UMD‐DYSF, a novel locus specific database for the compilation and interactive analysis of mutations in the dysferlin gene

Mutations in the dysferlin gene (DYSF) lead to a complete or partial absence of the dysferlin protein in skeletal muscles and are at the origin of dysferlinopathies, a heterogeneous group of rare autosomal recessive inherited neuromuscular disorders. As a step towards a better understanding of the DYSF mutational spectrum, and towards possible inclusion of patients in future therapeutic clinical trials, we set up the Universal Mutation Database for Dysferlin (UMD‐DYSF), a Locus‐Specific Database developed with the UMD® software. The main objective of UMD‐DYSF is to provide an updated compilation of mutational data and relevant interactive tools for the analysis of DYSF sequence variants, for diagnostic and research purposes. In particular, specific algorithms can facilitate the interpretation of newly identified intronic, missense‐ or isosemantic‐exonic sequence variants, a problem encountered recurrently during genetic diagnosis in dysferlinopathies. UMD‐DYSF v1.0 is freely accessible at www.umd.be/DYSF/. It contains a total of 742 mutational entries corresponding to 266 different disease‐causing mutations identified in 558 patients worldwide diagnosed with dysferlinopathy. This article presents for the first time a comprehensive analysis of the dysferlin mutational spectrum based on all compiled DYSF disease‐causing mutations reported in the literature to date, and using the main bioinformatics tools offered in UMD‐DYSF. ©2011 Wiley‐Liss, Inc. Hum Mutat 33:E2317–E2331, 2012. © 2012 Wiley Periodicals, Inc.

[1]  I. Richard,et al.  A Naturally Occurring Human Minidysferlin Protein Repairs Sarcolemmal Lesions in a Mouse Model of Dysferlinopathy , 2010, Science Translational Medicine.

[2]  J. Beckmann,et al.  Muscular dystrophy due to dysferlin deficiency in Libyan Jews. Clinical and genetic features. , 2000, Brain : a journal of neurology.

[3]  V. Mouly,et al.  Therapeutic exon ‘switching’ for dysferlinopathies? , 2010, European Journal of Human Genetics.

[4]  M. Baiget,et al.  Distal anterior compartment myopathy: A dysferlin mutation causing a new muscular dystrophy phenotype , 2001, Annals of neurology.

[5]  P. Lai,et al.  Identification and characterisation of human dysferlin transcript variants: implications for dysferlin mutational screening and isoforms , 2009, Human Genetics.

[6]  Y. Itoyama,et al.  Dysferlin mutations in Japanese Miyoshi myopathy , 2003, Neurology.

[7]  T. Maisonobe,et al.  Complete fatty degeneration of lumbar erector spinae muscles caused by a primary dysferlinopathy , 2008, Muscle & nerve.

[8]  C. Paradas,et al.  Symptomatic dysferlin gene mutation carriers: Characterization of two cases , 2007, Neurology.

[9]  C. Paradas,et al.  Dysferlin expression in monocytes: A source of mRNA for mutation analysis , 2007, Neuromuscular Disorders.

[10]  S. Salani,et al.  Clinical, molecular, and protein correlations in a large sample of genetically diagnosed Italian limb girdle muscular dystrophy patients , 2008, Human mutation.

[11]  G. Butler-Browne,et al.  Efficient bypass of mutations in dysferlin deficient patient cells by antisense‐induced exon skipping , 2010, Human mutation.

[12]  E. Leshinsky‐Silver,et al.  Dysferlinopathy in the Jews of the Caucasus: A frequent mutation in the dysferlin gene , 2007, Neuromuscular Disorders.

[13]  K. Bushby,et al.  Late onset in dysferlinopathy widens the clinical spectrum , 2008, Neuromuscular Disorders.

[14]  Peer Bork,et al.  SMART 6: recent updates and new developments , 2008, Nucleic Acids Res..

[15]  C. Béroud,et al.  Dysferlin mutations in LGMD2B, Miyoshi myopathy, and atypical dysferlinopathies , 2005, Human mutation.

[16]  S. Salani,et al.  Developmental and tissue‐specific regulation of a novel dysferlin isoform , 2004, Muscle and Nerve.

[17]  C. Paradas,et al.  A new phenotype of dysferlinopathy with congenital onset , 2009, Neuromuscular Disorders.

[18]  M. Baiget,et al.  Identification of a novel founder mutation in the DYSF gene causing clinical variability in the Spanish population. , 2005, Archives of neurology.

[19]  Jorge Oliveira,et al.  Private dysferlin exon skipping mutation (c.5492G>A) with a founder effect reveals further alternative splicing involving exons 49–51 , 2010, Journal of Human Genetics.

[20]  K. Bushby,et al.  Characterisation of the dysferlin skeletal muscle promoter , 2004, European Journal of Human Genetics.

[21]  Identification of different genomic deletions and one duplication in the dysferlin gene using multiplex ligation-dependent probe amplification and genomic quantitative PCR. , 2009, Genetic testing and molecular biomarkers.

[22]  J. Beckmann,et al.  Muscular dystrophy due to dysferlin deficiency in , 2000 .

[23]  Pieter J. de Jong,et al.  Dysferlin, a novel skeletal muscle gene, is mutated in Miyoshi myopathy and limb girdle muscular dystrophy , 1998, Nature Genetics.

[24]  N. Bresolin,et al.  Molecular analysis of LGMD-2B and MM patients: identification of novel DYSF mutations and possible founder effect in the Italian population , 2003, Neuromuscular Disorders.

[25]  J. Watson,et al.  Solution structure of the inner DysF domain of myoferlin and implications for limb girdle muscular dystrophy type 2b. , 2008, Journal of molecular biology.

