> ## Documentation Index
> Fetch the complete documentation index at: https://docs.catalog.igvf.org/llms.txt
> Use this file to discover all available pages before exploring further.

# Gene

# Genes

The official gene sets of the IGVF Catalog come from the following GENCODE releases:

* **Human:** [GENCODE v43](https://www.gencodegenes.org/human/release_43.html)
* **Mouse:** [GENCODE vM36](https://www.gencodegenes.org/mouse/release_M36.html)

Gene, transcript, and gene structure (UTRs, exons, etc.) entries are loaded from the comprehensive GENCODE annotation, including protein-coding, lncRNA, and other annotated gene types.

## Functional scoring overview

The page opens with a table summarizing how many coding variants have been scored per method.

* Columns: **Scoring method** (links to the source) and **Number of variants predicted/scored**.
* Selecting a row updates the downstream coding-variant preview to focus on that method.

## Coding variants preview

An interactive preview of coding variants with functional/predictive scores.

* Search by rsID, SPDI, HGVS, or chromosome/position.
* Quick filters: **Show rsID variants first**, **Sort by SPDI**, or **Only show variants with rsID**.
* Table columns: Variant label (links to the variant page when available), rsID, SPDI, Chromosome, Position, Ref, Alt, **MutPred2**, **ESM-1v**.
* Pagination shows three variants per page with Previous/Next controls; the first visible variant is auto-selected.
* Selecting a row reveals a details panel with rsID, SPDI, HGVS, coordinates/alleles, a link to the full variant page, headline MutPred2 and ESM-1v values, and a full score table with bar visualizations and source labels.
* Data source: `genes/coding-variants/scores` (verbose) for the selected gene.

## Enhancer–Gene Prediction

Predicted enhancers from ENCODE-rE2G for the selected gene (1,458 released ENCODE biosamples).

* Promoter and overlapping/self-promoter entries are filtered out; ENCODE\_EpiRaction rows are excluded.
* Distance is computed from enhancer coordinates to the gene body; overlapping elements (distance = 0) are removed.
* Table columns: Cell Type, Score (0–1), Start, End, Dataset (link), Model, **Element Class**, Distance (Enhancer to Gene).
* Default sort: Score descending. A score-distribution histogram is available alongside the table.

## Variant Associations (QTLs)

Variants linked to the gene through QTL evidence.

| Column              | Description                                                                 |
| ------------------- | --------------------------------------------------------------------------- |
| rsID                | Reference SNP ID(s) for the variant (links to variant pages when available) |
| Chromosome          | Chromosome where the variant is located                                     |
| Position            | Genomic position                                                            |
| Ref                 | Reference allele                                                            |
| Alt                 | Alternative allele                                                          |
| HGVS                | HGVS notation for the variant                                               |
| Evidence Sources    | Evidence types linking the variant to the gene                              |
| Biological Context  | Biological contexts where the relationship is observed                      |
| Max -log10(p-value) | Maximum -log10(p-value) across all evidence sources                         |

## Disease Associations (ClinGen, Orphanet)

Diseases linked to the gene from ClinGen and Orphanet submissions.

| Column              | Description                                                          |
| ------------------- | -------------------------------------------------------------------- |
| Disease             | Disease term (links to term page when available)                     |
| Association Status  | Curated association status                                           |
| Association Type    | Type of asserted relationship                                        |
| Inheritance Mode    | Reported inheritance pattern                                         |
| Supporting Variants | Variants supporting the association (links to variant or coordinate) |
| PMIDs               | PubMed references for the assertion                                  |
| Source              | Reporting source with an outbound link when available                |

## Molecular Networks

This section shows a notice: **“Perturb-seq and other CRISPR data coming soon!”** while network resources are being onboarded.