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Prediction of missense mutation

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https://www.readbyqxmd.com/read/28089752/three-novel-mutations-of-arg1-identified-in-chinese-patients-with-argininemia-detected-by-newborn-screening
#1
Ting Zhang, Jianbin Yang, Xiaoshan Yin, Ping Yu, Robert Mooney, Xinwen Huang, Ming Qi
Argininemia is a rare autosomal recessive genetic disorder caused by deficiency of arginase Ι, resulting from mutations in the ARG1 gene. Few genetic studies of ARG1 mutations in Chinese patients have been reported. In this study, two argininemia patients were initially diagnosed by tandem mass spectrometry in newborn screening. Mutation analysis of the ARG1 gene was performed by direct sequencing. Three novel mutations were identified and in silico methods were used to predict the impact of these mutations on the activity of enzyme...
January 12, 2017: Clinica Chimica Acta; International Journal of Clinical Chemistry
https://www.readbyqxmd.com/read/28087769/enzyme-efficiency-but-not-thermostability-drives-cefotaxime-resistance-evolution-in-tem-1-%C3%AE-lactamase
#2
Jennifer Knies, Fei Cai, Daniel M Weinreich
A leading intellectual challenge in evolutionary genetics is to identify the specific phenotypes that drive adaptation. Enzymes offer a particularly promising opportunity to pursue this question, because many enzymes' contributions to organismal fitness depend on a comparatively small number of experimentally accessible properties. Moreover, on first principles the demands of enzyme thermostability stand in opposition to the demands of catalytic activity. This observation, coupled with the fact that enzymes are only marginally thermostable, motivates the widely held hypothesis that mutations conferring functional improvement require compensatory mutations to restore thermostability...
January 12, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28087737/a-homozygous-mutation-in-trim36-causes-autosomal-recessive-anencephaly-in-an-indian-family
#3
Nivedita Singh, Vishwanath Kumble Bhat, Ankana Tiwari, Srinivas G Kodaganur, Sagar J Tontanahal, Astha Sarda, K V Malini, Arun Kumar
Anencephaly is characterized by the absence of brain tissues and cranium. During primary neurulation stage of the embryo, the rostral part of the neural pore fails to close, leading to anencephaly. Anencephaly shows a heterogeneous etiology, ranging from environmental to genetic causes. The autosomal recessive inheritance of anencephaly has been reported in several populations. In this study, we employed whole-exome sequencing and identified a homozygous missense mutation c.1522C>A (p.Pro508Thr) in the TRIM36 gene as the cause of autosomal recessive anencephaly (APH) in an Indian family...
January 13, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28074573/structural-functional-and-clinical-characterization-of-a-novel-ptpn11-mutation-cluster-underlying-noonan-syndrome
#4
Luca Pannone, Gianfranco Bocchinfuso, Elisabetta Flex, Cesare Rossi, Giuseppina Baldassarre, Christina Lissewski, Francesca Pantaleoni, Federica Consoli, Francesca Lepri, Monia Magliozzi, Massimiliano Anselmi, Giovanni Sorge, Kadri Karaer, Goran Cuturilo, Alessandro Sartorio, Sigrid Tinschert, Maria Accadia, Maria C Digilio, Giuseppe Zampino, Alessandro De Luca, Hélène Cavé, Martin Zenker, Bruce D Gelb, Bruno Dallapiccola, Lorenzo Stella, Giovanni B Ferrero, Simone Martinelli, Marco Tartaglia
Germline mutations in PTPN11, the gene encoding the Src-homology 2 (SH2) domain-containing protein tyrosine phosphatase (SHP2), cause Noonan syndrome (NS), a relatively common, clinically variable, multisystem disorder. Here, we report on the identification of five different PTPN11 missense changes affecting residues Leu(261) , Leu(262) and Arg(265) in 16 unrelated individuals with clinical diagnosis of NS or with features suggestive for this disorder, specifying a novel disease-causing mutation cluster. Expression of the mutant proteins in HEK293T cells documented their activating role on MAPK signaling...