[26]  B. Hyman,et al.  Dysferlin Interacts with Annexins A1 and A2 and Mediates Sarcolemmal Wound-healing* , 2003, Journal of Biological Chemistry.

[27]  L. Holm,et al.  The Pfam protein families database , 2005, Nucleic Acids Res..

[28]  H. Schulz,et al.  Dysfunction of dysferlin-deficient hearts , 2007, Journal of Molecular Medicine.

[29]  Gabor Matyas,et al.  Update of the UMD‐FBN1 mutation database and creation of an FBN1 polymorphism database , 2003, Human mutation.

[30]  C. Greenberg,et al.  Identical mutation in patients with limb girdle muscular dystrophy type 2B or Miyoshi myopathy suggests a role for modifier gene(s). , 1999, Human molecular genetics.

[31]  I. Nishino,et al.  Asymptomatic sporadic dysferlinopathy presenting with elevation of serum creatine kinase. Typical distribution of muscle involvement shown by MRI but not by CT. , 2008, Internal medicine.

[32]  C. Béroud,et al.  A new locus‐specific database (LSDB) for mutations in the TGFBR2 gene: UMD‐TGFBR2 , 2008, Human mutation.

[33]  J. Beckmann,et al.  Genomic organization of the dysferlin gene and novel mutations in Miyoshi myopathy , 2001, Neurology.

[34]  S. Antonarakis,et al.  Mutation nomenclature extensions and suggestions to describe complex mutations: A discussion , 2000 .

[35]  I. Nonaka,et al.  Protein and gene analyses of dysferlinopathy in a large group of Japanese muscular dystrophy patients , 2003, Journal of the Neurological Sciences.

[36]  K. Bushby,et al.  Limb-girdle muscular dystrophy: A follow-up study of 79 patients , 1996, Neuromuscular Disorders.

[37]  Thierry Soussi,et al.  UMD (Universal Mutation Database): 2005 update , 2005, Human mutation.

[38]  N. Lévy,et al.  Novel ancestral Dysferlin splicing mutation which migrated from the Iberian peninsula to South America , 2011, Neuromuscular Disorders.

[39]  K. Bushby,et al.  Dysferlin‐deficient muscular dystrophy features amyloidosis , 2008, Annals of neurology.

[40]  C. Béroud,et al.  Human Splicing Finder: an online bioinformatics tool to predict splicing signals , 2009, Nucleic acids research.

[41]  T. Kumamoto,et al.  Clinical heterogeneity in dysferlinopathy. , 2002, Internal medicine.

[42]  E. Birney,et al.  Pfam: the protein families database , 2013, Nucleic Acids Res..

[43]  D. Figarella-Branger,et al.  Phenotypic study in 40 patients with dysferlin gene mutations: high frequency of atypical phenotypes. , 2007, Archives of neurology.

[44]  J. Beckmann,et al.  A gene related to Caenorhabditis elegans spermatogenesis factor fer-1 is mutated in limb-girdle muscular dystrophy type 2B , 1998, Nature Genetics.

[45]  I. Illa,et al.  A novel, blood‐based diagnostic assay for limb girdle muscular dystrophy 2B and miyoshi myopathy , 2002, Annals of neurology.

[46]  C. Béroud,et al.  Analysis of the DYSF mutational spectrum in a large cohort of patients , 2009, Human mutation.

[47]  C Béroud,et al.  UMD (Universal Mutation Database): A generic software to build and analyze locus‐specific databases , 2000, Human mutation.

[48]  N. Lévy,et al.  Twenty-two year follow-up of an Indian family with dysferlinopathy-clinical, immunocytochemical, western blotting and genetic features. , 2008, Neurology India.

[49]  Christophe Béroud,et al.  UMD‐predictor, a new prediction tool for nucleotide substitution pathogenicity—application to four genes: FBN1, FBN2, TGFBR1, and TGFBR2 , 2009, Human mutation.

[50]  Matthew Mort,et al.  The Human Gene Mutation Database: providing a comprehensive central mutation database for molecular diagnostics and personalised genomics , 2009, Human Genomics.

[51]  Robert H. Brown,et al.  Membrane blebbing as an assessment of functional rescue of dysferlin-deficient human myotubes via nonsense suppression. , 2010, Journal of applied physiology.

[52]  M. Sinnreich,et al.  Mutation impact on dysferlin inferred from database analysis and computer-based structural predictions , 2006, Journal of the Neurological Sciences.

[53]  Mary Goldman,et al.  The UCSC Genome Browser database: extensions and updates 2011 , 2011, Nucleic Acids Res..

[54]  J. T. Dunnen,et al.  Therapeutic exon skipping for dysferlinopathies? , 2010, European Journal of Human Genetics.

[55]  S. Takeda,et al.  Identification and characterization of a novel human dysferlin transcript: dysferlin_v1 , 2006, Human Genetics.

[56]  K. Bushby Dysferlin and muscular dystrophy. , 2000, Acta neurologica Belgica.

[57]  M. Vorgerd,et al.  Variable reduction of caveolin-3 in patients with LGMD2B/MM , 2003, Journal of Neurology.

[58]  Chien-Chang Chen,et al.  Defective membrane repair in dysferlin-deficient muscular dystrophy , 2003, Nature.

[59]  K. Bushby,et al.  New aspects on patients affected by dysferlin deficient muscular dystrophy , 2009, Journal of Neurology, Neurosurgery & Psychiatry.

[60]  K. Bushby,et al.  Limb‐girdle muscular dystrophies – from genetics to molecular pathology , 2004, Neuropathology and applied neurobiology.