Answers.Body: <p>You can do this manually by looking up the protein variant on <a href="https://varsome.com" rel="nofollow noreferrer">https://varsome.com</a>. For your example, that would mean searching for <code>KRAS G12V</code> (change <code>V</code> for anything else, the idea is to give an HGVS protein notation for a variant, so any single letter amino acid code would work). That would take you to this page <a href="https://varsome.com/variant/hg19/KRAS%20G12V?annotation-mode=germline" rel="nofollow noreferrer">https://varsome.com/variant/hg19/KRAS%20G12V?annotation-mode=germline</a>, which includes:</p>
  <p><a href="https://i.sstatic.net/P590B.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/P590B.png" alt="screenshot of varsome.com" /></a></p>
  <p>Of course, I imagine you want to automate this. VarSome can help there too, through our API, but that is a paid service. If you have the option of paying for this, the VarSome API can be used to (among other things) look up arbitrary variants and translate between different notations, so you could easily adapt this to get the information you need.</p>
  <p><em><strong>Disclosure</strong></em>: I work for the company behind VarSome.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-08-07T17:27:26.827Z
Answers.LastActivityDate: 2022-08-07T17:27:26.827Z
Answers.UserDisplayName: terdon
Body: <p>Is there a function that can map genomic position (hg19) back from a protein position? I can have name of a particular transcript, and exon number.</p>
  <p>For example, I have KRAS gene for which I would like to know the exact genomic position of G12, and I expect to have an output saying:</p>
  <p>chr12, from 25398283 to 25398285.</p>
  <p><a href="https://github.com/zwdzwd/transvar" rel="nofollow noreferrer">transvar</a> could be an excellent solution if the current built was working (broken links for fasta annotations). The web search is working but not allowing files heavier than 5kB which is my case.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-08-07T17:28:30.657Z
Comments.Text: This is considerably more complicated since there can be more than one genomic position referring to G12 in the protein in cases where multiple transcripts use different exons and yet >1 of them result in a protein with a G at position 12.
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-09-02T13:22:11.300Z
Comments.Text: @lizaveta could you please review the answer? In my opinion this does answer your question (just my opinion), if it does please kindly consider "accepting" the answer.
Comments.UserDisplayName: M__
Tags: <sequence-annotation><codon><genomicranges>
Title: Find a genomic coordinates for a protein aminoacid position
ThreadText: # Find a genomic coordinates for a protein aminoacid position
  
  (Asked by: username_0 on 2022-08-02)
  
  Is there a function that can map genomic position (hg19) back from a protein position? I can have name of a particular transcript, and exon number.
  
  For example, I have KRAS gene for which I would like to know the exact genomic position of G12, and I expect to have an output saying:
  
  chr12, from 25398283 to 25398285.
  
  [transvar](https://github.com/zwdzwd/transvar) could be an excellent solution if the current built was working (broken links for fasta annotations). The web search is working but not allowing files heavier than 5kB which is my case.
  
  **Tags:** sequence-annotation, codon, genomicranges
  
  > **Comments:**
  > **username_1**: This is considerably more complicated since there can be more than one genomic position referring to G12 in the protein in cases where multiple transcripts use different exons and yet >1 of them result in a protein with a G at position 12.  
  > **username_2**: @username_0 could you please review the answer? In my opinion this does answer your question (just my opinion), if it does please kindly consider "accepting" the answer.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2022-08-07. Score: 1
  
  You can do this manually by looking up the protein variant on <https://varsome.com>. For your example, that would mean searching for `KRAS G12V` (change `V` for anything else, the idea is to give an HGVS protein notation for a variant, so any single letter amino acid code would work). That would take you to this page <https://varsome.com/variant/hg19/KRAS%20G12V?annotation-mode=germline>, which includes:
  
  [![screenshot of varsome.com](https://i.sstatic.net/P590B.png)](https://i.sstatic.net/P590B.png)
  
  Of course, I imagine you want to automate this. VarSome can help there too, through our API, but that is a paid service. If you have the option of paying for this, the VarSome API can be used to (among other things) look up arbitrary variants and translate between different notations, so you could easily adapt this to get the information you need.
  
  ***Disclosure***: I work for the company behind VarSome.
  
  
  ---
  
  