria Rossing, Åse K Rasmussen, Anne-Marie Gerdes, Anne-Bine Skytte, Uffe B Jensen, Finn C Nielsen, Thomas V O Hansen
BACKGROUND: Germline mutations in the succinate dehydrogenase complex genes SDHB, SDHC, and SDHD predispose to pheochromocytomas and paragangliomas. Here, we examine the SDHB, SDHC, and SDHD mutation spectrum in the Danish population by screening of 143 Danish pheochromocytoma and paraganglioma patients. METHODS: Mutational screening was performed by Sanger sequencing or next-generation sequencing. The frequencies of variants of unknown clinical significance, e...
2016: Hereditary Cancer in Clinical Practice
Shamim Saleha, Muhammad Ajmal, Muhammad Jamil, Muhammad Nasir, Abdul Hameed
AIM: To map Usher phenotype in a consanguineous Pakistani family and identify disease-associated mutation in a causative gene to establish phenotype-genotype correlation. METHODS: A consanguineous Pakistani family in which Usher phenotype was segregating as an autosomal recessive trait was ascertained. On the basis of results of clinical investigations of affected members of this family disease was diagnosed as Usher syndrome (USH). To identify the locus responsible for the Usher phenotype in this family, genomic DNA from blood sample of each individual was genotyped using microsatellite Short Tandem Repeat (STR) markers for the known Usher syndrome loci...
2016: International Journal of Ophthalmology
Jingrui Xing, Hiroki Kimura, Chenyao Wang, Kanako Ishizuka, Itaru Kushima, Yuko Arioka, Akira Yoshimi, Yukako Nakamura, Tomoko Shiino, Tomoko Oya-Ito, Yuto Takasaki, Yota Uno, Takashi Okada, Tetsuya Iidaka, Branko Aleksic, Daisuke Mori, Norio Ozaki
PSD-95 associated PSD proteins play a critical role in regulating the density and activity of glutamate receptors. Numerous previous studies have shown an association between the genes that encode these proteins and schizophrenia (SZ) and autism spectrum disorders (ASD), which share a substantial portion of genetic risks. We sequenced the protein-encoding regions of DLG1, DLG2, DLG4, DLGAP1, DLGAP2, and SynGAP in 562 cases (370 SZ and 192 ASD patients) on the Ion PGM platform. We detected 26 rare (minor allele frequency <1%), non-synonymous mutations, and conducted silico functional analysis and pedigree analysis when possible...
2016: Scientific Reports
Manuel Méndez, María-Isabel Moreno-Carralero, Marta Morado-Arias, María-Cristina Fernández-Jiménez, Silvia de la Iglesia Iñigo, María-José Morán-Jiménez
BACKGROUND: X-linked sideroblastic anemia (XLSA) is a disorder characterized by decreased heme synthesis and mitochondrial iron overload with ringed sideroblasts in bone marrow. XLSA is caused by mutations in the erythroid-specific gene coding 5-aminolevulinate synthase (ALAS2). Anemia in XLSA is extremely variable, characteristically microcytic and hypochromic with poikilocytosis, and the red blood cell distribution width is increased and prominent dimorphism of the red cell population...
May 2016: Molecular Genetics & Genomic Medicine
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