How to use this site

Examples - 13:20763071:T>C, 13:20763044, 13:20763045-20763071


Navigating by gene letter

Using the gene letter table When you click a letter on the table to the left, you will be shown all genes starting with that letter that have variants associated with them.

Navigating to gene page The “+” sign next to each gene indicates that you can click it to navigate to it's gene page.

The Gene Page

Gene page The Gene Page offers gene level information for review on the webpage as well as downloadable variant lists. On the webpage, you are be able to view all variants associated with that gene, view the gene in a genomic browser, and view the gene's 3D protein structure. For detailed information regarding the functionality of these interactive viewers, please see their individual sections of this page:

Navigating to gene page To download a variant table as a comma separated file (csv) directly, click the 'CSV' link to the right of the 'Variant List' heading. This will initiate a direct download of the variant table without the need of opening the table on the webpage. Clicking the 'Tab' link will initiate a download of the same information but in a tab delimited format.

Navigating by the variant search bar

The search bar featured at the top of most DVD pages enables you to search for a single specific variant, all variants at a position, all variants within a range of positions along the same chromosome, or any combination of those three options. The search bar hooks into the api so that a search of 13:20763071:T>C is equivalent to>C. For more information about the supporting API call, please review the API Documentation page.

The expected return of the search bar is a loading of a new page where,

  1. all of the search terms are displayed under the heading "Terms searched:" and
  2. all of the individual searched terms are displayed as faux-gene headings with api-links to their variant list results, similar to the gene page variant lists.
Clicking on one of these search term headings will cause the following to occur on the page:
  1. display a loading wait bar, with status messages for when the variant list data is requested from the DVD and when the data is being read into the variant list table.
  2. generate a table to view variant data resulting from the loaded search term(s) grouped by gene. For more information regarding use of the variant table and its capabilities please review the Variant Table Functionality Section of this page.
  3. Upon click of a search term heading, a grey message of "Loaded" or "No Data" will appear to the right of the clicked heading respective to the results returned by the search term.

Single Search Term Examples:

  • Single specific variant search - 13:20763071:T>C
  • "Fuzzy" search for all variants at a position - 13:20763044
  • Search for all variants within a range - 13:20763045-20763071
  • Single specific variant not found - X:79476000

The search bar also accepts several independent searches, separated by commas. Also, spaces are ignored. The results are in the same format as described above.

Multiple Search Term Examples:

  • Search of single specific variant and a 'fuzzy' search - 13:20763071:T>C, 13:20763044
  • Search a range and a 'fuzzy' search - 13:20763044, 13:20763045-20763071
  • Search a range that returns variants and a range that does not - 13:20763045-20763071,X:79477000-79477027
  • A mixture of all search permutations, found and not found - X:79476000:C>T,X:79476000,X:79477000-79477027,1:64239701:G>A,13:20763044,16:75661649-75661755

Variant Table Functionality

When either the 'Variant List' header or the searched term header, on a gene page or a search results page respectively, variant information will be requested from the DVD, returned, and a variant table will appear displaying the data similar to the picture shown below. To hide the variant table, click again the 'Variant List' header or the searched term header, on a gene page or a search results page respectively.
Using the variant list table

  1. Sorting: The variant table is sortable by column either in a ascending or descending order. The data sorted is across all data in the table (and across all pages if pagination is required). The sorting direction and column may be changed by clicking the grey arrow to the right of the column header being sorted by. Only a single column may dictate the sorting order at a time. By default when the table laods, the table is sorted in an ascending order by the 'Genomic Position' column.
  2. Filtering: The variant table is filterable by user input text (case insensitive) in the 'filter column...' field for any combination of columns. This filtering is applied across all data in the table (and across all pages if pagination is required). When filtered, only the rows that have partial or better text matcheds to the input text will be shown; the pagination number will also reflect this. The filtered data will be ordered according to any previously set sorting order as well. For example, to filter for only 'Likely benign' variants in exon '4': enter 'likely benign' into the 'Variant Classification' filter field and '4/' into the 'Exon Locale' filter field.
  3. Pagination: Often, there are more variants than displayable on a single page of the variant table. When this is the case, the variant table automatically paginates the display of the variants for more convenient viewing. The variant table loads up to 200 variants into a single page with a scrollable 23 rows of variants shown at any one time. To navigate between pages, use the buttons at the bottom right hand corner of the table.
    On click:
    • First: displays the first page of variants
    • Prev: displays the previous page of variants
    • 1...n: displays the nth page of variants
    • Next: displays the next page of variants
    • Last: displays the last page of variants
  4. Variant Specific Information: There are two methods of viewing more detailed information for a variant by interacting with a variant table.
    • Left Click - Compact Variant Overlay: Left clicking anywhere on a variant row will display an overlay with specific variant information in a compact format.
    • Right Click - Full Variant New Page: Right clicking anywhere on a variant row will redirect you to a new web page with specific variant information in a more detailed format. This variant page is persistant meaning that it may be referenced and revisited using its url.