January 10, 2017: Human Mutation
https://www.readbyqxmd.com/read/28073787/col6a5-variants-in-familial-neuropathic-chronic-itch
#5
Filippo Martinelli-Boneschi, Marina Colombi, Marco Castori, Grazia Devigili, Roberto Eleopra, Rayaz A Malik, Marco Ritelli, Nicoletta Zoppi, Chiara Dordoni, Melissa Sorosina, Paola Grammatico, Hassan Fadavi, Monique M Gerrits, Rowida Almomani, Catharina G Faber, Ingemar S J Merkies, Daniela Toniolo, Massimiliano Cocca, Claudio Doglioni, Stephen G Waxman, Sulayman D Dib-Hajj, Michela M Taiana, Jenny Sassone, Raffaella Lombardi, Daniele Cazzato, Andrea Zauli, Silvia Santoro, Margherita Marchi, Giuseppe Lauria
Itch is thought to represent the peculiar response to stimuli conveyed by somatosensory pathways shared with pain through the activation of specific neurons and receptors. It can occur in association with dermatological, systemic and neurological diseases, or be the side effect of certain drugs. However, some patients suffer from chronic idiopathic itch that is frequently ascribed to psychological distress and for which no biomarker is available to date. We investigated three multigenerational families, one of which diagnosed with joint hypermobility syndrome/Ehlers-Danlos syndrome hypermobility type (JHS/EDS-HT), characterized by idiopathic chronic itch with predominantly proximal distribution...
January 9, 2017: Brain: a Journal of Neurology
https://www.readbyqxmd.com/read/28072960/-novel-compound-heterozygous-tbc1d24-mutations-in-a-boy-with-infantile-focal-myoclonic-epilepsy-and-literature-review
#6
W H Li, S Z Zhou, L M Zhang, X H Wang, Y J Zhang, B B Wu, H J Wang, H W Yang
Objective: To investigate the clinical features and genetic characteristics of patients with TBC1D24 gene mutations. Method: The clinical data of a patient with novel TBC1D24 compound heterozygous mutations from Children's Hospital of Fudan University were collected, the related literature was searched from China National Knowledge Infrastructure, Wanfang Data Knowledge Service Platform, National Center from Biotechnology Information and Pubmed (up to April 2016) by using search terms "TBC1D24" "epilepsy" ...
January 2, 2017: Zhonghua Er Ke za Zhi. Chinese Journal of Pediatrics
https://www.readbyqxmd.com/read/28072499/in-silico-analysis-of-the-deleterious-nssnp-s-missense-in-the-homeobox-domain-of-human-hoxb13-gene-responsible-for-hereditary-prostate-cancer
#7
Gopalakrishnan Chandrasekaran, Eu Chang Hwang, Taek Won Kang, Dongdeuk Kwon, Kwangsung Park, Je-Jung Lee, Vinoth-Kumar Lakshmanan
The human HOXB13 gene encodes a transcription factor containing a DNA-binding homeobox domain and a HoxA13 N-terminal domain. SNP is considered to be the primary genetic cause for hereditary prostate cancer (PCa). The study of functional nsSNP's would give an insight into the exact cause underlying the onset of hereditary PCa and possible methodologies for the cure or early management of the disease. Several in silico tools were used to screen and map the deleterious nsSNP's to the protein structure for predicting the structure-function effects...
January 10, 2017: Chemical Biology & Drug Design
https://www.readbyqxmd.com/read/28063109/mutation-screening-of-ackr3-and-cops8-in-kidney-cancer-cases-from-the-confirm-study
#8
Maryam Mahmoodi, Tu Nguyen-Dumont, Fleur Hammet, Bernard J Pope, Daniel J Park, Melissa C Southey, John M Darlow, Fiona Bruinsma, Ingrid Winship
An apparently balanced t(2;3)(q37.3;q13.2) translocation that appears to segregate with renal cell carcinoma (RCC) has indicated potential areas to search for the elusive genetic basis of clear cell RCC. We applied Hi-Plex targeted sequencing to analyse germline DNA from 479 individuals affected with clear cell RCC for this breakpoint translocation and genetic variants in neighbouring genes on chromosome 2, ACKR3 and COPS8. While only synonymous variants were found in COPS8, one of the missense variants in ACKR3:c...
