Welcome to the Medical Genetics data browsers!

Please select a browser from the menu above to get started

These apps developed in shiny provide browsers for open access datasets.

Each dataset is filtered to contain only Loss of function, inframe indels, and predicted deleterious and damaging missense variants (by SIFT and PolyPhen respectively). Please see the VEP website for additional information about variant annotation.

Additional filters

Data can be interactively filtered and downloaded as per the users requirements. The following options can be applied.

Variant impact:

Protein affecting (default)

Loss of function
Inframe indels
predicted deleterious and damaging missense variants (by SIFT and PolyPhen respectively)

Loss of function

Stop gained
Stop lost
Start lost
Frameshift variant
Splice donor and splice acceptor variants

Variant allele frequency

Allows for additional filtering on variant rarity:

All (default)

< 0.05

Includes all variants with an allele frequency of < 0.05 within the entire ExAC non-TCGA set based on the AF column

< 0.01

Includes all variants with an allele frequency of < 0.01 within the entire ExAC non-TCGA set based on the AF column

Gene

Allows the input of incomplete strings and will return all genes within the data that contain that string. Has the option to match the gene name exactly from the search.

Data output

By default contains all protein affecting variants and is updated with filters. Hitting the download button downloads all data that match filters. It is currently not possible to download data without first selecting a gene of interest.

Summary Metrics

Summary metrics are generated after a gene name is input into the set. Counts of occurences (sum of ACs) are summarised for different impact and AF variants for different populations within the data. If the searched gene matches several genes then all genes will be summarised unless otherwise specified with the ‘Match gene name exactly’ button.