Other Table Features

  • Resizeable column widths by clicking and dragging.
  • Horizontal scrolling if not all columns fit into the width of the web page. The 'Genomic Position (Hg19)' column is frozen and acts as a row identifier.
  • Collapseable variant lists by clicking the arrow next to the gene name (ie. 'CLRN1 (7936 items)') within the table. To expand a collpased variant list, click the arrow again.

Table Column Descriptions

Genomic Position (Hg19) HGVS Nucleotdie Change HGVS Protein Change Exon Locale Intron Locale Variant Classification
Description (chromosome):(position):(reference)>(alternate) HGVS nucleotide only nomenclature (more info) HGVS protein only nomenclature (more info) (variant's exon) / (total number of exons in gene) (variant's intron) / (total number of introns in gene) Possible values:{Pathogenic,Likely pathogenic,Unknown significance,Benign*,
Likely benign,Benign}
Note Always has a value May have missing values May have missing values May have missing values (ie. intronic variant) May have missing values (ie. exonic variant) Always has one of the set of values

Phenotype Consequence CADD Phred Max MAF (%) Max MAF Source
Description Varying Combination of VEP consequence terms (more info) Phred-like scaled CADD score (more info) Maximum minor allele frequency across all sources and populations as a percentage (abbrv. source)_(abbrv. population)_AF
Note May have missing values May have missing values. Combinations of terms separated by '&' May have missing values Always has a value, set to 0.00000 if no data in any population from any source May have missing values

Genome Browser Functionality

Open the genome browser To open the genome browser, click the link-like button called 'Show Genome Browser' on the gene page. To hide the genome browser, click the link-like button called 'Close Genome Browser', which replaced the previous 'Show Genome Browser' button.

Using the genome browser

  1. Gene Range Highlight: After clicking to open the genome browser, the browser will load all of the default tracks independently. Once loaded, the browser will refocus to a range around to the gene of the gene page. The gene's range itself is highlighted in red.
  2. Zoom In and Out: This tool bar allow you to zoom in an out on the browser. Changes in the view of the browser are reflected in the coordinates input box to the left of the tool bar (see #3 below). The tool bar allows for two views to be temporarily 'saved' while viewing on this page. Which of the two views you are using is indicated by the slight blue dot on the tool bar track. By default, the right dot is selected on browser load and the left dot is set to the single base zoom level. Zooming in and out may be done so in steps using the '+' and '-' magnifying glasses, respectively, at the ends of the tool bar. Additionally, zooming in or out in a sliding fashion is also possible by clicking and dragging a tool bar dot. These positions only reset to defaults if the page is reloaded or navigated away from; closing the genome browser will not reset the two zoom settings.
  3. Specify Coordinates: In the input box is the current visible range of the format: (chromosome):(position start)..(position end). You may also search for genes by type the gene name into the field (case insensitive). Searching for a gene in this way will change the range of positions viewed and move the red highlight to encapsulate the gene's range.

NGL Protein Viewer Functionality

Open NGL Viewer To open the protein viewer, click the link-like button called 'Load NGL Viewer' on the gene page. To hide the protein viewer, click the bracketed link-like button called '[X]', which replaced the previous 'Load NGL Viewer' button.

Open NGL Viewer

  1. Protein Representation: On load, a pdb file is read and rendered into view. The filename of the structure can be seen in the top left of the NGL viewer. The filename nomenclature is as follows: (gene)_(residue range)_(model algorithm). For example: CLRN1_99-213_FFX indicates that the file loaded is for gene CLRN1 of residue range 99 to 213 as modeled by the FFX algorithm (more info). By clicking and dragging on the structure, you can change the perspective of the structure. Also, by scrolling up or down, you can zoom in or out on the structure, respectively.
  2. Hover For Residue: You can view information of a specific residue by hovering the pointer over a part of the structure. When doing so, a grey tooltip box will appear with residue specific information.
  3. Switching Representations: By hovering the pointer over 'Switch Representation', a grey tooltip box will appear with a list of representations available for viewing the structure as. To load the representation for the current structure, click on one of the options in the list. Switch Representation

  4. Switching Structures: By hovering the pointer over 'Switch Structure', a grey tooltip box will appear with a list of structures available for that gene. To load the structure, click on one of the options in the list. Switch Representation

Getting Support

Please get in touch if you experience any issues with using this site.