Only two XPC variants were experimentally validated to affect actual BP sites. The remaining spliceogenic variants were inferred to abrogate a BP site due to nucleotide position, i.e. located within the -18 to -44 nucleotide BP window, and/or positive BP site prediction.
All deep intronic variants listed here create a new 5’ splice site or activate a cryptic 5’ splice site except LRG_135t1:c.2839-581_2839-578del, which introduces an intron-splicing processing element.
§Reported as c.1236-405C>T, in intron 11, with NM_000051.3 as reference transcript. However, the first base of exon 12 in the NM_000051.3 transcript is c.1803. Mutalyzer (https://mutalyzer.nl/) maps c.1236-405C>T in intron 11 of U82828.1 reference sequence.
Authors did not indicate the reference sequence and HGVS nomenclature. The published pseudoexon sequence maps to intron 18 of LRG_135. This variant was described as ATMIVS20-579_IVS20-576delGTAA by Coutinho et al. (2005).
††Reported as U82828.1:g.75117A>G, IVS28-159A>G
‡‡Reported as 5762ins137 caused by A>G variant. Published pseudoexon sequence maps to intron 38 of LRG_135. This variant was described as ATM IVS40-1126G>A by Coutinho et al. (2005).
§§Reported as NG_009057.1:g.74409T>A, NM_000268.3:c.1447-240T>A. However, inspection of the NG_009057.1 sequence (16-NOV-2019 version) revealed two sequence errors in the published illustration of the pseudoexon with flanking intronic regions: G deletion (+1 position) and A insertion (+4 position). Based on the publication’s illustration of variant location and reported sequence of pseudoexon boundaries, the variant is located at g.74408 in NG_009057.1, 233 bp upstream of exon 14.
¶¶Reported as IVS23-1398A>G