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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
  1. M male, F female, AD Alzheimer’s disease, FTD Frontotemporal dementia, MCI mild cognitive impairment, AAO age at onset, CN copy number, 0 homozygous deletion, 1 heterozygous deletion, 3 duplication, 4 triplication. Neurogenes and genes previously reported are in bold lettering. No UKBB CNVs were significantly associated with dementia based on Fisher’s exact test