serine palmitoyltransferase, long chain base subunit 1 (SPTLC1) - coding DNA reference sequence

(used for mutation description)

(last modified July 13, 2012)


This file was created to facilitate the description of sequence variants in the SPTLC1 gene based on a coding DNA reference sequence following the HGVS recommendations.

The sequence was taken from NG_007950.1, covering SPTLC1 transcript NM_006415.2.


Please note that introns are available by clicking on the exon numbers above the sequence.
 (upstream sequence)
                               .         .         .                g.5038
                       gcgcttgtgacccgccttccggaaggaagcggctaact       c.-1

          .         .         .         .         .        | 02.    g.7849
 ATGGCGACCGCCACGGAGCAGTGGGTTCTGGTGGAGATGGTACAGGCGCTTTACGAG | GCT    c.60
 M  A  T  A  T  E  Q  W  V  L  V  E  M  V  Q  A  L  Y  E   | A      p.20

          .         .         .         .         .         .       g.7909
 CCTGCTTACCATCTTATTTTGGAAGGGATTCTGATCCTCTGGATAATCAGACTTCTTTTC       c.120
 P  A  Y  H  L  I  L  E  G  I  L  I  L  W  I  I  R  L  L  F         p.40

          .         .         .         .      | 03  .         .    g.11589
 TCTAAGACTTACAAATTACAAGAACGATCTGATCTTACAGTCAAG | GAAAAAGAAGAACTG    c.180
 S  K  T  Y  K  L  Q  E  R  S  D  L  T  V  K   | E  K  E  E  L      p.60

          .         .         .         .         .         .       g.11649
 ATTGAAGAGTGGCAACCAGAACCTCTTGTTCCTCCTGTCCCAAAAGACCATCCTGCTCTC       c.240
 I  E  E  W  Q  P  E  P  L  V  P  P  V  P  K  D  H  P  A  L         p.80

          .         . | 04       .         .         .         .    g.39485
 AACTACAACATCGTTTCAGG | CCCTCCAAGCCACAAAACTGTGGTGAATGGAAAAGAATGT    c.300
 N  Y  N  I  V  S  G  |  P  P  S  H  K  T  V  V  N  G  K  E  C      p.100

          .         .         .         .         .     | 05   .    g.40326
 ATAAACTTCGCCTCATTTAATTTTCTTGGATTGTTGGATAACCCTAGGGTTAAG | GCAGCA    c.360
 I  N  F  A  S  F  N  F  L  G  L  L  D  N  P  R  V  K   | A  A      p.120

          .         .         .         .         .         .       g.40386
 GCTTTAGCATCTCTAAAGAAGTATGGCGTGGGGACTTGTGGACCCAGAGGATTTTATGGC       c.420
 A  L  A  S  L  K  K  Y  G  V  G  T  C  G  P  R  G  F  Y  G         p.140

         | 06.         .         .         .         .         .    g.52363
 ACATTTG | ATGTTCATTTGGATTTGGAAGACCGCCTGGCAAAATTTATGAAGACAGAAGAA    c.480
 T  F  D |   V  H  L  D  L  E  D  R  L  A  K  F  M  K  T  E  E      p.160

          .         .         .         .         .         .       g.52423
 GCCATTATATACTCATATGGATTTGCCACCATAGCCAGTGCTATTCCTGCTTACTCTAAA       c.540
 A  I  I  Y  S  Y  G  F  A  T  I  A  S  A  I  P  A  Y  S  K         p.180

          .         . | 07       .         .         .         .    g.61140
 AGAGGGGACATTGTTTTTGT | AGATAGAGCTGCCTGCTTTGCTATTCAGAAAGGATTACAG    c.600
 R  G  D  I  V  F  V  |  D  R  A  A  C  F  A  I  Q  K  G  L  Q      p.200

          .         .         .         .         .         .       g.61200
 GCATCCCGTAGTGACATTAAGTTATTTAAGCATAATGACATGGCTGACCTCGAGCGACTA       c.660
 A  S  R  S  D  I  K  L  F  K  H  N  D  M  A  D  L  E  R  L         p.220

