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Nucleotide collagen - DOC


Nucleotide collagen

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									                                    SUPPLEMENTARY TABLE 4. Splicing defects in COL1A2
     Nucleotide                                               Phenotype b                                        Unpublished
      Change a         IVS location     Transcript Change Lethal Non-Lethal       References              (personal communications)
     g.8927A>G         IVS5-2A>G             multiple             EDSVIIB (Byers, et al., 1997)
     g.8927A>G         IVS5-2A>G       Skips 1st 15bp exon 6      EDSVIIB                                 Marini, Cabral and Pals
     g.8928G>A          IVS5-1>A             multiple             EDSVIIB (Byers, et al., 1997)
     g.8928G>C          IVS5-1G>C       cryptic site +14 e6       EDSVIIB (Chiodo, et al., 1992)
     g.8982G>A           8982G>A           Skips exon 6           EDSVIIB (Weil, et al., 1989)
     g.8982G>A           8982G>A           Skips exon 6           EDSVIIB (Byers, et al., 1997)
     g.8983G>A         IVS6+1G>A           Skips exon 6           EDSVIIB (Weil, et al., 1990)
     g.8983G>A         IVS6+1G>A           Skips exon 6           EDSVIIB (Vasan, et al., 1991)
     g.8983G>A         IVS6+1G>A           Skips exon 6           EDSVIIB (Nicholls, et al., 1991)
     g.8983G>A         IVS6+1G>A           Skips exon 6           EDSVIIB (Watson, et al., 1992)
     g.8983G>A         IVS6+1G>A           Skips exon 6           EDSVIIB (Lehmann, et al., 1994)
     g.8983G>A         IVS6+1G>A           Skips exon 6           EDSVIIB (Giunta, et al., 1999)
     g.8983G>T         IVS6+1G>T           Skips exon 6           EDSVIIB (Byers, et al., 1997)
     g.8983G>T         IVS6+1G>T           Skips exon 6           EDSVIIB (Byers, et al., 1997)
     g.8983G>T         IVS6+1G>T           Skips exon 6           EDSVIIB (Nicholls, et al., 2000)
     g.8984T>C         IVS6+2T>C           Skips exon 6           EDSVIIB (Weil, et al., 1988)
     g.8984T>C         IVS6+2T>C           Skips exon 6           EDSVIIB (Ho, et al., 1994)
     g.8984T>C         IVS6+2T>C           Skips exon 6           EDSVIIB (Giunta, et al., 1999)
    g.12256G>T         IVS9+1G>T           Skips exon 9              IV                 Byers
 g.12258_12268del11   IVS9+3^13del11       Skips exon 9            OI/EDS    (Nicholls, et al., 1992)
g.12259_12262delAGTA IVS9+4^7delAGTA       Skips exon 9              IV                                   Byers
    g.12260G>A         IVS9+5G>A           Skips exon 9            OI/EDS    (Feshchenko, et al., 1998)
    g.12256G>A         IVS9+5G>A           Skips exon 9            OI/EDS                                 Byers
   g.12260G>A          IVS9+5G>A        more complex?          IV                                  Byers
    g.12561G>C          IVS9-1G>C                            OI/EDS                                Hyland and Prockop
g.13031_13050del20   13031_13050del20   Skips exon 11        OI/EDS   (Kuivaniemi, et al., 1988)
   g.13668T>G          IVS12+2T>G       Skips exon 12          IV     (Chipman, et al., 1992)
g.13667_13685del19   IVS12+1^19del19    Skips exon 12          IV                                  Byers
   g.15214T>A          IVS12-3T>A                              IV     (Ward, et al., 2001)
g.15265_15283del19   IVS13+4^22del19    Skips exon 13          I      (Zhuang, et al., 1993)
   g.15607G>A          IVS14+1G>A       Skips exon 14          I                                   Korkko and Prockop
   g.15608T>C          IVS14+2T>C       Skips exon 14          IV                                  Byers
   g.15608T>A          IVS14+2T>A       Skips exon 14          IV                                  Byers
   g.16138A>G          IVS15-2A>G       Skips exon 16          IV                                  Byers
   g.16194G>A          IVS16+1G>A       Skips exon 16          IV     (Filie, et al., 1993)
   g.16194G>T          IVS16+1G>T       Skips exon 16          IV     (Ward, et al., 2001)
   g.16195T>C          IVS16+2T>C       Skips exon 16        III/IV   (Zolezzi, et al., 1995)
   g.16195T>A          IVS16+2T>A       Skips exon 16          I                                   Korkko and Prockop
   g.17611G>C          IVS19-1G>C       Skips exon 20          I      (Mottes, et al., 1994)
