Table 3 of Scavello, Mol Vis 2005; 11:97-110.


Table 3. Gene sequence variants

A list of observed sequence polymorphisms found in the 9 genes screened. In the first column, numbers prefixed with "rs" are public reference SNP numbers from the dbSNP database. Items not found in this database are listed as "Novel." The wild type sequence is derived from the scaffold sequence NT_010859 of chromosome 18p. Amino acid changes are for relevant splice variants. Sample numbers for affected individual appear in red. Sample numbers beginning with the letter "C" are controls.

                    Position      Wild type                                         Site of
                     on DNA      nucleotide        Observed                        nucleotide   Amino acid
      RefSNP ID      Contig       sequence       base changes     Sample number      change       change
    -------------   ---------   -------------   --------------   ---------------   ----------   ----------

CLUL1 (No polymorphisms observed)

EMILIN2
     rs592120       2875118     A/G             A/G              5-9, 5-6, 7-5,    base 157     Asn>Asn
                                                                 C-2               of exon 3
     rs592120       2875118     A/G             G                1-15              base 157     Asn>Asn
                                                                                   of exon 3
     rs592120       2875118     A/G             A                4-7, 6-4          base 157     Asn>Asn
                                                                                   of exon 3
     rs601071       2903579     A/G             A/G              7-5, 6-4          base 515     3' UTR
                                                                                   exon 9
     rs601071       2903579     A/G             G                5-9, 5-6, 1-15,   base 515     3' UTR
                                                                 4-7, C-2          of exon 9
     rs1059281      2903896     C/G             C/G              5-9, 1-15         base 832     3' UTR
                                                                                   of exon 9
     rs1059281      2903896     C/G             C                5-6, 7-5, 4-7,    base 832     3' UTR
                                                                 6-4, C-2          of exon 9
     rs1059282      2903918     A/G             A/G              5-9               base 854     3' UTR
                                                                                   exon 9
     rs1059282      2903918     A               A                1-15              base 854     3' UTR
                                                                                   of exon 9
     rs1059282      2903918     G               G                5-6, 7-5, 4-7,    base 854     3' UTR
                                                                 6-4, C-2          of exon 9
     rs1790994      2903431     C/T             T                5-9, 5-6, 1-15,   base 367     3' UTR
                                                                 4-7, C-2          of exon 9
     rs1790994      2903431     C/T             C/T              7-5, 6-6          base 367     3' UTR
                                                                                   of exon 9
     rs3810066      2882201     C/T             C                5-9, 5-6, 7-5,    base 1643    Thr>Thr
                                                                 1-15, 4-7, 6-4,   of exon 4
                                                                 C-2
     rs3810067      2881478     A/G             A                5-9, 5-6, 7-5,    base 920     Asn>Asn
                                                                 4-7, 6-4, C-2     of exon 4
     rs3810067      2881478     A/G             A/G              1-15              base 920     Asn>Ser
                                                                                   of exon 4
     rs3826638      2881847     A/G             G                C008, C0014,      base 1289    Arg>Arg
                                                                 5-9, 5-6, C-2     of exon 4
     rs3826638      2881847     A/G             A/G              7-5, 1-15, 4-7,   base 1289    Arg>Arg
                                                                 6-4               of exon 4