January 6, 2017: Familial Cancer
https://www.readbyqxmd.com/read/28062663/a-population-based-analysis-of-germline-bap1-mutations-in-melanoma
#9
Sally J O'Shea, Carla Daniela Robles-Espinoza, Lauren McLellan, Jeanine Harrigan, Xavier Jacq, James Hewinson, Vivek Iyer, Will Merchant, Faye Elliott, Mark Harland, D Timothy Bishop, Julia Newton-Bishop, David J Adams
Germline mutation of the BRCA1 associated protein-1 (BAP1) gene has been linked to uveal melanoma, mesothelioma, meningioma, renal cell carcinoma and basal cell carcinoma. Germline variants have also been found in familial cutaneous melanoma pedigrees, but their contribution to sporadic melanoma has not been fully assessed. We sequenced BAP1 in 1,977 melanoma cases and 754 controls and used deubiquitinase assays, a pedigree analysis, and a histopathological review to assess the consequences of the mutations found...
January 5, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28061006/confirmation-of-promise-a-simple-genomics-based-clinical-classifier-for-endometrial-cancer
#10
Aline Talhouk, Melissa K McConechy, Samuel Leung, Winnie Yang, Amy Lum, Janine Senz, Niki Boyd, Judith Pike, Michael Anglesio, Janice S Kwon, Anthony N Karnezis, David G Huntsman, C Blake Gilks, Jessica N McAlpine
BACKGROUND: Classification of endometrial carcinomas (ECs) by morphologic features is irreproducible and imperfectly reflects tumor biology. The authors developed the Proactive Molecular Risk Classifier for Endometrial Cancer (ProMisE), a molecular classification system based on The Cancer Genome Atlas genomic subgroups, and sought to confirm both feasibility and prognostic ability in a new, large cohort of ECs. METHODS: Immunohistochemistry (IHC) for the presence or absence of mismatch repair (MMR) proteins (to identify MMR deficiency [MMR-D]), sequencing for polymerase-ɛ (POLE) exonuclease domain mutations (POLE EDMs), and IHC for tumor protein 53 (p53) (wild type vs null/missense mutations; p53 wt and p53 abn, respectively) were performed on 319 new EC samples...
January 6, 2017: Cancer
https://www.readbyqxmd.com/read/28059152/identification-of-a-novel-missense-mutation-of-mip-in-a-chinese-family-with-congenital-cataracts-by-target-region-capture-sequencing
#11
Bo Jiang, Yanhua Chen, Baisheng Xu, Nan Hong, Rongrong Liu, Ming Qi, Liping Shen
Congenital cataract is both clinically diverse and genetically heterogeneous. To investigate the underlying genetic defect in three-generations of a Chinese family with autosomal dominant congenital cataracts, we recruited family members who underwent comprehensive ophthalmic examinations. A heterozygous missense mutation c.634G > C (p.G212R) substitution was identified in the MIP gene through target region capture sequencing. The prediction results of PolyPhen-2 and SIFT indicated that this mutation was likely to damage the structure and function of MIP...
January 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28057753/a-novel-kleefstra-syndrome-associated-variant-that-affects-the-conserved-tplx-motif-within-the-ankyrin-repeat-of-ehmt1-leads-to-abnormal-protein-folding
#12
Patrick R Blackburn, Alexander Tischer, Michael T Zimmermann, Jennifer L Kemppainen, Sujatha Sastry, Amy E Knight Johnson, Margot A Cousin, Nicole J Boczek, Gavin Oliver, Vinod K Misra, Ralitza H Gavrilova, Gwen A Lomberk, Matthew Auton, Raul A Urrutia, Eric W Klee
Kleefstra syndrome (KS) (MIM# 610253), also known as 9q34 deletion syndrome, is an autosomal dominant disorder caused by haploinsufficiency of euchromatic histone methyltransferase-1 (EHMT1). The clinical phenotype of KS includes moderate to severe intellectual disability with absent speech, hypotonia, brachycephaly, congenital heart defects, and dysmorphic facial features with hypertelorism, synophrys, macroglossia, protruding tongue, and prognathism. Only a few cases of de novo missense mutations in EHMT1 giving rise to KS have been described...
