# How is the isDeleterious column in the CCLE\_mutations.csv file determined?

**URL:** <https://forum.depmap.org/t/how-is-the-isdeleterious-column-in-the-ccle-mutations-csv-file-determined/129>\
**Category:** Q&A\
**Tags:** data\
**Created:** [July 30, 2020, 3:36pm UTC](https://forum.depmap.org/t/how-is-the-isdeleterious-column-in-the-ccle-mutations-csv-file-determined/129 "2020-07-30T15:36:18Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![ytakemon](https://yyz1.discourse-cdn.com/flex035/user_avatar/forum.depmap.org/ytakemon/32/549_2.png) [@ytakemon](https://forum.depmap.org/u/ytakemon)\
**Post date:** [July 30, 2020, 3:36pm UTC](https://forum.depmap.org/t/how-is-the-isdeleterious-column-in-the-ccle-mutations-csv-file-determined/129/1 "2020-07-30T15:36:18Z")

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I am curious to know how TRUE/FALSE is determined in the `isDeleterious` column of the CCLE\_mutations.csv file. Is it a combined score of multiple variant predictors? Apologies, if this is already written up in a publication.

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**Author:** ![jnoorbak](https://yyz1.discourse-cdn.com/flex035/user_avatar/forum.depmap.org/jnoorbak/32/12_2.png) [@jnoorbak](https://forum.depmap.org/u/jnoorbak)\
**Post date:** [August 6, 2020, 6:01pm UTC](https://forum.depmap.org/t/how-is-the-isdeleterious-column-in-the-ccle-mutations-csv-file-determined/129/2 "2020-08-06T18:01:56Z")

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The isDeleterious is an outdated annotation which we do not recommend using. We will drop this in a future release. Please use the column ‘Variant\_annotation’ instead.

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**Author:** ![ytakemon](https://yyz1.discourse-cdn.com/flex035/user_avatar/forum.depmap.org/ytakemon/32/549_2.png) [@ytakemon](https://forum.depmap.org/u/ytakemon)\
**Post date:** [August 13, 2020, 12:13am UTC](https://forum.depmap.org/t/how-is-the-isdeleterious-column-in-the-ccle-mutations-csv-file-determined/129/3 "2020-08-13T00:13:19Z")

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Thanks for getting back to me @jnoorbak, are there plans to include a SIFT/PolyPhen scores to these mutations? Perhaps this was the original intent of `isDeleterious`?

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**Author:** ![jnoorbak](https://yyz1.discourse-cdn.com/flex035/user_avatar/forum.depmap.org/jnoorbak/32/12_2.png) [@jnoorbak](https://forum.depmap.org/u/jnoorbak)\
**Post date:** [August 13, 2020, 1:35pm UTC](https://forum.depmap.org/t/how-is-the-isdeleterious-column-in-the-ccle-mutations-csv-file-determined/129/4 "2020-08-13T13:35:23Z")

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The original goal has been somewhat to get the damaging effect of the mutation. This column in most cases corresponds to one of the following mutation types from ‘Variant\_Classification’ column (Oncotator annotations), but there are exceptions to that:

_‘De\_novo\_Start\_OutOfFrame’, ‘Nonsense\_Mutation’, ‘Nonstop\_Mutation’, ‘Splice\_Site’, ‘Frame\_Shift\_Del’, ‘Frame\_Shift\_Ins’, ‘Start\_Codon\_Del’, ‘Start\_Codon\_Ins’, ‘Stop\_Codon\_Del’, ‘Stop\_Codon\_Ins’_

We do have a plan to update the mutation functional annotations in the future, but its timeline is unclear right now. We do generate SIFT/PolyPhen scores that are not reported right now. I’ll keep in mind including them once we get to that. -Thanks

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**Author:** ![ytakemon](https://yyz1.discourse-cdn.com/flex035/user_avatar/forum.depmap.org/ytakemon/32/549_2.png) [@ytakemon](https://forum.depmap.org/u/ytakemon)\
**Post date:** [August 13, 2020, 3:13pm UTC](https://forum.depmap.org/t/how-is-the-isdeleterious-column-in-the-ccle-mutations-csv-file-determined/129/5 "2020-08-13T15:13:06Z")

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> [@jnoorbak](#):
>
> Variant\_Classification

Thank you for the clarification, I will mark your response here as the solution.  
Cheers