          .         .         . | 08       .         .         .    g.64944
 CTAAAAGAACAAGAGATCGAAGATCAAAAG | AATCCTCGCAAGGCTCGTGTAACTCGGCGT    c.720
 L  K  E  Q  E  I  E  D  Q  K   | N  P  R  K  A  R  V  T  R  R      p.240

          .         .         .         .         .         .       g.65004
 TTCATTGTAGTAGAAGGATTGTATATGAATACTGGAACTATTTGTCCTCTTCCAGAATTG       c.780
 F  I  V  V  E  G  L  Y  M  N  T  G  T  I  C  P  L  P  E  L         p.260

  | 09       .         .         .         .         .         .    g.70401
  | GTTAAGTTAAAATACAAATACAAAGCAAGAATCTTCCTGGAGGAAAGCCTTTCATTTGGA    c.840
  | V  K  L  K  Y  K  Y  K  A  R  I  F  L  E  E  S  L  S  F  G      p.280

          .         .         .         .         | 10         .    g.72712
 GTCCTAGGAGAGCATGGCCGAGGAGTCACTGAACACTATGGAATCAAT | ATTGATGATATT    c.900
 V  L  G  E  H  G  R  G  V  T  E  H  Y  G  I  N   | I  D  D  I      p.300

          .         .         .         .         .         .       g.72772
 GATCTTATCAGTGCCAACATGGAGAATGCACTTGCTTCTATTGGAGGTTTCTGCTGTGGC       c.960
 D  L  I  S  A  N  M  E  N  A  L  A  S  I  G  G  F  C  C  G         p.320

          .         .     | 11   .         .         .         .    g.73176
 AGGTCTTTTGTAATTGACCATCAG | CGACTTTCCGGCCAGGGATACTGCTTTTCAGCTTCG    c.1020
 R  S  F  V  I  D  H  Q   | R  L  S  G  Q  G  Y  C  F  S  A  S      p.340

          .         .         .         .         .         .       g.73236
 TTACCTCCCCTGTTAGCTGCTGCAGCAATTGAGGCCCTCAACATCATGGAAGAGAATCCA       c.1080
 L  P  P  L  L  A  A  A  A  I  E  A  L  N  I  M  E  E  N  P         p.360

   | 12      .         .         .         .         .       | 13 . g.82047
 G | GTATTTTTGCAGTGTTGAAGGAAAAGTGCGGACAAATTCATAAAGCTTTACAAGG | CATT c.1140
 G |   I  F  A  V  L  K  E  K  C  G  Q  I  H  K  A  L  Q  G  |  I   p.380

          .         .         .         .         .         .       g.82107
 TCTGGATTAAAAGTGGTGGGGGAGTCCCTTTCTCCAGCCTTTCACCTACAACTGGAAGAG       c.1200
 S  G  L  K  V  V  G  E  S  L  S  P  A  F  H  L  Q  L  E  E         p.400

          .         .         .         .         .     | 14   .    g.85531
 AGCACTGGGTCTCGCGAGCAAGATGTCAGACTGCTTCAGGAAATTGTAGATCAA | TGCATG    c.1260
 S  T  G  S  R  E  Q  D  V  R  L  L  Q  E  I  V  D  Q   | C  M      p.420

          .         .         .         .         .         .       g.85591
 AACAGAAGTATTGCATTAACTCAGGCGCGCTACTTGGAGAAAGAAGAGAAGTGTCTCCCT       c.1320
 N  R  S  I  A  L  T  Q  A  R  Y  L  E  K  E  E  K  C  L  P         p.440

          | 15         .         .         .         .         .    g.87902
 CCTCCCAG | CATTCGGGTTGTGGTCACGGTGGAACAAACAGAGGAAGAACTGGAGAGAGCT    c.1380
 P  P  S  |  I  R  V  V  V  T  V  E  Q  T  E  E  E  L  E  R  A      p.460

