You take the list of genes from the probes used for capture (all vendors provide them) and use biomart to get all the annotations you have mention.
The definition of clinical exome is vage and confusing, and in my opinion should not be use.
First you need to choose what means clinical exome to you:
a) the whole exome? Then the atribute "clinical" does not mean anything, perhaps it only states that is going to be used in a diagnostic environment and probably the threshold for base coverage would be over 40.
b) You do an exome but only analyze the clinical relevant genes (400-7000, the ones in OMIM, HGMD....)
- you can do a whole exome but only describe mutation in those genes (and only in the core refseq transcripts)
- you use some ad-hoc exome capture sets like agilent focus-exome or illumina TruSightOne that constains only probes for these genes and you save in secuencing.
c) It is the whole exome but the clinical relevant genes has improved capture and an effort has been made to achieve maximum coverage on them, like Agilent Sure Select Clinical Research V2
Now that you have chosen your capture set, ¿How to obtain the genes and data you want?
The list of genes are usually stored in files called manifest, or files in bed format. You can obtain Illumina TruSightOne from here, and the agilents ones from SureDesign register yourself there, go to "find_design" tab, select "SureSelect DNA", and click in "Agilent Catalog" tab.
I you don't have bionformatics knowledge you can extract the gene column in Excel and use biomart (filters-> gene-> imput external references [select "gene name" from the options]) and paste them in groups of 500;