LPIN2
     Novel          2951033     T               A                C-6               Intron 1
     rs652587       2951033                     T/A              1-15, 3-6,
                                                                 4-7, 5-6,
                                                                 5-10, 6-4, C-3
     Novel          2951049     C               C/A              1-15, 5-6, C-1    Intron 1
     Novel          2950970     TATTAA/TATTAA   del/del          C-5               Intron 1
     Novel          2950970                     TATTAA/del       1-15, 1-16,
                                                                 3-6, 5-6, 5-10,
                                                                 6-4, 5-9, C-1,
                                                                 C-3
     Novel          2950692     G               G/A              C-1               base 25      His>His
                                                                                   of exon 2
     Novel          2924536     G               C                C-2               Intron 7
     rs3765622      2924536                     G/C              1-15, 3-6, 4-7,
                                                                 6-4, 7-5, C-1,
                                                                 C-3
     Novel          2924436     C               T/C              1-15              base 78      Lys>Lys
                                                                                   of exon 8
     rs607549       2909606     A               T                1-15, 5-6, C-1,   3' UTR       3' UTR
                                                                 C-5
     rs3840906      2909343     DIP             T                1-15, 5-6, C-1,   3' UTR       3' UTR
                                                                 C-5
     rs8091401      2907798     G               G/C              1-15              3' UTR       3' UTR
     Novel          2907425     T               T/G              5-6               3' UTR       3' UTR
     rs1164         2907152     T               T/C              5-6, C-5          3' UTR       3' UTR

MYOM1
     rs1042731      3056944     A               A/G              5-6, 1-15, C-3    base 611     3' UTR
                                                                                   of exon 36
     rs10667835     3065503                     TTT ins          All               Intron 32
     rs2298540      3065554     A               A/G              5-6, 1-15         Intron 32
     Novel          3065712     G               A/G              5-6, 1-15         Intron 32
     rs1143657      3065746     C               C/T              C-2, 1-15         base 14      Ala>Ala
                                                                                   of exon 32
     rs2298539      3065778     T               G/T              C-2, 1-15         Intron 31
     rs9966837      3074007     T               C/T              1-15, C-2         base 20      Met>Thr
                                                                                   of exon 29
     Novel          3074052     G               A/G              1-15              Intron 28
     Novel          3074052     G               A/A              5-6, C-2          Intron 28
     rs5822736      3079522     C               C/A              1-15              Intron 25
     Novel          3079611     T               C/T              C-2               Intron 24
     rs8098020      3083974     T               C/T              C-3               Intron 23
     Novel          3084007     T               A/T              C-3, 5-6          Intron 23
     rs9955413      3090049     A               A/G              5-6               Intron 22
     rs4798067      3090051     A               G/G              C-3, 5-6, 1-15,   Intron 22
                                                                 C-2
     rs6506059      3090429     C               C/T              5-6, 1-15, C-2    Intron 20
     rs8096115      3102120     A               G/G              C-3, 5-6, 1-15    Intron 19
     rs8084318      3102231     C               G/G              C-3, 5-6, 1-15    Intron 19
     Novel          3102313     T               G/T              C-3               base 99      Trp>Gly
                                                                                   of exon 19
     rs4129036      3106539     T               C/T              C-2               Intron 17
     rs9954421      3116632     G               A/G              C-3, C-2          Intron 16
     rs9954421      3116632     G               A/A, A/G         5-6, 1-15
     rs7505146      3124555     A               A/G              C-3               Intron 14
     Novel          3124610     T               C/T              C-2               Intron 14
     rs6506072      3139096     G               A/G              C-3               Intron 11
     Novel          3139220     C               C/T              C-3               Intron 10
     Novel          3139267     T               C/T              1-15              Intron 10
     rs8087321      3158741     G               A/G              C-2               Intron 6
     rs11873066     3163816     G               A/G              C-3               Intron 6
     rs10153415     3163873     C               C/T              C-3               Intron 6
     rs10153407     3163964     C               C/T              C-3               base 36      His>His
                                                                                   of exon 6
                    3164018     G               A/G              C-3               Intron 5
     rs11665082     3165911     G               A/A, A/G         C-2               Intron 4
     Novel          3166017     G               A/G              C-3               Intron 4
     rs11664-7      3166040     G               C/C              C-3               base 94      Trp>Cys
                                                                                   of exon 4
     rs11664-7      3166040     G               C/G              5-6, 1-15, C-2    base 94      Trp>Cys
                                                                                   of exon 4
     rs8099021      3166063     G               A/G              C-3               base 71      Gly>Gly
                                                                                   of exon 4
     rs10538262     3178857     T               C/T              C-2               base 230     Ser>Ser
                                                                                   of exon 2
     rs2230166      3178873     C               C/T              C-2               base 214     Thr>Met
                                                                                   of exon 2
     rs2230165      3178976     T               C/C              1-15, C-3         base 111     Ser>Ser
                                                                                   of exon 2
     rs2230165      3178976     T               C/T              5-6               base 111     Ser>Ser
                                                                                   of exon 2
     rs1962519      3179169     A               A/A, A/G         C-2               Intron 1
     rs11664065     3179170     G               G/G, T/T         C-2               Intron 1

