Right tool for identifying mutations

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Filippo Pullara

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Mar 29, 2017, 2:12:36 PM3/29/17

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Hi,

I have a list of thousands of nucleotides mutation (either single nucleotide or a sequence of them) in a specific gene that I know correspond to a protein and I need to identify the corresponding amino-acid mutations. Ideally, I’d like to be able to input a list of mutation of nucleotides and have as output a list of the corresponding amino acid mutation.

Can you, please, suggest which tool is more appropriate to use?

Thank you very much,

Filippo

Christopher Lee

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Mar 29, 2017, 7:30:05 PM3/29/17

to Filippo Pullara, UCSC Genome Browser Discussion List

Hi Filippo,

Thank you for your question about finding the amino acid changes corresponding to your mutations. You can use the Variant Annotation Integrator (VAI): http://genome.ucsc.edu/cgi-bin/hgVai to find the amino acid changes associated with your variants, as long as you have less than 100,000 variants and you have either a list of rsID's or a Personal Genome SNP (pgSnp)/VCF custom track/track hub to use as input.

To start, navigate over to the VAI: http://genome.ucsc.edu/cgi-bin/hgVai, and then select your genome and assembly of interest. Then, from the "region to annotate" dropdown, input the region of your gene of interest. Depending on whether you have a list of rsID's or a pgSNP/VCF Custom track/track hub, use the appropriate buttons to add your custom track/hub, or change the variants dropdown to "Variant Identifiers" and paste in your rsID input. After adding your input, select the gene track you are annotating, and select any extra annotations of interest that may be available for your assembly.

Finally click "get results" where you will see an output column: "Amino acid change" and the effect of your mutation on the protein. Here is an example line of output, indicating an inframe deletion of the chr9:133255668-133255670 region of the GRCh38 Human assembly:

## ENSEMBL VARIANT EFFECT PREDICTOR format (UCSC Variant Annotation Integrator)
## Output produced at 2017-03-29 16:10:10
## Connected to UCSC database hg38
## Variants: Artificial Example Variants
## Transcripts: GENCODE v24 Comprehensive Transcript Set (only Basic displayed by default) (hg38.knownGene)
## dbSNP: Simple Nucleotide Polymorphisms (dbSNP 147) (/gbdb/hg38/vai/snp147.bed4.bb)
Uploaded Variation    Location    Allele    Gene    Feature    Feature type    Consequence    Position in cDNA    Position in CDS    Position in protein    Amino acid change    Codon change    Co-located Variation    Extra
ex_codonLeftDel    chr9:133255668-133255670    -    ABO    uc064wua.1    Transcript    inframe_deletion    1079-1081    1054-1056    352    R/-    CGT/-    -    EXON=9/9

For more information about using the Variant Annotation Integrator, please see the VAI user guide:
http://genome.ucsc.edu/cgi-bin/hgVai#intro

Please let us know if you have any further questions!

Thank you again for your inquiry and using the UCSC Genome Browser. If
you have any further questions, please reply to gen...@soe.ucsc.edu.
All messages sent to that address are archived on a
publicly-accessible forum. If your question includes sensitive data,
you may send it instead to genom...@soe.ucsc.edu.

Christopher Lee
UCSC Genomics Institute

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