Table 3.
De novo CNVs identified in this study.
| Case ID | Chromosome region | Type of CNV | Gene involved | Gene functions and supportive evidence |
|---|---|---|---|---|
| 2715 | 9q21.11-9q21.2 | 7.88 Mb loss | 22 OMIM genes | 9q21.13 microdeletion syndrome including RORB, which is a strong candidate gene for neurological disorders82. |
| TM41-3 | 1p35.2 | 220 kb gain | FABP3 | - FABP3 is a candidate tumor suppressor gene for human breast cancer and plays a role in mammary gland differentiation. |
| - FABP3 knockout mice showed decreased social memory and novelty seeking58. | ||||
| SNRNP40 | SNRNP40 is a component of the U5 small nuclear ribonucleoprotein (snRNP) particle which is involved in the removal of introns from nuclear pre-mRNAs83. | |||
| NKAIN1 | - NKAIN1 can interact with the β subunit of Na, K-ATPase. | |||
| - NKAIN1 protein highly expressed in hippocampus and cerebellar granular cell layer59. | ||||
| SERINC2 | - SERINC2 encodes transmembrane proteins that facilitate incorporation of serine into membrane lipid synthesis. SERINC2 mRNA was upregulated by kainate-induced seizures in the dentate gyrus of the hippocampus in the rat brain60. | |||
| TM18-3 | 2q14.1 | 127 kb gain | DPP10 | - DPP10 encodes a protein which binds specific voltage-gated potassium channels (KCND2) and alters their expression and biophysical properties84. |
| - Loss and gain of the DPP10 gene have been identified in patients with autism49. | ||||
| TM4-3 | 3p26.3 | 159 kb gain | CHL1 | - CHL1 encodes a member of the L1 family of neural cell adhesion molecules, which plays a role in nervous system development and synaptic plasticity85,86. |
| - Loss and gain of the CHL1 gene have been identified in patients with autism and ID50,51. | ||||
| AR12-3 | 18q22.3 | 217 kb gain | ZNF407 | - ZNF407 encodes a zinc finger protein which may be involved in transcriptional regulation. |
| - Balanced translocation and point mutations in the ZNF407 gene have been identified in ID patients with autism52. | ||||
| CNDP2 | CNDP2 is a nonspecific dipeptidase rather than a selective carnosinase53. | |||
| CNDP1 | - CNDP1 protein present in pyramidal neurons of the hippocampus and neurons of the temporal cortex53. | |||
| - Decreased serum CNDP1 activity has been associated with ID, DD, multiple sclerosis and Parkinson’s disease54–57. |
Abbreviations: ID, intellectual disability; DD, developmental delay.