Table 2.
List of all qPCR confirmed rare biallelic deletions (CNV0) among individuals with ASD in the HMCA collection.
| # of CNV | chr | Start | Size (Kb) | Histone peak | Gene location | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| ENCODE project | Primary neuron | Road map neuron | Road map brain | Exonic | Intronic | On the left | On the right | ||||
| 1 | 1 | 189,959,475 | 6.9 | Y | FAM5C | ||||||
| 1 | 1 | 191,473,007 | 179.0 | Y | Y | Y | Y | FAM5C | RGS18, RGS21 | ||
| 1 | 2 | 167,346,017 | 47.1 | Y | Y | Y | Y | SCN7A | |||
| 1 | 2 | 184,794,451 | 8.0 | Y | DUSP19, NCKAP1, NUP35 | ZNF804A | |||||
| 1 | 2 | 227,341,510 | 6.1 | Y | Y | Y | Y | NYAP2 | IRS1, RHBDD1 | ||
| 1 | 2 | 242,915,454 | 119.2 | Y | Y | Y | CXXC11, D2HGDH, DTYMK, GAL3ST2, ING5, NEU4, PDCD1 | ||||
| 1 | 3 | 1,782,524 | 5.1 | CNTN6 | CNTN4 | ||||||
| 1 | 3 | 75,394,265 | 149.8 | Y | Y | Y | Y | CNTN3 | ZNF717 | ||
| 1 | 3 | 143,637,504 | 853.2 | Y | Y | Y | Y | C3orf58 | SLC9A9 | ||
| 1 | 4 | 134,871,302 | 321.4 | Y | Y | Y | Y | PABPC4L | |||
| 1 | 5 | 9,904,421 | 20.6 | Y | Y | TAS2R1 | CCT5, CMBL, FAM173B, MARCH6 | ||||
| 1 | 6 | 154,121,271 | 10.1 | Y | Y | FBXO5, MTRF1L, RGS17 | IPCEF1, OPRM1 | ||||
| 3 | 7 | 16,900,135 | 15.3 | Y | AGR3 | AGR2, BZW2, TSPAN13 | |||||
| 1 | 7 | 80,157,064 | 141.8 | Y | Y | Y | Y | CD36 | GNAT3 | SEMA3C | |
| 1 | 7 | 159,049,219 | 13.1 | No data | Y | VIPR2, WDR60 | |||||
| 1 | 8 | 15,937,585 | 88.5 | Y | Y | MSR1 | |||||
| 1 | 8 | 18,852,675 | 9.6 | Y | Y | Y | Y | PSD3 | |||
| 1 | 8 | 34,800,058 | 43.0 | Y | Y | Y | UNC5D | ||||
| 1 | 10 | 81,512,254 | 85.7 | Y | Y | Y | Y | AK302451, EIF5AL1, SFTPA1, SFTPA2, ZCCHC24 | PLAC9, SFTPD, TMEM254 | ||
| 1 | 12 | 112,432,874 | 5.6 | Y | Y | Y | TMEM116 | ALDH2, MAPKAPK5 | ERP29, HECTD4, NAA25, TRAFD1 | ||
| 1 | 14 | 28,475,766 | 25.0 | Y | Y | Y | Y | FOXG1 | |||
| 1 | 14 | 47,966,854 | 2.6 | MDGA2 | |||||||
| 2 | 20 | 52,643,162 | 20.2 | Y | Y | Y | Y | BCAS1 | CYP24A1, PFDN4 | ||
| 1 | 21 | 18,802,512 | 19.7 | Y | Y | Y | Y | BTG3, CXADR | |||
| 1 | 22 | 30,336,496 | 30.3 | Y | Y | Y | Y | MTMR3 | ASCC2, CABP7, NF2, , UQCR10, ZMAT5 | HORMAD2 | |
The table notes overlap with histone peaks as defined by the ENCODE Project33, by ChIP-seq data from Primary–Neuron34, and both Brain and Neuron epigenomes from Roadmap Project (ChromHMM state model36. Neighboring genes are shown, and genes with bibliographic evidence linking them to neurodevelopmental disorders are noted in bold. Table S5a list rare homozygous deletions (CNV0) for unaffected siblings.