Where can I get hg19.omimAvSnp and hg19.omimAv tables?

Question

[o3964fn4n]

Hi, I have an assignment where I have to find this:

"A table of the 4 mutations (listed in the NCBI OMIM database) in the TMPRSS3 protein causing deafness, their dbSNP id, their consequence for the protein coding sequence of TMPRSS3 and their genomic coordinates (hg19). Use information present in hg19.omimAvSnp and hg19.omimAv tables (available at the UCSC table browser) to generate your table"

I have found the 4 mutations and information about them. But what is "omimAvSnp"?

[GenoMax]

While you should be able to find them at UCSC Table Browser, the specific omim related tables appear to be grayed out (not sure if there is some access restriction from OMIM now). You should email UCSC genome browser support about this question (genome at soe.ucsc.edu)

Answer 1

[genecats.ucsc]

You will want to use the UCSC Table Browser to find this data.

From the Table Browser page, select the hg19 assembly, then in the position box, enter your gene of interest and click the "lookup" button, then choose your transcript of interest (probably the top one). Once this region has been selected, change the group dropdown to "Phenotype and Literature", and then select "OMIM Alleles" from the track dropdown. Note that the table selected is now "omimAvSnp".

From here you will need to explore linked tables and their fields to find the rest of the information you are looking for. Note that you may need to use the Data Integrator if you need to intersect more than a few tables. Also note that these OMIM tables (as well as a few others) are unavailable for genome-wide queries, due to restrictions by the data providers, although position queries will work just fine.

If you need more of an explanation feel free to send an email to our help-desk at [e-mail], or, if your message contains private information, [e-mail] instead.

ChrisL, UCSC Genome Browser

[o3964fn4n]

Thank you ! It helped a lot