Hereditary Cancer Gene Variants with Validated Splicing Effects

A review paper by Daffodil M. Canson from QIMR Berghofer Medical Research Institute presents a catalog of germline variants affecting mRNA splicing. It lists 81 exonic variants impacting splicing regulatory elements in BRCA1, BRCA2, MLH1, MSH2, MSH6, and PMS2 genes. The work also includes an analysis of 283 variants using a pre-existing BRCA1 functional dataset to assess bioinformatic prediction tools.

Use Cases

• Benchmarking bioinformatic prediction tools based on a set of 283 variants with functional data
• Prioritizing variants for experimental validation based on the described generic workflow for splicing regulatory elements
• Studying the impact of non-canonical splice site variants on disease causation using the catalog of 81 exonic variants

Strengths

• Includes a specific list of 81 exonic variants with experimentally validated splicing effects
• Benchmarks prediction tools using a dataset of 283 variants from a pre-existing large-scale BRCA1 functional study

Limitations

• Row count and column-level documentation are unknown; field semantics must be inferred after download
• Description metadata is limited; actual data quality requires manual inspection after download

Provenance

Source

QIMR Berghofer Medical Research Institute

Collection Method

Review and analysis of existing experimental data and bioinformatic predictions.