Table 1 January 2018 freeze of G2P datasets

From: Flexible and scalable diagnostic filtering of genomic variants using G2P with Ensembl VEP

  G2P-DD number G2P-DD percent G2P-cancer number G2P-cancer percent
 Reportablea LGMDET 2044 100 123 100.0
 Different reportable genes 1517 NA 92 NA
LGMDET confidence     
 Confirmed 1551 75.9 114 92.7
 Probable 403 19.7 9 7.3
 Possibleb [257] NA [5] NA
 RD and IF 90 4.4 0 0.0
LGMDET allelic requirementc     
 Monoallelic 701 34.3 80 65.0
 Biallelic 1123 54.9 38 30.9
 Digenic 2 0.1 0  
 Imprinted 7 0.3 0  
 Mitochondrial 1 0.0 0  
 Mosaic 12 0.6 0  
 Hemizygous 166 8.1 2 1.6
 X-linked dominant and X-linked over-dominance 32 1.6 0  
 Uncertain 0   3 2.4
LGMDET mutation consequence     
 Loss-of-function 1446 70.7 107 87.0
 Activating 114 5.6 0  
 Dominant negative 53 2.6 0  
 5’ or 3’UTR mutation 5 0.2 0  
 Cis-regulatory or promotor mutation 5 0.2 0  
 Increased gene dosage 3 0.1 0  
 All missense/in-frame 287 14.0 6 4.9
 Uncertain 131 6.4 10 8.1
  1. aReportable genes are those with a LGMDET confidence level categorized as probable, confirmed or relevant and incidental.
  2. bPossible LGMDETs (see Supplementary Table 1 for definitions) are not reported in the pipelines used here.
  3. cAn individual gene may have more than one reportable LGMDET e.g. monoallelic/activating and biallelic/loss-of-function