          .         .         .         .                           g.87944
 GCGTCCACCATCAAGGAGGTAGCCCAGGCCGTCCTGCTCTAG                         c.1422
 A  S  T  I  K  E  V  A  Q  A  V  L  L  X                           p.473

          .         .         .         .         .         .       g.88004
 gcagagtcccgggaccatggcctcctgccacacaacacgcagagaggactcaagactccc       c.*60

          .         .         .         .         .         .       g.88064
 gctggccatggagtggcctgaaagagagcaagaacatgtggatctttgataggattgtta       c.*120

          .         .         .         .         .         .       g.88124
 ccaaatggtgtcagtatggaccaattgtgtgaccatgagaaggatgcttattttttttaa       c.*180

          .         .         .         .         .         .       g.88184
 aaagaaaacacatctaaaagcccaggaactgatttttttaagaggaaaactaatgacagt       c.*240

          .         .         .         .         .         .       g.88244
 gtataactgatgtttaaattgtgcatttagtactatttaaatgttttcttatactagtat       c.*300

          .         .         .         .         .         .       g.88304
 tttatattcttttgttgtcgtttaaaactggagcttcagtgtctcttccctccctctaat       c.*360

          .         .         .         .         .         .       g.88364
 agtaatggttcagtaagcactccttaactccttagtatttcatagaaaaatgactgcaac       c.*420

          .         .         .         .         .         .       g.88424
 attaaagctaagaggaacacttcaacatatgtggtacaaatttatattgaagatctaaat       c.*480

          .         .         .         .         .         .       g.88484
 aaaccacgtattttccagtcttcgttgtgtgaagctaaatggtggctaaaaggaacactt       c.*540

          .         .         .         .         .         .       g.88544
 tttgtgtgattattataaactttgcattgtatttgaatcttagaacttttgtacacacta       c.*600

          .         .         .         .         .         .       g.88604
 aatattgatgtcacaccatttctaatctgagcatccttagccagagaatattcattatac       c.*660

          .         .         .         .         .         .       g.88664
 ttcctaagtgagcaataatttaaatcagaagctattttattttaatgtaattaacctttc       c.*720

          .         .         .         .         .         .       g.88724
 tttacatttcttatgtgttcacctctaatctgttttaggaagagagttggttattatgtt       c.*780

          .         .         .         .         .         .       g.88784
 gatcccataatataaatcatatcctttatattttagaatatctcaaatgtattccttttt       c.*840

          .         .         .         .         .         .       g.88844
 tgtatggtgggtttgcctagggacgtgtaactacaggcttttactaagccaaggaaaaag       c.*900

          .         .         .         .         .         .       g.88904
 agaatttttcttttcatcttacaaattccagatatctacaaaagatgtgaaagcactaaa       c.*960

          .         .         .         .         .         .       g.88964
 aataccatttttaagcagtactttacctgttttttctttagcaaaccaggttatgtggtg       c.*1020

          .         .         .         .         .         .       g.89024
 taaaggtttgttatacgtgccacaatatagcatataaatattatgccatcattccttctc       c.*1080

          .         .         .         .         .         .       g.89084
 ttgttaaaggtagaagaataaaattgtgatttttataacctgtgcttattactcaaatgg       c.*1140

          .         .         .         .         .         .       g.89144
 tcttcaacatctttttaaacaacacatactttttgaatgttcagtttctattttgcttga       c.*1200

          .         .         .         .         .         .       g.89204
 ggtattttgtacatatgtgccttgtgattgctgctgctttaaaggataaagtactctttg       c.*1260

          .         .         .         .         .         .       g.89264
 ggggatgagtctggtttgttttgttttattttttaatgaaataaacctatattcctgatt       c.*1320

 

 (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 10th nucleotide is indicated by a "." above the sequence. The Serine palmitoyltransferase, long chain base subunit 1 protein sequence is shown below the coding DNA sequence, with numbering indicated at the right starting with 1 for the translation initiating Methionine. Every 10th 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 mutations, all stop codons in the +1 frame are shown in bold while all stop codons in the +2 frame are underlined.

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