MRLC2
     rs6146192      3252107     GTGCGCCTTCCG    GTGCGCCTTCCG/    5-1, 5-6, 7-5,    5' UTR       5' UTR
                                                del              1-15, 6-4, C-2,
                                                                 C-3
     rs6146192      3252107     GTGCGCCTTCCG    GTGCGCCTTCCG/    4-7               5' UTR       5' UTR
                                                (GTGCGCCTTCCG)
                                                x3 ins
     rs11650        3252193     T               C/C              5-6, 7-5, 1-15,   base 32      5' UTR
                                                                 4-7, 6-4, C-3     of exon 1
     rs11650        3252193     T               C/T              5-1/C-2           base 32      5' UTR
                                                                                   of exon 1
     rs4133582      3252379     G               A/A              All               Intron 1     None
     rs7407072      362874      T               A/A              All               Intron 1     None
     rs6506099      3262855     C               T/T              5-6, 7-5, 1-15,   Intron 1     None
                                                                 6-4, C-2, C-3
     rs6506099      3262855     C               C/T              4-7               Intron 1     None
     rs6506098      3262799     G               C/C              All               Intron 1     None
     rs1954838      3267077     C               A/A              5-1, 5-6, 7-5,    Intron 2     None
                                                                 1-15, 6-4, C-2
     rs10853294     3267237     G               T/T              5-1, 5-6, 7-5,    Intron 2     None
                                                                 1-15, 4-7, C-2,
                                                                 C-3
     rs10853294     3267237     G               G/T              6-4               Intron 2     None
     rs6506100      3267466     T               C/T              4-7               Intron 3     None
     rs6506100      3267466     T               C/C              5-1, 5-6, 7-5,    Intron 3     None
                                                                 1-15, 6-4, C-2,
                                                                 C-3
     rs6506101      3267467     G               A/G              4-7                            None
     rs6506101      3267467     G               A/A              5-1, 5-6, 7-5,    Intron 3     None
                                                                 1-15, 6-4, C-2,
                                                                 C-3
     rs1372996      3268475     A               G/G              5-1, 5-6, 1-15,   3' UTR       3' UTR
                                                                 6-4
     rs7506285      3268480     T               C/C              5-1, 5-6, 1-15,   3' UTR       3' UTR
                                                                 6-4

MRCL3
     rs716351       3243048     T               C/T              C-2               Intron 1     None
     rs716351       3243048     T               C/C              5-1, 5-6, 7-5,    Intron 1     None
                                                                 1-15, 6-4, C-3
     rs1791105      3243543     G               A/G              5-1, C-2, 4-7     Intron 2     None
     rs2304926      3243628     G               A/G              C-2, 4-7          Intron 2     None
     rs7811         3246112     A               A/G              5-1               3' UTR       3' UTR

