---
title: Gene lists
description: "VarSome Clinical offers 3 ways of creating a new gene list: The options to manage the existing gene lists are the following: Gene lists can be copied by clicking on the "Copy" button . Genes can be a"
---
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# Gene lists
VarSome Clinical offers three ways of creating a new gene list:
1. Copy and modify an existing gene list.
2. Create a new gene list.
3. Create a gene list from phenotypes.
### 
### **1. Copy and modify an existing gene list**
The options to manage the existing gene lists are the following:
Gene lists can be copied by clicking on the "**Copy**" button .
Genes can be added or removed by clicking on the "**Edit**" button . Once you have finished editing the gene list, you can save the list with either the original name or with a new one.
[****](https://lh6.googleusercontent.com/7F7yreqd0qRkedEZFvCcLPofyV0iT9FsQ_BHxTlLu3ngZgq1I8RaVyT0_wiVcQ0sgFyu3VEgh2TwFw-9jmh0Ot4pWAjEMz6FhQ2QVE1r1Vr_jt-fRZy9fIAH9Hu10D10G72PW5YIq7DsS0QqpBGVz7U1Mmr-pBhi)
All the gene lists are editable, regardless of who created them. The system displays the name of the last person who made changes and the date of the last modification.
Gene lists can be exported to excel by clicking on the "**Excel**" button .
Finally, these gene lists can also be deleted by clicking on the "**Trash**" button .
Only the user who created a list can delete it. For all other users, the Delete option appears greyed out and cannot be selected. Deleted lists cannot be recovered.
### **2. Create a new gene list**
- Click on "**Create new gene list**".
- Enter a name for the gene list and paste the list of genes to be analyzed.
- You can also add a note or comment before clicking **Save List.**
The gene names need to follow the HGNC (Hugo Gene Nomenclature Committee) standard ([http://www.genenames.org/](http://www.genenames.org/)), otherwise an error message will appear after clicking **Save list.**
****
### **3. Create a gene list from phenotypes**
- Click on "**Create gene list from phenotypes**"
- Start by typing a phenotype, or use the bulk input or paste an entire list of HPO, MONDO and OMIM® identifiers (separated by commas, spaces, or line breaks), or full phenotype terms (separated by line breaks), directly into the field. By selecting **All**, phenotype matching records from HPO, MONDO and OMIM® will be available.
[](https://lh3.googleusercontent.com/pvODx-aF7GJ1h9bS88pNOgzw3DNH1oZGSaim04XO8-OVVUNxVJOypHHTWlKJaW5FFrXM4-ZoAX4B48Agj07hDarUu8tBO84g2aSHm3oema8IjLU9gCCa53N1DEK66_iMejIueVQlYjKfjrwFSVouq9yTfR6F24MJ4uLncOArWOByxgaLb6KoP9cp_txaig)
- If typing, click on phenotype from the drop down menu to add it to your phenotypes list. If pasting a list, the system will automatically parse the content and provide immediate visual feedback indicating which terms were successfully added (blue ones) and which were unrecognized (red ones).
Please note that you can right click any phenotype to remove it from the list.
- Select one or more phenotypes from your list to view the associated genes.
[](https://lh4.googleusercontent.com/A8iWbJWrARcwOTDfVzAtF_DEhH1DvDJApv9Mm3JnYcp0xqzMEo8ChQVHNliBEZ42JoCTkMb6KM1J7gI-jBeFzey6833JNHQP-sKdY_Ts6CiWJ7jMkdMMrsdNslXw0JLouQSVcu9ubF2y5kmmF_DHtNr5VwkazAvLyIpCGrj--yti4aN5xgXzL8-W9RGLyQ)
- Finally select one or more genes to be added to your gene list.
[](https://lh3.googleusercontent.com/8DQKrcgeflbl_liQWh7Gd8ik6dL8-KlvPuv2tYD6IeFAd3LQxxquT8Y9SNnpmqpI6O1VspyZled79jREc8fVFcy06IOXeVMo3dj5s8vvcjh_cSrB3mlJ9UJvA8RiNuqMdYwl6c46lWfponE_Otpbh83MRooIosVNaeuUW75ci7uSzzC5dQ_xpzxcrpNYxQ)
The methodology to generate a gene list from phenotype(s) has been changed. Previously, when making a gene list from phenotypes, we would include only those genes that are directly annotated with that phenotype. We have now extended this and instead first collect all diseases linked to the phenotype and then all genes linked to those diseases, as well as any genes directly linked to the phenotype. We already worked this way when adding phenotypes to analyses, so this change ensures we are consistent and also makes sure we don’t miss any genes when creating gene lists.
To filter your gene list, go to the Variant table page of the CNV analysis you performed and click on the filter icon  on the left. Click on "**Create**" and you will see a screen like the one below:
Click to add a Gene list filter for the chosen phenotype. Add a name to the filter set and save it in order to be applied to your analysis.
### **Browsing through gene lists**
- Search gene lists by name:
[](https://lh7-us.googleusercontent.com/7cZfAVuB2QE-SR5aT1R4O9ms_oKoU5HOw0v6zaj--E9HLo4NoBY5IMAUF15IMXp2B5p-JiAPUyuP3LIiUJveG8zXmnWhfM0WBIiRR4Bu7C_gUkwNHbgL45VBoFUrq3-5PrDQVSs_Bqq7xnYG0wEyb04)
- Toggle custom view:
**[](https://docs.varsome.com/hubfs/image-png-Apr-28-2026-09-52-20-4915-AM.png?hsLang=en)**
- Display gene lists sorted by name, owner and update date:
[](https://docs.varsome.com/hubfs/image-png-Apr-28-2026-09-53-59-4632-AM.png?hsLang=en)
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