about synonymous and non-synonymous mutations

[Ya Hu]

Dear sir or madam,

I am trying to check whether a mutation on a site is synonymous or non-synonymous in human genome, (given position and allele status before and after mutation), which files could I refer to from UCSC download site, please?

Many thanks,

Ya Hu

[Matthew Speir]

Hi Ya,

Thank you for your question about finding information on synonymous and
non-synonymous variants in the UCSC Genome Browser. You can use the
Variant Annotation Integrator, http://genome.ucsc.edu/cgi-bin/hgVai, to
get information on how your variants effect genes along side a great
deal of other information. The Variant Annotation Integrator can take
rsIDs, VCF, or pgSnp files as input. If you have a list of rsIDs that
you are interested in, use the following steps to get information on
these variants:

1. Navigate to the Variant Annotation Integrator,
http://genome.ucsc.edu/cgi-bin/hgVai.
2. Select “Variant Identifiers” from the drop-down next to “variants”.
3. Paste your identifiers into the box.
4. Select the number of variants to be processed (up to 100,000).
5. Select the gene track you would like to use as a reference for
the variant effects.
6. Select any of the other variant information options you are
interested in.
7. Select your output options.
8. Click “Get results”.

However, if you do not have a list of rsIDs, you will have to input your
variant positions using either the pgSnp or VCF formats as input. You
can find out more about the pgSnp format here:
http://genome.ucsc.edu/FAQ/FAQformat.html#format10, and the VCF format
here: http://genome.ucsc.edu/goldenPath/help/vcf.html. Once your have
your variant positions in one of these two formats, you can upload them
as a custom track here: http://genome.ucsc.edu/cgi-bin/hgCustom. After
you have uploaded them as a custom track, use the following steps to get
information on these variants:

1. Navigate to the Variant Annotation Integrator,
http://genome.ucsc.edu/cgi-bin/hgVai.
2. Select your custom track from the drop-down next to “variants”.
3. Select the number of variants to be processed (up to 100,000).
4. Select the gene track you would like to use as a reference for
the variant effects.
5. Select any of the other variant information options you are
interested in.
6. Select your output options.
7. Click “Get results”.

I hope this is helpful. 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 Google Groups forum. If your question includes
sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Matthew Speir
UCSC Genome Bioinformatics Group

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