Question: What Is Ivsi Number Of A Mutation?
3
gravatar for Edi
6.5 years ago by
Edi120
Sri Lanka
Edi120 wrote:

Hi, I need to find out the SNP (rs#) associated with IVSI-5. I searched in the ENTREZ of NCBI but I couldnt locate it. Can anybody help me to find this. Thank you in advance.

snp • 6.6k views
ADD COMMENTlink written 6.5 years ago by Edi120
5
gravatar for Fabio Marroni
6.5 years ago by
Fabio Marroni1.5k
Italy
Fabio Marroni1.5k wrote:

IVS means InterVening Sequence (i.e. an intron). Your mutation is located in the gene you are studying, in the first intron, five nucleotides before the consensus intron site AG.
You might give a look here for further details (http://www.hgvs.org/mutnomen/history-1996.html). I paste the sentence about IVS below for reference. Intron mutations when the full genomic sequence is not known can be designated by the intron (IVS) number, positive numbers starting from the G of the donor site invariant GT, negative numbers starting from the G of the acceptor site invariant AG. IVS4+1G>T denotes the G to T substitution at nt +1 of intron 4. IVS4-2A>C denotes the A to C substitution at nt -2 of intron 4. When the full length genomic sequence is known, the mutation can also be simply designated by the nt number of the reference sequence.

ADD COMMENTlink written 6.5 years ago by Fabio Marroni1.5k
3
gravatar for Giulietta - Ensembl Helpdesk
6.5 years ago by
Cambridge, UK

You can search for your gene of interest in Ensembl, then have a look at the intronic variations either using the variation table (showing all variations for a gene) and choosing 'intronic'

http://www.ensembl.org/Homo_sapiens/Gene/Variation_Gene/Table?g=ENSG00000139618;r=13:32889611-32973805

then pay attention to the coordinate to determine which falls in your first intron.

Or, you can go to the Location view for your gene of interest and zoom in to the first intron of your gene. Turn on the variation track and see what overlaps your position of interest:

http://www.ensembl.org/Homo_sapiens/Location/View?db=core;g=ENSG00000139618;r=13:32889611-32973805

I hope that helps.

ADD COMMENTlink written 6.5 years ago by Giulietta - Ensembl Helpdesk1.2k
2
gravatar for Larry_Parnell
6.5 years ago by
Larry_Parnell16k
Boston, MA USA
Larry_Parnell16k wrote:

Good question - trying to convert a common name of a genetic variant into a standard ID.

This sounds a lot like a rather generic name for an insertion/deletion variant. You could check the Database of Genomic Variants but I doubt it is there. So, I would suggest that you carefully read the Methods section of the articles in which this variant is studied, keeping in mind that you may have to reconstruct electronically the PCR and other protocols used to detect the variant.

In the end, you may find that there is no rs#.

Please reply if you need more help as this is something we have done a lot in our group.

Fabio gives a good answer +1. However, one must still check the Methods because what those authors thought was 5 bases away from teh splice site may not be according to corrected gene models. I once studied a SNP that was called a promoter SNP that was later placed in an intron by the corrected gene model. So, I map the variant to the reference genome and cross-check with dbSNP entries to be 100% certain of the SNP ID.

ADD COMMENTlink modified 6.5 years ago • written 6.5 years ago by Larry_Parnell16k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1067 users visited in the last hour