Curate Gene page

1. Top bar

2. Gene Information section

3. Interpretation section

4. Transcript section

5. Gene Metrics section

6. Variants Summary section

7. RefSeq Summary section

8. Gene's related diseases section

9. Activities panel

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1. The Top bar lists:

   a. Gene symbol;

   b. DNA strand orientation;

   c. Gene type;

   d. Clickable HGNC ID (links to HGNC);

   e. Clickable NCBI ID (links to NCBI Gene).

   

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2. The Gene Information section features:

   a. Official full gene name approved by the HGNC;

   b. Alias symbols;

   c. Location relative to GRCh37 and GRCh38 (with links to UCSC Genome Browser);

   d. Gene type;

   e. Gene family.

   

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1. The Interpretation section features:

   a. 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 (30.0+);

   b. The Note tab for your draft notes on the gene.

   Note: to edit your notes, select the tab (Curated or Note), and press the Edit button. Edit the text and apply the formatting. Don't forget to click Save!

   

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2. The Transcript section includes:

   a. Canonical transcript;

   b. Exon count;

   c. Organization preferred transcript;

   d. 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;

   e. A Copy button to conveniently copy transcript details to your clipboard.

   

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3. The Gene Metrics section (30.0+) displays

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

   a. RVIS - Residual variation intolerance score,

   b. p(LoF intolerant) - Probability of loss of function intolerance,

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

   d. O/E score - Ratio of the observed/expected number of LoF variants,

   e. HI - Haploinsufficiency,

   f. TS - Triplosensitivity,

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

   

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4. The Variants summary section features:

   a. A percent bar that illustrates trends in previous Pathogenicity classification;

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

   c. A link to See Related Variants.

   

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1. The RefSeq Summary section showcases:

   a. Gene summary sourced from RefSeq;

   b. A link to the respective NCBI Gene page;

   c. A convenient Copy button for quick data retrieval.

   

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1. The Gene's related diseases section includes:

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

   b. The list of Gene's Related Diseases with links to data sources,

   c. Icons representing inheritance modes, when available.

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

   

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2. Activities panel

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

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