ceroid-lipofuscinosis, neuronal 6, late infantile, variant (CLN6) - coding DNA reference sequence

(used for variant description)

(last modified October 23, 2014)

This file was created to facilitate the description of sequence variants on transcript NM_017882.2 in the CLN6 gene based on a coding DNA reference sequence following the HGVS recommendations.

The sequence was taken from NG_008764.1, covering CLN6 transcript NM_017882.2.

Please note that introns are available by clicking on the exon numbers above the sequence.

 (upstream sequence)
                               .         .         .                g.5038
                       gtccgcagccccgcctgttcctcccgagggccgcgcgc       c.-121

 .         .         .         .         .         .                g.5098
 tctcgccggcccgccccgaaccgccccgcgctgggaatttgcggcggcctccgccggggc       c.-61

 .         .         .         .         .         .                g.5158
 agccgagctgaaccggtctcttcctcggaaaggcagggccgaggggcctgcggggcagcc       c.-1

          .         .         .         .         .         .       g.5218
 ATGGAGGCGACGCGGAGGCGGCAGCACCTGGGAGCGACGGGCGGCCCAGGCGCGCAGCTG       c.60
 M  E  A  T  R  R  R  Q  H  L  G  A  T  G  G  P  G  A  Q  L         p.20

          .         .    | 02    .         .         .         .    g.16129
 GGCGCCTCCTTCCTGCAGGCCAG | GCATGGCTCTGTGAGCGCTGATGAGGCTGCCCGCACG    c.120
 G  A  S  F  L  Q  A  R  |  H  G  S  V  S  A  D  E  A  A  R  T      p.40

          .         .         .         .         .         .       g.16189
 GCTCCCTTCCACCTCGACCTCTGGTTCTACTTCACACTGCAGAACTGGGTTCTGGACTTT       c.180
 A  P  F  H  L  D  L  W  F  Y  F  T  L  Q  N  W  V  L  D  F         p.60

          .         | 03         .         .         .         .    g.20396
 GGGCGTCCCATTGCCATG | CTGGTATTCCCTCTCGAGTGGTTTCCACTCAACAAGCCCAGT    c.240
 G  R  P  I  A  M   | L  V  F  P  L  E  W  F  P  L  N  K  P  S      p.80

          .         .         .         .         .        | 04.    g.22882
 GTTGGGGACTACTTCCACATGGCCTACAACGTCATCACGCCCTTTCTCTTGCTCAAG | CTC    c.300
 V  G  D  Y  F  H  M  A  Y  N  V  I  T  P  F  L  L  L  K   | L      p.100

          .         .         .         .         .         .       g.22942
 ATCGAGCGGTCCCCCCGCACCCTGCCACGCTCCATCACGTACGTGAGCATCATCATCTTC       c.360
 I  E  R  S  P  R  T  L  P  R  S  I  T  Y  V  S  I  I  I  F         p.120

          .         .         .         .         .         .       g.23002
 ATCATGGGTGCCAGCATCCACCTGGTGGGTGACTCTGTCAACCACCGCCTGCTCTTCAGT       c.420
 I  M  G  A  S  I  H  L  V  G  D  S  V  N  H  R  L  L  F  S         p.140

          .         .         .         .         .         .       g.23062
 GGCTACCAGCACCACCTGTCTGTCCGTGAGAACCCCATCATCAAGAATCTCAAGCCGGAG       c.480
 G  Y  Q  H  H  L  S  V  R  E  N  P  I  I  K  N  L  K  P  E         p.160

        | 05 .         .         .         .         .         .    g.23478
 ACGCTG | ATCGACTCCTTTGAGCTGCTCTACTATTATGATGAGTACCTGGGTCACTGCATG    c.540
 T  L   | I  D  S  F  E  L  L  Y  Y  Y  D  E  Y  L  G  H  C  M      p.180

    | 06     .         .         .         .         .         .    g.25041
 TG | GTACATCCCCTTCTTCCTCATCCTCTTCATGTACTTCAGCGGCTGCTTTACTGCCTCT    c.600
 W  |  Y  I  P  F  F  L  I  L  F  M  Y  F  S  G  C  F  T  A  S      p.200

          .         .         .         .         .         .       g.25101
 AAAGCTGAGAGCTTGATTCCAGGGCCTGCCCTGCTCCTGGTGGCACCCAGTGGCCTGTAC       c.660
 K  A  E  S  L  I  P  G  P  A  L  L  L  V  A  P  S  G  L  Y         p.220

       | 07  .         .         .         .         .         .    g.26387
 TACTG | GTACCTGGTCACCGAGGGCCAGATCTTCATCCTCTTCATCTTCACCTTCTTCGCC    c.720
 Y  W  |  Y  L  V  T  E  G  Q  I  F  I  L  F  I  F  T  F  F  A      p.240

          .         .         .         .         .         .       g.26447
 ATGCTGGCCCTCGTCCTGCACCAGAAGCGCAAGCGCCTCTTCCTGGACAGCAACGGCCTC       c.780
 M  L  A  L  V  L  H  Q  K  R  K  R  L  F  L  D  S  N  G  L         p.260

