Protein Visualization

VarLens includes an interactive protein visualization modal for exploring variant context at the protein and gene level. Access it from the Variant Details panel by clicking the DNA icon next to the gene symbol.

Opening the Viewer

1. Click any variant row in the variant table to open the Details panel
2. In the panel header, click the DNA icon (next to the gene name)
3. The protein visualization modal opens fullscreen with three tabs

Lollipop Plot

The default tab shows your variant on a protein backbone alongside population and clinical data.

Tracks (top to bottom)

• Your variant — Highlighted lollipop above the backbone with amino acid change label and gold border
• Protein backbone — Horizontal bar scaled to protein length with InterPro domain annotations (colored rectangles)
• ClinVar track — Diamond-shaped markers colored by clinical significance (red = Pathogenic, orange = Likely Pathogenic, yellow = VUS, green = Benign)
• gnomAD track — Population variant dots colored by consequence type, sized by density at each position

Filters

Filter each track independently using the legend chips:

• gnomAD Variants — Filter by consequence type (Missense, Truncating, Inframe, Splice, Synonymous). Click a chip to toggle, click only to isolate one category, click All to reset.
• ClinVar Significance — Filter by pathogenicity (Pathogenic, Likely P., VUS, Likely B., Benign)
• ClinVar Consequence — Filter ClinVar variants by consequence type
• AF filter — Dropdown in the toolbar to filter gnomAD variants by allele frequency threshold

Toolbar

• Zoom — Zoom in/out/reset buttons, or scroll-wheel to zoom, drag to pan
• gnomAD toggle — Show/hide the gnomAD population variant track (on by default)
• Case variants — Toggle to show other variants from the same case in the same gene
• Export — Download the plot as SVG or PNG

Gene Structure

The Gene Structure tab shows exon/intron architecture from the canonical Ensembl transcript.

Features

• Exons — Blue rectangles with exon numbers, sized proportionally
• Introns — Thin connecting lines between exons
• Variant — Your variant shown as a highlighted lollipop at its genomic position
• ClinVar — Diamond markers below the exon track (when loaded), with significance filters
• Coordinates — Chromosome position axis with assembly label (GRCh38)
• Scale bar — Shows the genomic distance scale

Toolbar

Zoom controls, exon count indicator, gene length, and SVG/PNG export.

3D Structure

The 3D Structure tab renders the protein's predicted structure from AlphaFold using the Mol* (pdbe-molstar) viewer.

Representations

Switch between three molecular representation styles:

• Cartoon — Secondary structure ribbons (default)
• Surface — Molecular surface envelope
• Ball+Stick — Atomic-level detail

Variant Highlighting

• Your variant residue is highlighted in its consequence color on the 3D structure
• ClinVar P/LP variants are shown in the sidebar and highlighted on the structure
• Click any variant in the sidebar to zoom to its position

Sidebar Filters

• Your Variant chip — Toggle visibility of your variant on the structure
• ClinVar chips — Filter by significance (Pathogenic, Likely P., VUS, Likely B., Benign) with only / All controls

Confidence Coloring

AlphaFold structures display pLDDT confidence scores:

Confidence	pLDDT Range	Color
Very high	> 90	Dark blue
Confident	70-90	Light blue
Low	50-70	Yellow
Very low	< 50	Orange

Data Sources

All data is fetched on demand and cached locally in SQLite:

Source	Data	Cache
UniProt	Gene-to-protein mapping	90 days
InterPro	Protein domain annotations	90 days
AlphaFold DB	Predicted 3D structures	90 days
Ensembl	Gene/exon coordinates	90 days
gnomAD	Population variant frequencies	30 days
gnomAD ClinVar	ClinVar variant annotations	30 days

Network Required

gnomAD and ClinVar data require an internet connection on first load. Subsequent views use cached data (even offline) until the cache expires.