We have performed an exome for a genetically heterogeneous disorder.
There is a certain gene of interest which spans more than 150 kb and has >100 exons.
Looking in the variants of the gene (incl. also synonymous and intronic) there appear to be approx. 30 SNVs within the first half (5' part) of the gene but no variant at all in the rest. 30 variants within the first 50 exons and introns but no variant thereafter.
There appear to be reads within the exons which do not have variants and the coverage for the entire coding region appears to be >97% at 30x. Coverage appears to be insufficient for a single or two exons at most.
Would you have any idea why this may be happening ?
Thank you in advance.