January 5, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28056872/a-limb-girdle-myopathy-phenotype-of-runx2-mutation-in-a-patient-with-cleidocranial-dysplasia-a-case-study-and-literature-review
#13
Sung-Ju Hsueh, Ni-Chung Lee, Shu-Hua Yang, Han-I Lin, Chin-Hsien Lin
BACKGROUND: Cleidocranial dysplasia (CCD) is a rare hereditary disorder that arises from heterozygous loss of function mutations in the runt-related transcription factor 2 (RUNX2) gene. As RUNX2 is mainly expressed in osteoblasts, CCD typically affects the skeletal and dental systems. Few studies have investigated RUNX2 mutation effects on non-skeletal systems. Here, we describe limb-girdle myopathy, an uncommon phenotype of CCD, in a patient with a heterozygous missense mutation (p.R225Q) in the RUNX2 gene...
January 6, 2017: BMC Neurology
https://www.readbyqxmd.com/read/28054173/association-of-ahsg-with-alopecia-and-mental-retardation-apmr-syndrome
#14
M Reza Sailani, Fereshteh Jahanbani, Jafar Nasiri, Mahdiyeh Behnam, Mansoor Salehi, Maryam Sedghi, Majid Hoseinzadeh, Shinichi Takahashi, Amin Zia, Joshua Gruber, Janet Linnea Lynch, Daniel Lam, Juliane Winkelmann, Semira Amirkiai, Baoxu Pang, Shannon Rego, Safoura Mazroui, Jonathan A Bernstein, Michael P Snyder
Alopecia with mental retardation syndrome (APMR) is a very rare autosomal recessive condition that is associated with total or partial absence of hair from the scalp and other parts of the body as well as variable intellectual disability. Here we present whole-exome sequencing results of a large consanguineous family segregating APMR syndrome with seven affected family members. Our study revealed a novel predicted pathogenic, homozygous missense mutation in the AHSG (OMIM 138680) gene (AHSG: NM_001622:exon7:c...
January 4, 2017: Human Genetics
https://www.readbyqxmd.com/read/28051077/fig4-variants-in-central-european-patients-with-amyotrophic-lateral-sclerosis-a-whole-exome-and-targeted-sequencing-study
#15
Alma Osmanovic, Isolde Rangnau, Anne Kosfeld, Susanne Abdulla, Claas Janssen, Bernd Auber, Peter Raab, Matthias Preller, Susanne Petri, Ruthild G Weber
We aimed to identify the genetic cause of the devastating neurodegenerative disease amyotrophic lateral sclerosis (ALS) in a German family with two affected individuals, and to assess the prevalence of variants in the identified risk gene, FIG4, in a central European ALS cohort. Whole-exome sequencing (WES) and an overlapping data analysis strategy were performed in an ALS family with autosomal dominant inheritance and incomplete penetrance. Additionally, 200 central European ALS patients were analyzed using whole-exome or targeted sequencing...
January 4, 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28042953/cervical-small-cell-neuroendocrine-tumor-mutation-profiles-via-whole-exome-sequencing
#16
Soo Young Cho, Minhye Choi, Hyo-Jeong Ban, Chang Hyeon Lee, Soojun Park, HanKyeom Kim, Young-Sik Kim, Young Seek Lee, Ji-Yun Lee
Cervical small cell neuroendocrine tumors (CSCNETs) are rare, aggressive neuroendocrine tumors (NETs). Reliable diagnostic and prognostic CSCNET markers are lacking, making diagnosis and prognosis prediction difficult, and treatment strategies limited. Here we provide mutation profiles for five tumor-normal paired CSCNETs using whole exome sequencing (WES). We expanded our assessment of frequently mutated genes to include publicly available data from 55 small intestine neuroendocrine tumors, 10 pancreatic neuroendocrine tumors, 42 small cell lung cancers, six NET cell lines, and 188 cervical cancers, along with our five CSCNETs...