                                                                      (Superti-Furga, et al.,
g.17900_17938del39   IVS21+2^40del39    Skips exon 21          I      1993)
   g.17903G>A          IVS21+5G>A       Skips exon 21          I      (Nicholls, et al., 1996)
   g.17903G>C          IVS21+5G>C       Skips exon 21          IV                                  Byers
   g.17903G>A          IVS21+5G>A       Skips exon 21          IV                                  Byers
       ND                  ND           Skips exon 26          IV     (Wenstrup, et al., 1990)
   g.20451G>C          IVS25-1G>C       Skips exon 26          III                                 Lund
   g.20508A>G          IVS26+3A>G       Skips exon 26          IV     (Zolezzi, et al., 1997)
                                                                      (Tromp and Prockop,
   g.21261A>G          IVS27-2A>G       Skips exon 28   II            1988)
       ND                  ND           Skips exon 30   II                                         Nuytinck and De Paepe
      g.22641G>A              IVS30+1G>A              Skips exon 30          II                                            Byers
                                                  del32, ins last 6nt IVS                       (Kuslich and Byers,
      g.25198G>A              IVS32+1G>A                    32                        III/IV    2000)
      g.25198G>A              IVS32+1G>A              Skips exon 32          II                                            Byers
      g.25924A>G              IVS33+4A>G          first 18 nt ins IVS33                IV       (Wenstrup, et al., 1993)
      g.25925G>A              IVS33+5G>A              Skips exon 33          II                 (Ganguly, et al., 1991)
          ND                      ND                  Skips exon 34          II                                            Cohn, King and Krakow
g.27647T>A;27649A>C IVS35+6T>A;+8A>C                Skips exon 35                    III                                 De Paepe
      g.27801T>C              IVS36+2T>C              Skips exon 36                    III                                 Korkko and Prockop
      g.28004G>T              IVS37+1G>T              Skips exon 37          II                                            Byers
      g.28363A>G              IVS37-2A>G          del38 + cryptic site?                IV                                  Byers
      g.30439G>A              IVS40+5G>A            del last 66nt e40        II                 (Ward, et al., 2001)
      g.32424T>G              IVS41-3T>G              Skips exon 42          II                                            Byers
      g.32974G>A              IVS43+1G>A            del43, ins IVS 43                  IV                                  Byers
      g.32974G>A              IVS43+1G>A              Skips exon 43                    IV                                  De Paepe
      g.32974G>A              IVS43+1G>A              Skips exon 43                    IV                                  Cohn, King and Krakow
      g.32974G>A              IVS43+1G>A                                               IV       (Hartikka, et al., 2004)
          ND                      ND                  Skips exon 47          II                                            Cohn, King and Krakow
      g.34370G>C              IVS47+5G>C              Skips exon 47          II                                            Korkko and Prockop
The Nucleotide changes: described at the genomic level. Numbered from the first base of the transcript.
Phenotype: is based on the callsification proposed by Sillence (Sillence, et al., 1979).
ND=mutation detected only at mRNA level.

Byers PH, Duvic M, Atkinson M, Robinow M, Smith LT, Krane SM, Greally MT, Ludman M, Matalon R, Pauker S and others. 1997.
        Ehlers-Danlos syndrome type VIIA and VIIB result from splice-junction mutations or genomic deletions that involve exon 6 in
        the COL1A1 and COL1A2 genes of type I collagen. Am J Med Genet 72:94-105.
Chiodo AA, Hockey A, Cole WG. 1992. A base substitution at the splice acceptor site of intron 5 of the COL1A2 gene activates a
        cryptic splice site within exon 6 and generates abnormal type I procollagen in a patient with Ehlers-Danlos syndrome type VII.
