Novel high-risk missense mutations identification in FAT4 gene causing Hennekam syndrome and Van Maldergem syndrome 2 through molecular dynamics simulation
Tài liệu tham khảo
Hennekam, 1989, Autosomal recessive intestinal lymphangiectasia and lymphedema, with facial anomalies and mental retardation, Am J Med Genet, 34, 593, 10.1002/ajmg.1320340429
Rao, 2015, Hennekam lymphangiectasia syndrome, Int J Res Med Sci, 3, 516, 10.5455/2320-6012.ijrms20150229
Van Balkom, 2002, Lymphedema-lymphangiectasia-mental retardation (Hennekam) syndrome: a review, Am J Med Genet, 112, 412, 10.1002/ajmg.10707
Erkan, 1998, Syndrome de Hennekam [Hennekam syndrome], Arch Pediatr, 5, 1344, 10.1016/S0929-693X(99)80054-2
Cormier-Daire, 1995, Craniosynostosis and kidney malformation in a case of Hennekam syndrome, Am J Med Genet, 57, 66, 10.1002/ajmg.1320570115
Nişli, 2008, Hennekam sendromlu bir olguda başvuru nedeni olarak perikard efüzyonu [A case of Hennekam syndrome presenting with massive pericardial effusion], Turk Kardiyol Dernegi Arsivi, 36, 325
Musumeci, 2006, Cutaneous manifestations and massive genital involvement in Hennekam syndrome, Pediatr Dermatol, 23, 239, 10.1111/j.1525-1470.2006.00225.x
Bellini, 2003, Hennekam syndrome presenting as nonimmune hydrops fetalis, congenital chylothorax, and congenital pulmonary lymphangiectasia, Am J Med Genet, 120A, 92, 10.1002/ajmg.a.20180
Rockson, 1999, Lymphoscintigraphic manifestations of Hennekam syndrome--a case report, Angiology, 50, 1017, 10.1177/000331979905001207
Al-Gazali, 2003, Further delineation of Hennekam syndrome, Clin Dysmorphol, 12, 227, 10.1097/00019605-200310000-00003
Huppke, 2000, Two brothers with Hennekam syndrome and cerebral abnormalities, Clin Dysmorphol, 9, 21, 10.1097/00019605-200009010-00004
Al Sinani, 2012, Octreotide in Hennekam syndrome-associated intestinal lymphangiectasia, World J Gastroenterol, 18, 6333, 10.3748/wjg.v18.i43.6333
Bellini, 2003, Hennekam syndrome presenting as nonimmune hydrops fetalis, congenital chylothorax, and congenital pulmonary lymphangiectasia, Am J Med Genet, 120, 92, 10.1002/ajmg.a.20180
VanBalkom, 2002, Lymphedema–lymphangiectasia–mental retardation (Hennekam) syndrome: a review, Am J Med Genet, 112, 412, 10.1002/ajmg.10707
Boopathy, 2019, Role of hippo pathway-YAP/TAZ signaling in angiogenesis, Front Cell Dev Biol, 7, 49, 10.3389/fcell.2019.00049
Cha, 2021, A novel role of Hippo-Yap/TAZ signaling pathway in lymphatic vascular development, BMB Rep, 54, 285, 10.5483/BMBRep.2021.54.6.020
Alders, 2009, Mutations in CCBE1 cause generalized lymph vessel dysplasia in humans, Nat Genet, 41, 1272, 10.1038/ng.484
Alders, 2014, Hennekam syndrome can be caused by FAT4 mutations and be allelic to Van Maldergem syndrome, Hum Genet, 133, 1161, 10.1007/s00439-014-1456-y
Brouillard, 2017, Loss of ADAMTS3 activity causes Hennekam lymphangiectasia-lymphedema syndrome 3, Hum Mol Genet, 26, 4095, 10.1093/hmg/ddx297
Shah, 2013, CCBE1 mutation in two siblings, one manifesting lymphedema-cholestasis syndrome, and the other, fetal hydrops, PLoS One, 8, 10.1371/journal.pone.0075770
Hogan, 2009, Ccbe1 is required for embryonic lymphangiogenesis and venous sprouting, Nat Genet, 41, 396, 10.1038/ng.321
Bos, 2011, CCBE1 is essential for mammalian lymphatic vascular development and enhances the lymphangiogenic effect of vascular endothelial growth factor-C in vivo, Circ Res, 109, 486, 10.1161/CIRCRESAHA.111.250738
Sandbank, 2019, Oral and topical sirolimus for vascular anomalies: a multicentre study and review, Acta Derm Venereol, 99, 10.2340/00015555-3262