          .         .         .         .         .         .       g.26507
 TTCCTCTTCTCCTCCTTCGCACTGACCCTCTTGCTTGTGGCGCTCTGGGTCGCCTGGCTG       c.840
 F  L  F  S  S  F  A  L  T  L  L  L  V  A  L  W  V  A  W  L         p.280

          .         .         .         .         .         .       g.26567
 TGGAATGACCCTGTTCTCAGGAAGAAGTACCCGGGTGTCATCTACGTCCCTGAGCCCTGG       c.900
 W  N  D  P  V  L  R  K  K  Y  P  G  V  I  Y  V  P  E  P  W         p.300

          .         .         .                                     g.26603
 GCTTTCTACACCCTTCACGTCAGCAGTCGGCACTGA                               c.936
 A  F  Y  T  L  H  V  S  S  R  H  X                                 p.311

          .         .         .         .         .         .       g.26663
 gtccctggcaccaggctctggcgctctgctgggtgggagggtgggccatggagggcatct       c.*60

          .         .         .         .         .         .       g.26723
 gaatacaggagtagggggggtgtgggtgtgtaaccagagaccgagagcatgagtggggtg       c.*120

          .         .         .         .         .         .       g.26783
 tgcctcgtgtgcgtggattcgtgtgtgtgtgtgtgtgtgtcttgtatatgtgtgcgcaga       c.*180

          .         .         .         .         .         .       g.26843
 gtgcatcattttcagactctactatttccgtcaagtttctgtttgatttggatcatctca       c.*240

          .         .         .         .         .         .       g.26903
 ggatcggattctgttttagagtgtttctgggccaggatccgggcccctgccctcctctgc       c.*300

          .         .         .         .         .         .       g.26963
 acctgaccacactccctactcagggctagtctgttcttcccggacatcttctggtagccg       c.*360

          .         .         .         .         .         .       g.27023
 tgcaggagagggctgggtggggcagaggccaggaggggacctggtgtgtcacctgcccac       c.*420

          .         .         .         .         .         .       g.27083
 cacctggctcatccctcaggcccaccctgaccctacattacataggttacgtcagcctac       c.*480

          .         .         .         .         .         .       g.27143
 tgtggctgttgagcaaagcatttctcctttctgggcctcatttgcactagatgggcctgt       c.*540

          .         .         .         .         .         .       g.27203
 ggtcccaaagtaggtcagtaggttggggttgctgacaccccttgggtgcagctttgggac       c.*600

          .         .         .         .         .         .       g.27263
 agatgagtggctctgtcctgtcactgccctctccctgcctgggggctatgtgcactccag       c.*660

          .         .         .         .         .         .       g.27323
 acccctgcccaggctcaggcccatgaggtatggagacaccctggcccccaggagctggag       c.*720

          .         .         .         .         .         .       g.27383
 gcaccgcccactcccctggcattccagctttgcaggtgaccctcctctacccaaagctct       c.*780

          .         .         .         .         .         .       g.27443
 gtccccctgctcccactccagaagaactgcggcacgcgcttcgggcagcctagccacagg       c.*840

          .         .         .         .         .         .       g.27503
 ctttgagcgcctgcattcctgggggctggagggtggggtgccaaaggccctgagcaaaag       c.*900

          .         .         .         .         .         .       g.27563
 ccagagctcctctcatcaaagcctttacaaggtgctgggcccagaggctttgccttgaca       c.*960

          .         .         .         .         .         .       g.27623
 gagtggcccagggtttcaagggaggaggaacctccccctacctaggacccttcctgtggg       c.*1020

          .         .         .         .         .         .       g.27683
 gggtctacagagtcagggacagaagggaagggacccacaggaagtcacagtggtgcccag       c.*1080

          .         .         .         .         .         .       g.27743
 ggatgtgtcagcccccagccacggggacgcgggattcaagaatgaagtaaatacagtcac       c.*1140

                                                                    g.27751
 agccccaa                                                           c.*1148

 (downstream sequence)

Legend:
Nucleotide numbering (following the rules of the HGVS for a 'Coding DNA Reference Sequence') is indicated at the right of the sequence, counting the A of the ATG translation initiating Methionine as 1. Every 10^th nucleotide is indicated by a "." above the sequence. The Ceroid-lipofuscinosis, neuronal 6, late infantile, variant protein sequence is shown below the coding DNA sequence, with numbering indicated at the right starting with 1 for the translation initiating Methionine. Every 10^th amino acid is shown in bold. The position of introns is indicated by a vertical line, splitting the two exons. The start of the first exon (transcription initiation site) is indicated by a '\', the end of the last exon (poly-A addition site) by a '/'. The exon number is indicated above the first nucleotide(s) of the exon. To aid the description of frame shift variants, all stop codons in the +1 frame are shown in bold while all stop codons in the +2 frame are underlined.