December 22, 2016: Oncotarget
https://www.readbyqxmd.com/read/28032242/molecular-pathological-study-on-lrrc10-in-sudden-unexplained-nocturnal-death-syndrome-in-the-chinese-han-population
#17
Lei Huang, Shuangbo Tang, Yili Chen, Liyong Zhang, Kun Yin, Yeda Wu, Jinxiang Zheng, Qiuping Wu, Jonathan C Makielski, Jianding Cheng
Sudden unexplained nocturnal death syndrome (SUNDS) is a perplexing disorder to both forensic pathologists and clinic physicians. Clinical features of SUNDS survivors suggested that SUNDS is similar to Brugada syndrome (BrS). Leucine-rich repeat containing 10 (LRRC10) gene was a newly identified gene linked to dilated cardiomyopathy, a disease associated with sudden cardiac death. To investigate the prevalence and spectrum of genetic variants of LRRC10 gene in SUNDS and BrS, the coding regions of LRRC10 were genetically screened in 113 sporadic SUNDS victims (from January 2005 to December 2015, 30...
December 28, 2016: International Journal of Legal Medicine
https://www.readbyqxmd.com/read/28031081/restrictive-cardiomyopathy-resulting-from-a-troponin-i-type-3-mutation-in-a-chinese-family
#18
Yan-Ping Ruan, Chao-Xia Lu, Xiao-Yi Zhao, Rui-Juan Liang, Hui Lian, Michael Routledge, Wei Wu, Xue Zhang, Zhong-Jie Fan
Objective To identify the pathogenic variant responsible for restrictive cardiomyopathy (RCM) in a Chinese family.Methods Next generation sequencing was used for detecting the mutation and Results verified by sequencing. We used restriction enzyme digestion to test the mutation in the family members and 200 unrelated normal subjects without any cardiac inherited diseases when the mutation was identified.Results Five individuals died from cardiac diseases, two of whom suffered from sudden cardiac death. Two individuals have suffered from chronic cardiac disorders...
March 20, 2016: Chinese Medical Sciences Journal, Chung-kuo i Hsüeh K'o Hsüeh Tsa Chih
https://www.readbyqxmd.com/read/28030592/a-novel-missense-mutation-224g-t-r75m-in-sry-coding-region-interferes-with-nuclear-import-and-results-in-46-xy-complete-gonadal-dysgenesis
#19
Wufang Fan, Bei Wang, Shanshan He, Tengfei Zhang, Chenxing Yin, Yunping Chen, Shuqi Zheng, Jixia Zhang, Lin Li
SRY-mutation-caused sex reversal is a rare disease and mostly associated with a de novo mutation since the patients with defective SRY is infertile. There are many reports about SRY-mutation associated 46, XY ovarian disorder of sex development (DSD), but few described their molecular mechanism. Here we report a de novo mutation 224G>T (R75M) in SRY associated with a phenotypic female, 46, XY karyotype and dysgerminoma. The wild and mutated SRY were cloned into recombinant plasmid and expressed in cells in vitro, the result showed the mutated SRY is greatly accumulated in cytoplasm while the wild type SRY is mostly localized in nucleus...
2016: PloS One
https://www.readbyqxmd.com/read/28028996/genetic-profiles-of-korean-patients-with-glucose-6-phosphate-dehydrogenase-deficiency
#20
Jaewoong Lee, Joonhong Park, Hayoung Choi, Jiyeon Kim, Ahlm Kwon, Woori Jang, Hyojin Chae, Myungshin Kim, Yonggoo Kim, Jae Wook Lee, Nack Gyun Chung, Bin Cho
BACKGROUND: We describe the genetic profiles of Korean patients with glucose-6-phosphate dehydrogenase (G6PD) deficiencies and the effects of G6PD mutations on protein stability and enzyme activity on the basis of in silico analysis. METHODS: In parallel with a genetic analysis, the pathogenicity of G6PD mutations detected in Korean patients was predicted in silico. The simulated effects of G6PD mutations were compared to the WHO classes based on G6PD enzyme activity...
March 2017: Annals of Laboratory Medicine
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