Table 2 Results of intersecting CNVs detected in the Turkish dementia cohort and both neurodegenerative disease-associated genes and genes previously reported in CNV analyses of similar disease cohorts
From: A comprehensive analysis of copy number variation in a Turkish dementia cohort
Position | # SNPs | Length (bases) | CN | Sample | GnomAD-SV spanning the entire CNV? | # DGV observations | Genes (neuro/lit gene) | Total # intersects with CNVs from UKBB dementia (CN=0|CN=1|CN=3|CN=4) | Total # intersects with CNVs from UKBB non-dementia (CN=0|CN=1|CN=3|CN=4) | Pathogenicity |
|---|---|---|---|---|---|---|---|---|---|---|
Chr1:12850542-12915847 | 16 | 65,306 | 3 | F ;AD; AAO: 72 | No | 309 | PRAMEF1, PRAMEF11, HNRNPCL1 | 21 (0|9|12|0) | 46(0|19|27|0) | Likely benign |
Chr15:22750305-23226254 | 113 | 475,950 | 3 | F ;FTD | Loss of function deletion in 41 | 452 | TUBGCP5, CYFIP1, NIPA2, NIPA1 | 22 (0|9|13|0) | 44(0|16|28|0) | Likely benign |
M; AD; AAO: 64 | ||||||||||
Chr2:185421477-185564834 | 24 | 143,358 | 3 | M ;AD ;AAO: 71 | Inversion in 1 | 4 | ZNF804A | No overlap | No overlap | Uncertain significance |
Chr2:61448493-61929733 | 59 | 481,241 | 3 | F; AD; AAO: 52 | No | 0 | SNORA70B, USP34, XPO1 | No overlap | No overlap | Uncertain significance |
Chr22:18886915-19037734 | 59 | 150,820 | 3 | M; AD; AAO: 77 | No | 50 | DGCR6, PRODH, DGCR2 | 41 (0|8|33|0) | 67(0|8|59|0) | Uncertain significance |
Chr3:1154559-2400967 | 605 | 1,246,409 | 3 | M; MCI ;AAO: 73 | No | 1 | CNTN6, CNTN4 | 11 (0|7|4|0) | 20(0|7|13|0) | Uncertain significance |
Chr4:172006196-172792316 | 140 | 786,121 | 3 | F; AD; AAO: 75 | No | 0 | GALNTL6 | 1 (0|1|0|0) | 2(0|2|0|0) | Uncertain significance |
Chr6:31360254-31451679 | 161 | 91,426 | 1 | F; RISK | No | 657 | MICA | 7 (0|5|2|0) | 17(0|10|7|0) | Likely benign |
Chr6:31360254-31454364 | 168 | 94,111 | 3 | F; AD; AAO: 77 | No | 122 | MICA | 7 (0|5|2|0) | 17(0|10|7|0) | Uncertain significance |
M; AD; AAO: 65 | ||||||||||
Chr6:4805260-5449240 | 201 | 643,981 | 3 | M; MCI; AAO: 73 | No | 0 | MIR3691, CDYL, RPP40, PPP1R3G, LYRM4, FARS2 | 1 (0|1|0|0) | 1(0|1|0|0) | Uncertain significance |
Chr9:107311368-107699196 | 246 | 387,829 | 1 | M; MCI; AAO: 73 | Copy gain in 1 | 1 | OR13C8, OR13C5, OR13C2, OR13C9, OR13D1, NIPSNAP3A, NIPSNAP3B, ABCA1, LOC286367 | 1 (0|0|1|0) | No overlap | Uncertain significance |