# Gene panels
Analyses in ELLA are restricted to genes included in predefined gene panels. In addition to which genes to investigate, the gene panels defines default transcripts, phenotype relationships and inheritance mode for each gene.
# Genes
Genes to include, using HGNC ID (opens new window).
# Transcripts
Transcript(s) to use as default for each gene (multiple choices possible). Default transcripts affect how variants and annotation are displayed in the user interface, especially regarding HGVS cDNA/protein naming and VEP consequence (opens new window) calculation.
Note that ELLA also uses consequences calculated for alternative transcripts in the same gene, but these will be less visible unless they are "worse" (i.e. more likely to cause damage) than in the default transcript(s).
# Phenotypes
Phenotypes linked to each gene, based on OMIM (opens new window). Tied to:
# Inheritance
The inheritance mode to use for each gene, based on OMIM (opens new window). These are important for certain rules in variant filtering and suggesting ACMG criteria.
The modes are grouped like this for the purpose of both filtering and ACMG suggestions:
- Autosomal dominant (AD)
- Other (autosomal recessive (AR), x-linked dominant/recessive (XD/XR), combinations)
Note that although mixed modes are possible (e.g. AD/AR), using pure AD whenever reasonable generally means more accurate results in filtering and ACMG suggestions.