Is it possible to get the Codons for an intron/splice mutation given the chromosome and position?
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10 months ago
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Hello,

I have annotated my VCF files using VEP from Ensembl. I have obtained the following lines (please copy paste them in a file for a better view):

CHROM  POS       REF  ALT  QUAL     DP   Consequence              IMPACT    SYMBOL  Gene  Feature_type  Transcript  Transcript_version  BIOTYPE         EXON  INTRON  HGVSc                      HGVSp  cDNA_position  CDS_position  Protein_position  Amino_acids  Codons  Existing_variation
chr7   44145448  C    T    2539.77  180  intron_variant           MODIFIER  GCK     2645  Transcript    NM_000162   NM_000162.5         protein_coding  -     9/9     NM_000162.5:c.1253+49G>A   -      -              -             -                 -            -       rs13306387
chr7   44146057  G    T    3229.77  323  intron_variant           MODIFIER  GCK     2645  Transcript    NM_000162   NM_000162.5         protein_coding  -     8/9     NM_000162.5:c.1020-327C>A  -      -              -             -                 -            -       rs887688&COSV56267186
chr7   44146206  C    G    1619.77  145  intron_variant           MODIFIER  GCK     2645  Transcript    NM_000162   NM_000162.5         protein_coding  -     8/9     NM_000162.5:c.1019+257G>C  -      -              -             -                 -            -       rs887687
chr7   44146619  C    G    4788.77  431  splice_acceptor_variant  HIGH      GCK     2645  Transcript    NM_000162   NM_000162.5         protein_coding  -     7/9     NM_000162.5:c.864-1G>C     -      -              -             -                 -            -       CS001424&CS109126
chr7   44149675  T    C    1305.77  116  intron_variant           MODIFIER  GCK     2645  Transcript    NM_000162   NM_000162.5         protein_coding  -     6/9     NM_000162.5:c.679+85A>G    -      -              -             -                 -            -       rs2268575
chr7   44149722  A    G    6190.77  217  intron_variant           MODIFIER  GCK     2645  Transcript    NM_000162   NM_000162.5         protein_coding  -     6/9     NM_000162.5:c.679+38T>C    -      -              -             -                 -            -       rs2268574&COSV60787932

Clearly, those mutations are located in introns but there's one found in a splice site by looking at the Consequence column. I would like to know if there are any tools available (or any means necessary) to provide the Codons information for these mutations.

For example, the Codons column in the following lines where the impacted nucleotide is shown in uppercase:

CHROM  POS     REF  ALT  QUAL     DP   Consequence         IMPACT    SYMBOL  Gene   Feature_type  Transcript  Transcript_version  BIOTYPE         EXON   INTRON  HGVSc                  HGVSp                    cDNA_position  CDS_position  Protein_position  Amino_acids  Codons   Existing_variation
chr1   952421  A    G    4279.77  146  synonymous_variant  LOW       NOC2L   26155  Transcript    NM_015658   NM_015658.4         protein_coding  10/19  -       NM_015658.4:c.1182T>C  NP_056473.3:p.Thr394=    1198           1182          394               T            acT/acC  rs3828047
chr1   953259  T    C    1984.77  69   synonymous_variant  LOW       NOC2L   26155  Transcript    NM_015658   NM_015658.4         protein_coding  9/19   -       NM_015658.4:c.918A>G   NP_056473.3:p.Glu306=    934            918           306               E            gaA/gaG  rs3748596
chr1   953279  T    C    1769.77  61   missense_variant    MODERATE  NOC2L   26155  Transcript    NM_015658   NM_015658.4         protein_coding  9/19   -       NM_015658.4:c.898A>G   NP_056473.3:p.Ile300Val  914            898           300               I/V          Atc/Gtc  rs3748597

Thank you in advance

codons introns • 233 views
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Hello badredda!

It appears that your post has been cross-posted to another site: https://bioinformatics.stackexchange.com/questions/13449/is-it-possible-to-get-the-codons-for-an-intron-splice-mutation-given-the-chromos

This is typically not recommended as it runs the risk of annoying people in both communities.

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@Pierre thanks for the note, I deleted the post there.

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