Table 2. Genes included in different types of CNV have different genetic and functional characteristics.
| Class B genes (1,075)* | Class P genes (6,367)† | Class X genes (523)‡ | BL/PG genes (94) | BG/PL genes (110) | P-value (χ2-test)§ | P-value (Mann–Whitney U-test)‖ | |
|---|---|---|---|---|---|---|---|
| Developmental genes | 14.3% (154) | 25.2% (1,606) | 22.4% (117) | 20.2% (19) | 25.5% (28) | 2.7 × 10−11 | |
| Protein complex members | 23.4% (251) | 33.9% (2,156) | 28.7% (150) | 33.0% (31) | 35.5% (39) | 7.5 × 10−9 | |
| Ohnologues | 26.9% (289) | 37.6% (2,395) | 30.4% (159) | 29.8% (28) | 41.8% (46) | 4.1 × 10−10 | |
| Haploinsufficient genes¶ | 12.0% (104) | 19.5% (1,138) | 13.9% (63) | 13.4% (11) | 14.9% (15) | 4.3 × 10−6 | |
| Haploinsufficiency score (median)# | 0.014 | 0.028 | 0.009 | 0.002 | 0.001 | ||
| · | · | 0.005 | |||||
| Maximal expression in RPKMs (median) | 9.6 | 19.6 | 12.6 | 20.4 | 14.1 | ||
| · | · | <1.0 × 10−16 | |||||
| · | · | 0.005 | |||||
| · | · | 4.5 × 10−13 |
BG/PL, genes exclusively overlapped by benign gain CNVRs and pathogenic loss peak CNVRs; BL/PG, genes exclusively overlapped by benign loss CNVRs and pathogenic gain peak CNVRs; CNV, copy number variant; CNVR, CNV regions; RPKM, reads per kilobase of transcript per million mapped reads.
*Genes exclusively observed in benign CNVRs.
†Gene exclusively observed in pathogenic CNVRs.
‡Genes observed in contradictory CNV types and clinical interpretations.
§All P-values are Bonferroni corrected. Values in bold have adjusted residuals >±2 in the χ2-test.
‖Pairwise comparisons are indicated with dots. All P-values are Bonferroni corrected.
¶Genes with probability of loss-of-function mutation intolerance >90% inferred in ref. 49.
#Probability of loss-of-function mutation intolerance inferred in ref. 49.