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Chipman SD, Shapiro JR, McKinstry MB, Stover ML, Branson P, Rowe DW. 1992. Expression of mutant  (I)-procollagen in
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Feshchenko S, Brinckmann J, Lehmann HW, Koch HG, Muller PK, Kugler S. 1998. Identification of a new heterozygous point
        mutation in the COL1A2 gene leading to skipping of exon 9 in a patient with joint laxity, hyperextensibility of skin and blue
        sclerae. Mutations in brief no. 166. Online. Hum Mutat 12:138.
Filie JD, Orrison BM, Wang Q, Lewis MB, Marini JC. 1993. A de novo G+1-->A mutation at the 2(I) exon 16 splice donor site
        causes skipping of exon 16 in the cDNA of one allele of an OI type IV proband. Hum Mutat 2:380-8.
Ganguly A, Baldwin CT, Strobel D, Conway D, Horton W, Prockop DJ. 1991. Heterozygous mutation in the G+5 position of intron
        33 of the pro-2(I) gene (COL1A2) that causes aberrant RNA splicing and lethal osteogenesis imperfecta. Use of carbodiimide
        methods that decrease the extent of DNA sequencing necessary to define an unusual mutation. J Biol Chem 266:12035-40.
Giunta C, Superti-Furga A, Spranger S, Cole WG, Steinmann B. 1999. Ehlers-Danlos syndrome type VII: clinical features and
        molecular defects. J Bone Joint Surg Am 81:225-38.
Hartikka H, Kuurila K, Korkko J, Kaitila I, Grenman R, Pynnonen S, Hyland JC, Ala-Kokko L. 2004. Lack of correlation between the
        type of COL1A1 or COL1A2 mutation and hearing loss in osteogenesis imperfecta patients. Hum Mutat 24:147-54.
Ho KK, Kong RY, Kuffner T, Hsu LH, Ma L, Cheah KS. 1994. Further evidence that the failure to cleave the aminopropeptide of type
        I procollagen is the cause of Ehlers-Danlos syndrome type VII. Hum Mutat 3:358-64.
Kuivaniemi H, Sabol C, Tromp G, Sippola-Thiele M, Prockop DJ. 1988. A 19-base pair deletion in the pro-2(I) gene of type I
        procollagen that causes in-frame RNA splicing from exon 10 to exon 12 in a proband with atypical osteogenesis imperfecta
        and in his asymptomatic mother. J Biol Chem 263:11407-13.
Kuslich CD, Byers PH. An IVS32+1G>A mutation in a type I collagen gene, COL1A2, results in use of a rare AT/AC splice system
        and may ameliorate the osteogenesis imperfecta phenotype caused by exon-skipping; 2000; ASHG Conference, Philadelphia,
        Pennsylvania. p 196.
Lehmann HW, Mundlos S, Winterpacht A, Brenner RE, Zabel B, Muller PK. 1994. Ehlers-Danlos syndrome type VII: phenotype and
        genotype. Arch Dermatol Res 286:425-8.
Mottes M, Sangalli A, Valli M, Forlino A, Gomez-Lira M, Antoniazzi F, Constantinou-Deltas CD, Cetta G, Pignatti PF. 1994. A base
        substitution at IVS-19 3'-end splice junction causes exon 20 skipping in pro 2(I) collagen mRNA and produces mild
        osteogenesis imperfecta. Hum Genet 93:681-7.
Nicholls AC, Oliver J, McCarron S, Winter GB, Pope FM. 1996. Splice site mutation causing deletion of exon 21 sequences from the
        pro 2(I) chain of type I collagen in a patient with severe dentinogenesis imperfecta but very mild osteogenesis imperfecta.
        Hum Mutat 7:219-27.
Nicholls AC, Oliver J, Renouf DV, Heath DA, Pope FM. 1992. The molecular defect in a family with mild atypical osteogenesis
        imperfecta and extreme joint hypermobility: exon skipping caused by an 11-bp deletion from an intron in one COL1A2 allele.
        Hum Genet 88:627-33.
Nicholls AC, Oliver J, Renouf DV, McPheat J, Palan A, Pope FM. 1991. Ehlers-Danlos syndrome type VII: a single base change that
        causes exon skipping in the type I collagen  2(I) chain. Hum Genet 87:193-8.
Nicholls AC, Sher JL, Wright MJ, Oley C, Mueller RF, Pope FM. 2000. Clinical phenotypes and molecular characterisation of three
        patients with Ehlers-Danlos syndrome type VII. J Med Genet 37:E33.