Mahoney, 1991, The fat tumor suppressor gene in Drosophila encodes a novel member of the cadherin gene superfamily, Cell, 67, 853, 10.1016/0092-8674(91)90359-7
Clark, 1995, Dachsous encodes a member of the cadherin superfamily that controls imaginal disc morphogenesis in Drosophila, Genes Dev, 9, 1530, 10.1101/gad.9.12.1530
Katoh, 2006, Comparative integromics on FAT1, FAT2, FAT3 and FAT4, Int J Mol Med, 18, 523
Tanoue, 2005, New insights into Fat cadherins, J Cell Sci, 118, 2347, 10.1242/jcs.02398
2004, Finishing the euchromatic sequence of the human genome, Nature, 431, 931, 10.1038/nature03001
Dabhi, 2014, In silico analysis of single nucleotide polymorphism (SNP) in human TNF-α gene, Meta Gene, 2, 586, 10.1016/j.mgene.2014.07.005
Barroso, 1999, Dominant negative mutations in human PPARgamma associated with severe insulin resistance, diabetes mellitus and hypertension, Nature, 402, 880, 10.1038/47254
Chasman, 2001, Predicting the functional consequences of non-synonymous single nucleotide polymorphisms: structure-based assessment of amino acid variation, J Mol Biol, 307, 683, 10.1006/jmbi.2001.4510
Lander, 1996, The new genomics: global views of biology, Science, 274, 536, 10.1126/science.274.5287.536
Smith, 1994, Estrogen resistance caused by a mutation in the estrogen-receptor gene in a man [published correction appears in N Engl J Med 1995 Jan 12;332(2):131], N Engl J Med, 331, 1056, 10.1056/NEJM199410203311604
Sherry, 2001, dbSNP: the NCBI database of genetic variation, Nucleic Acids Res, 29, 308, 10.1093/nar/29.1.308
Stenson, 2017, The human gene mutation database: towards a comprehensive repository of inherited mutation data for medical research, genetic diagnosis and next generation sequencing studies, Hum Genet, 136, 665, 10.1007/s00439-017-1779-6
Pinero, 2017, DisGeNET: a comprehensive platform integrating information on human disease-associated genes and variants, Nucleic Acids Res, 45, 10.1093/nar/gkw943
Ng, 2006, Predicting the effects of amino acid substitutions on protein function, Annu Rev Genom Hum Genet, 7, 61, 10.1146/annurev.genom.7.080505.115630
Adzhubei, 2013, Predicting functional effect of human missense mutations using PolyPhen‐2, Curr Protocols Human Genetics, 76, 7, 10.1002/0471142905.hg0720s76
Kumar, 2009, Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm, Nat Protoc, 4, 1073, 10.1038/nprot.2009.86
Li, 2018, VarCards: an integrated genetic and clinical database for coding variants in the human genome, Nucleic Acids Res, 46, D1039, 10.1093/nar/gkx1039
Choi, 2012, Predicting the functional effect of amino acid substitutions and indels, PLoS One, 7, 10.1371/journal.pone.0046688
Hecht, 2015, Better prediction of functional effects for sequence variants, BMC Genom, 16, 1, 10.1186/1471-2164-16-S8-S1
Niroula, 2015, PON-P2: prediction method for fast and reliable identification of harmful variants, PLoS One, 10, 10.1371/journal.pone.0117380
Ferrer-Costa, 2005, PMUT: a web-based tool for the annotation of pathological mutations on proteins, Bioinformatics, 21, 3176, 10.1093/bioinformatics/bti486
Calabrese, 2009, Functional annotations improve the predictive score of human disease-related mutations in proteins, Hum Mutat, 30, 1237, 10.1002/humu.21047
Tang, 2016, PANTHER-PSEP: predicting disease-causing genetic variants using position-specific evolutionary preservation, Bioinformatics, 32, 2230, 10.1093/bioinformatics/btw222
Bendl, 2014, PredictSNP: robust and accurate consensus classifier for prediction of disease-related mutations, PLoS Comput Biol, 10, 10.1371/journal.pcbi.1003440
