Genes
The official gene sets of the IGVF Catalog come from the following GENCODE releases:- Human: GENCODE v43
- Mouse: GENCODE vM36
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 |