TGIF
     Novel          3402167     C               C/T, T/T         1-23, 1-15,       base 96      5' UTR
                                                                 1-16, 1-19,       of exon 1
                                                                 2-10, 5-6, C-2,
                                                                 C-3
     rs8092903      3402386     C               C/T              C-2               Intron 1
     Novel          3402523     C               C/T, T/T         5-6, 7-5, C-2     Intron 1
     Novel          3408219     T               C/T              7-5               Intron 2
     rs238137       3437725     C               C/T              1-16, 1-21, C-2   base 118     5' UTR
                                                                                   of exon 3
     rs151472       3437871     T               C/T              1-15, 1-19,       Intron 3
                                                                 4-7, 5-6, 7-5,
                                                                 1-21, 1-23,
                                                                 2-10, C-2
     rs238132       3440455     C               C/A              4-8, 6-4, C-2,    base 284     5' UTR
                                                                 C-3, C-4          of exon 5
     rs238533       3441762     C               C/T, T/T         4-7, 6-4, 4-8,    base 172     5' UTR
                                                                 C-4               of exon 6
     Novel          3441896     G               G/A, A/A         4-7, 6-4, 4-8     base 306
                                                                                   of exon 6
     rs2238536      3442978     C               C/T, T/T         4-7, 6-4, 4-8     base 374      UTR
                                                                                   of exon 7
     Novel          3442216     C               C/C del          C-1               base 626     Early
                                                                                   of exon 6    truncation
     Novel          3442223     T               T/T del          3-6, C-1          base 633     Early
                                                                                   of exon 6    truncation
     Novel          3443789     T               G/T              1-16, 1-21, 2-6   base 18      5' UTR
                                                                                   of exon 8
     rs2229337      3447539     A               G/A, G/G         4-7, 6-4, C-2,    base 177     None
                                                                 C-4, C-5          of exon 10
     Novel          3447598     C               C/T              6-6, C-1          base 236     Pro>Leu
                                                                                   of exon 10
     rs4468717      3447606     C               C/T              3-6               base 44      Pro>Ser
                                                                                   of exon 10
     rs2229333      3447607     C               C/T, T/T         4-7, 6-4, 4-8     base 245     Pro>Leu
                                                                                   of exon 10
     rs2229335      3447695     C               C/T              C-1, C-4          base 333     None
                                                                                   of exon 10
     rs2229336      3447776     T               T/G              C-1, C-4          base 414     3' UTR
                                                                                   of exon 10
     Novel          3448161     G               G/A              5-9               base 799     3' UTR
                                                                                   of exon 10
     Novel          3448260     G               G/A              4-7, 5-6, 5-9,    base 898     3' UTR
                                                                 6-4, 7-5, C-2     of exon 10

DLGAP1
     rs3786431      3804148     G               C/G              2852              base 126     Thr>Thr
                                                                                   of exon 2
     rs3745051      3719175     G               A/A              5472              base 201     Val>Met
                                                                                   of exon 4
     rs3745051      3719175     G               A/G              C008, 2141,       base 201     Val>Met
                                                                 2852              of exon 4
                    3571966     C               C/T              5-6, 5472         base 281     Thr>Thr
                                                                                   of exon 5

Zinc Finger 161
     rs620652       5282030     T               C/C              5-1, 7-5, 1-15,   base 174     Thr>Thr
                                                                 6-4, C48          of exon 2
                                T               C/T              5-6, 4-7          base 174     Thr>Thr
                                                                                   of exon 2
     rs12522        5280282     T               C/T              7-5, 5-1          base 1922    3' UTR
                                                                                   of exon 2
                                T               C/C              C48               base 1922    3' UTR
                                                                                   of exon 2
     rs990072       5280198     A               A/G              4-7, 7-5, 5-1     base 2006    3' UTR
                                                                                   of exon 2
                                A               G/G              C48, 6-4          base 2006    3' UTR
                                                                                   of exon 2
     rs12343        5280174     C               C/T              7-5, 5-1          base 2030    3' UTR
                                                                                   of exon 2
                                C               T/T              C48               base 2030    3' UTR
                                                                                   of exon 2
     rs2789         5279887     G               G/C              C48, 5-1          base 2317    3' UTR
                                                                                   of exon 2

Scavello, Mol Vis 2005; 11:97-110 <http://www.molvis.org/molvis/v11/a11/>
©2005 Molecular Vision <http://www.molvis.org/molvis/>
ISSN 1090-0535