Apweiler, 2001, The InterPro database, an integrated documentation resource for protein families, domains and functional sites, Nucleic Acids Res, 29, 37, 10.1093/nar/29.1.37
Warde-Farley, 2010, The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function, Nucleic Acids Res, 38, W214, 10.1093/nar/gkq537
Capriotti, 2005, I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure, Nucleic Acids Res, 33, 10.1093/nar/gki375
Cheng, 2006, Prediction of protein stability changes for single-site mutations using support vector machines, Proteins, 62, 1125, 10.1002/prot.20810
Källberg, 2012, Template-based protein structure modeling using the RaptorX web server, Nat Protoc, 7, 1511, 10.1038/nprot.2012.085
Yang, 2013, Protein-ligand binding site recognition using complementary binding-specific substructure comparison and sequence profile alignment, Bioinformatics, 29, 2588, 10.1093/bioinformatics/btt447
Yang, 2013, BioLiP: a semi-manually curated database for biologically relevant ligand-protein interactions, Nucleic Acids Res, 41, D1096
Ashkenazy, 2016, Ben-Tal N. ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules, Nucleic Acids Res, 44, W344, 10.1093/nar/gkw408
Venselaar, 2010, Protein structure analysis of mutations causing inheritable diseases. An e-Science approach with life scientist friendly interfaces, BMC Bioinf, 11, 548, 10.1186/1471-2105-11-548
Geourjon, 1995, SOPMA: significant improvements in protein secondary structure prediction by consensus prediction from multiple alignments, Comput Appl Biosci, 11, 681
Deng, 2017, Computational prediction of methylation types of covalently modified lysine and arginine residues in proteins, Briefings Bioinf, 18, 647
Blom, 1999, Sequence and structure-based prediction of eukaryotic protein phosphorylation sites, J Mol Biol, 294, 1351, 10.1006/jmbi.1999.3310
Radivojac, 2010, Identification, analysis, and prediction of protein ubiquitination sites, Proteins, 78, 365, 10.1002/prot.22555
Zhao, 2014, GPS-SUMO: a tool for the prediction of sumoylation sites and SUMO-interaction motifs, Nucleic Acids Res, 42, W325, 10.1093/nar/gku383
Kelley, 2015, The Phyre2 web portal for protein modeling, prediction and analysis, Nat Protoc, 10, 845, 10.1038/nprot.2015.053
Wang, 2016, RaptorX-Property: a web server for protein structure property prediction, Nucleic Acids Res, 44, W430, 10.1093/nar/gkw306
Yang, 2015, Protein structure and function prediction using I-TASSER, Curr Protoc Bioinformatics, 52
Benkert, 2011, Toward the estimation of the absolute quality of individual protein structure models, Bioinformatics, 27, 343, 10.1093/bioinformatics/btq662
Wiederstein, 2007, ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins, Nucleic Acids Res, 35, 10.1093/nar/gkm290
Laskowski, 1993, Procheck - a program to check the stereochemical quality of protein structures, J. App. Cryst., 26, 283, 10.1107/S0021889892009944
Bowers, 2006
Ferreira, 2015, Molecular docking and structure-based drug design strategies, Molecules, 20, 13384, 10.3390/molecules200713384
Hildebrand, 2019, Bringing molecular dynamics simulation data into view, Trends Biochem Sci, 44, 902, 10.1016/j.tibs.2019.06.004
Rasheed, 2021, Identification of lead compounds against Scm (fms10) in Enterococcus faecium using computer aided drug designing, Life, 11, 10.3390/life11020077
Shivakumar, 2010, Prediction of absolute solvation free energies using molecular dynamics free energy perturbation and the OPLS force field, J Chem Theor Comput, 6, 1509, 10.1021/ct900587b