Sillence DO, Rimoin DL, Danks DM. 1979. Clinical variability in osteogenesis imperfecta-variable expressivity or genetic
        heterogeneity. Birth Defects Orig Artic Ser 15:113-29.
Superti-Furga A, Raghunath M, Pistone FM, Romano C, Steinmann B. 1993. An intronic deletion leading to skipping of exon 21 of
        COL1A2 in a boy with mild osteogenesis imperfecta. Connect Tissue Res 29:31-40.
Tromp G, Prockop DJ. 1988. Single base mutation in the pro  2(I) collagen gene that causes efficient splicing of RNA from exon 27
        to exon 29 and synthesis of a shortened but in-frame pro  2(I) chain. Proc Natl Acad Sci U S A 85:5254-8.
Vasan NS, Kuivaniemi H, Vogel BE, Minor RR, Wootton JA, Tromp G, Weksberg R, Prockop DJ. 1991. A mutation in the pro 2(I)
        gene (COL1A2) for type I procollagen in Ehlers-Danlos syndrome type VII: evidence suggesting that skipping of exon 6 in
        RNA splicing may be a common cause of the phenotype. Am J Hum Genet 48:305-17.
Ward LM, Lalic L, Roughley PJ, Glorieux FH. 2001. Thirty-three novel COL1A1 and COL1A2 mutations in patients with
        osteogenesis imperfecta types I-IV. Hum Mutat 17:434.
Watson RB, Wallis GA, Holmes DF, Viljoen D, Byers PH, Kadler KE. 1992. Ehlers Danlos syndrome type VIIB. Incomplete
        cleavage of abnormal type I procollagen by N-proteinase in vitro results in the formation of copolymers of collagen and
        partially cleaved pNcollagen that are near circular in cross-section. J Biol Chem 267:9093-100.
Weil D, Bernard M, Combates N, Wirtz MK, Hollister DW, Steinmann B, Ramirez F. 1988. Identification of a mutation that causes
       exon skipping during collagen pre-mRNA splicing in an Ehlers-Danlos syndrome variant. J Biol Chem 263:8561-4.
Weil D, D'Alessio M, Ramirez F, Eyre DR. 1990. Structural and functional characterization of a splicing mutation in the pro- 2(I)
       collagen gene of an Ehlers-Danlos type VII patient. J Biol Chem 265:16007-11.
Weil D, D'Alessio M, Ramirez F, Steinmann B, Wirtz MK, Glanville RW, Hollister DW. 1989. Temperature-dependent expression of
       a collagen splicing defect in the fibroblasts of a patient with Ehlers-Danlos syndrome type VII. J Biol Chem 264:16804-9.
Wenstrup R, Shrago A, Phillips CL, Byers PH, Cohn D. 1990. Osteogenesis Imperfecta Type IV analysis for mutations in  -2(I) of
       type I collagen by specific -2(I) cDNA synthesis and polymerase chain-reaction. Annal NY Acad Sci 580:546-8.
Wenstrup RJ, Lever LW, Phillips CL, Quarles LD. 1993. Mutations in the COL1A2 gene of type I collagen that result in nonlethal
       forms of osteogenesis imperfecta. Am J Med Genet 45:228-32.
Zhuang J, Tromp G, Kuivaniemi H, Nakayasu K, Prockop DJ. 1993. Deletion of 19 base pairs in intron 13 of the gene for the pro 
       2(I) chain of type-I procollagen (COL1A2) causes exon skipping in a proband with type-I osteogenesis imperfecta. Hum Genet
Zolezzi F, Forlino A, Mottes M, Valli M, Sensi A, Calzolari E, Pignatti PF, Cetta G. 1995. A 931 + 2T-->C transition in one COL1A2
       allele causes exon 16 skipping in PRO  2(I) mRNA and produces moderately severe OI. Hum Mutat 6:268-71.
Zolezzi F, Valli M, Clementi M, Mammi I, Cetta G, Pignatti PF, Mottes M. 1997. Mutation producing alternative splicing of exon 26
       in the COL1A2 gene causes type IV osteogenesis imperfecta with intrafamilial clinical variability. Am J Med Genet 71:366-

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