How to find the chromosomal coordinate of a mutation in a gene?

Question

[Cerebelle]

I have information on the Codon number, Amino acid change and the corresponding nucleotide change for a mutation in a gene. I need the exact chromosomal coordinate for that mutation.Can someone please tell me how to find the chromosomal coordinate of that particular mutation? What tools are available to find the coordinates?

[Pierre Lindenbaum]

using backlocate: http://lindenb.github.io/jvarkit/BackLocate.html

see also Amino Acid Change To Genomic Location: using 'backlocate'

[cocchi.e89]

@Pierre I tried to use back locate but when I run the example it gives me an error:

echo -e "INF2\tA13T" | java -jar dist/backlocate.jar -R hg19.fa
[WARN][BackLocate]ici
[WARN][BackLocate]ici
[INFO][BackLocate]loading genes
[INFO][BackLocate]genes:99813
[INFO][BackLocate]loading http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/kgXref.txt.gz
[INFO][BackLocate]kgxref:0 . Count ignored because not found in kg file: 82960

Do you have any clue?

[Pierre Lindenbaum]

Yes, that's because the --kg parameter should be http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/knownGene.txt.gz . try with this URL. I'm going to update the code on my side.

[Pierre Lindenbaum]

#User.Gene  AA1 petide.pos.1    AA2 knownGene.name  knownGene.strand    knownGene.AA    index0.in.rna   wild.codon  potential.var.codons    base.in.rna chromosome  index0.in.genomic   exon    messages    extra.user.data
INF2    Ala 13  Thr uc001yoy.4  +   A   36  GCG ACG G   14  105167738   Exon 2  .   .
INF2    Ala 13  Thr uc001yoy.4  +   A   37  GCG ACG C   14  105167739   Exon 2  .   .
INF2    Ala 13  Thr uc001yoy.4  +   A   38  GCG ACG G   14  105167740   Exon 2  .   .
INF2    Ala 13  Thr uc001ypb.2  +   A   36  GCG ACG G   14  105167738   Exon 2  .   .
INF2    Ala 13  Thr uc001ypb.2  +   A   37  GCG ACG C   14  105167739   Exon 2  .   .
INF2    Ala 13  Thr uc001ypb.2  +   A   38  GCG ACG G   14  105167740   Exon 2  .   .
INF2    Ala 13  Thr uc001ypc.2  +   A   36  GCG ACG G   14  105167738   Exon 2  .   .
INF2    Ala 13  Thr uc001ypc.2  +   A   37  GCG ACG C   14  105167739   Exon 2  .   .
INF2    Ala 13  Thr uc001ypc.2  +   A   38  GCG ACG G   14  105167740   Exon 2  .   .

Answer 1

[genecats.ucsc]

If this is for some Human assembly you can make an HGVS term out of your information and paste into the search box on the UCSC Genome Browser. The highlighted base(s) will be your mutation coordinate(s).

If you have further questions about UCSC data or tools feel free to send your question to one of the below mailing lists:

• General questions: [e-mail]
• Questions involving private data: [e-mail]
• Questions involving mirror sites: [e-mail]

ChrisL from the UCSC Genome Browser

Answer 2

[finswimmer]

Hello,

if you have a transcript id you could use mutalyzer. If you don't have a transcript id use ensembl's VEP.

But be careful. Without a transcript id the result could be ambiguous.

fin swimmer