Maiorov, 1994, Significance of root-mean-square deviation in comparing three-dimensional structures of globular proteins, J Mol Biol, 235, 625, 10.1006/jmbi.1994.1017
El Khatabi, 2022
Shinwari, 2022, Novel disease-associated missense single-nucleotide polymorphisms variants predication by algorithms tools and molecular dynamics simulation of human TCIRG1 gene causing congenital neutropenia and osteopetrosis, Front Mol Biosci, 9, 10.3389/fmolb.2022.879875
Pedersen, 2021, Effective variant filtering and expected candidate variant yield in studies of rare human disease, NPJ Genomic Med, 6, 60, 10.1038/s41525-021-00227-3
Venselaar, 2010, Protein structure analysis of mutations causing inheritable diseases. An e-Science approach with life scientist friendly interfaces, BMC Bioinf, 11, 548, 10.1186/1471-2105-11-548
AbdulAzeez, 2016, In-silico computing of the most deleterious nsSNPs in HBA1 gene, PLoS One, 11, 10.1371/journal.pone.0147702
Abdulazeez, 2019, The rs61742690 (S783N) single nucleotide polymorphism is a suitable target for disrupting BCL11A-mediated foetal-to-adult globin switching, PLoS One, 14, 10.1371/journal.pone.0212492
Khafizov, 2015, Computational approaches to study the effects of small genomic variations, J Mol Model, 21, 251, 10.1007/s00894-015-2794-y
Kucukkal, 2015, Structural and physico-chemical effects of disease and non-disease nsSNPs on proteins, Curr Opin Struct Biol, 32, 18, 10.1016/j.sbi.2015.01.003
Takano, 2012, An X-linked channelopathy with cardiomegaly due to a CLIC2 mutation enhancing ryanodine receptor channel activity, Hum Mol Genet, 21, 4497, 10.1093/hmg/dds292
Hsu, 2008, Two distinct Omp85 paralogs in the chloroplast outer envelope membrane are essential for embryogenesis in Arabidopsis thaliana, Plant Signal Behav, 3, 1134, 10.4161/psb.3.12.7095
Vihinen, 1987, Relationship of protein flexibility to thermostability, Protein Eng, 1, 477, 10.1093/protein/1.6.477
Bond, 2010, Gene repression by minimal lac loops in vivo, Nucleic Acids Res, 38, 8072, 10.1093/nar/gkq755
Dai, 2010, p53 post-translational modification: deregulated in tumorigenesis, Trends Mol Med, 16, 528, 10.1016/j.molmed.2010.09.002
Shiloh, 2013, The ATM protein kinase: regulating the cellular response to genotoxic stress, and more, Nat Rev Mol Cell Biol, 14, 197, 10.1038/nrm3546
Deutscher, 2005, Ser/Thr/Tyr protein phosphorylation in bacteria - for long time neglected, now well established, J Mol Microbiol Biotechnol, 9, 125
Puttick, 2008, Histidine phosphorylation in biological systems, Biochim Biophys Acta, 1784, 100, 10.1016/j.bbapap.2007.07.008
Cieśla, 2011, Phosphorylation of basic amino acid residues in proteins: important but easily missed, Acta Biochim Pol, 58, 137, 10.18388/abp.2011_2258
Sawicka, 2014, Sensing core histone phosphorylation - a matter of perfect timing, Biochim Biophys Acta, 1839, 711, 10.1016/j.bbagrm.2014.04.013
Gallo, 2017, The importance of regulatory ubiquitination in cancer and metastasis, Cell Cycle, 16, 634, 10.1080/15384101.2017.1288326
Essadssi, 2019, Computational analysis of nsSNPs of ADA gene in severe combined immunodeficiency using molecular modeling and dynamics simulation, J Immunol Res, 10.1155/2019/5902391
Zhang, 2020, In silico analysis of non-synonymous single nucleotide polymorphisms (nsSNPs) in the human GJA3 gene associated with congenital cataract, BMC Mol Cell Biol, 21, 12, 10.1186/s12860-020-00252-7
Shinwari, 2021, Predicting the most deleterious missense nonsynonymous single-nucleotide polymorphisms of Hennekam syndrome-causing CCBE1 gene, in silico analysis, Sci World J, 10.1155/2021/6642626