Curate Gene page

The Top bar lists:

• Gene symbol

• DNA strand orientation

• Gene type

• Clickable HGNC ID (links to HGNC)

• Clickable NCBI ID (links to NCBI Gene)

The Gene Information card features:

• Official full gene name approved by the HGNC

• Alias symbols

• Location relative to GRCh37 and GRCh38 (with links to UCSC Genome Browser)

• Gene type

• Gene family

The Interpretation card features:

• The Curated tab to be used for your curated gene interpretation. This text can be reused in the Variant Interpretation notes or Gene interpretation notes within a case

• The Note tab for your draft notes on the gene

The Transcript card includes:

• Canonical transcript

• Exon count

• Organization preferred transcript

• A dropdown list featuring all known transcripts. This is where you can select a preferred transcript to be used in case analysis instead of the default one. The organization's preferred transcript is indicated by a star icon, while the canonical transcript is marked by a checkmark icon

• A Copy button to conveniently copy transcript details to your clipboard

The Gene Metrics card displays gene metrics from ExAC, gnomAD and ClinGen that assess the potential pathogenic impact of gene alterations:

• RVIS - Residual variation intolerance score

• p(LoF intolerant) - Probability of loss of function intolerance

• p(REC) - Probability of being intolerant to homozygous, but not heterozygous LoF variants

• O/E score - Ratio of the observed/expected number of LoF variants

• HI - Haploinsufficiency

• TS - Triplosensitivity

• Z missense - Intolerance to missense variants based on the deviation of observed missense variants versus the expected number

The Variants summary card features:

• A percent bar that illustrates trends in previous Pathogenicity classification

• A table summarizing Pathogenicity and severity across variants in the gene that have been previously added to Curate in a table view

• A link to See Related Variants

The RefSeq Summary card showcases:

• Gene summary sourced from RefSeq

• A link to the respective NCBI Gene page

• A convenient Copy button for quick data retrieval

The Gene's related diseases card includes:

• The number of gene-associated diseases sourced from OMIM, ORPHANET, CGD, ClinVar, and academic papers incorporated in Emedgene knowledge graph

• The list of Gene's Related Diseases with links to data sources

• Icons representing inheritance modes, when available

• An expandable condition summary from Uniprot (accessible via dropdown) along with a link to Uniprot and a copy button for convenient data extraction

Activities panel

The Activities panel records a history of user activities on the Curate Variant page. Click on the Activities button to open it.