Table 2.
Summary of all pathogenic CNVs and VOUS identified in this study.
| Case ID | Sex | Clinical diagnosis | Additional clinical features | Chromosome region | Coordinates (hg19) | Gain/loss | Size | Gene involved* | Inheritance |
|---|---|---|---|---|---|---|---|---|---|
| A. Pathogenic CNVs (N = 7 of 114) | |||||||||
| AR82-3 | M | Non-syndromic ASD | Macrocephaly | 1q21.1-1q21.2 | chr1:146571244-147825548 | Gain | 1.25 Mb | 9 OMIM genes | Maternal |
| TU22 | M | ASD, ID | Microcephaly, seizures | 4p16.3 | chr4:49450-1997786 | Loss | 1.95 Mb | 22 OMIM genes | NA |
| 2715 | M | ASD, ID | Dysmorphic features, seizures | 9q21.11-9q21.2 | chr9:72066646–79948984 | Loss | 7.88 Mb | 22 OMIM genes | De novo |
| AR83-3 | F | Non-syndromic ASD | None | 15q13.2-15q13.3 | chr15:30371774-32514341 | Loss | 2.14 Mb | 8 OMIM genes | Maternal |
| TM50-3 | M | Non-syndromic ASD | None | 16p13.11 | chr16:15129970-16633361 | Gain | 1.50 Mb | 11 OMIM genes | Paternal |
| TU17 | F | ASD, ID, MCA | Microcephaly, cleft lip and palate, absent philtrum, abnormal ear canal, hypotelorism, flat nasal root, prominent nose | 18q21.33-18q23 | chr18:59030666-78015180 | Loss | 18.9 Mb | 43 OMIM genes | NA |
| 2950 | F | ASD | Familial history of lissencephaly | 22q13.33 | chr22:50537901-51211392 | Loss | 673 kb | 23 OMIM genes | NA |
| *OMIM genes are shown in Supplementary Table S1. | |||||||||
| B. VOUS, likely pathogenic CNVs (N = 7 of 114) | |||||||||
| TM41-3 | M | Non-syndromic ASD | None | 1p35.2 | chr1:31707971-31928387 | Gain | 220 kb | FABP3, SNRNP40, NKAIN1,SERINC2 | De novo |
| AR44-3 | M | Non-syndromic ASD | Macrocephaly | 1q42.2 | chr1:231763496-231877073 | Loss | 113 kb | DISC1 | NA |
| TM18-3 | F | Non-syndromic ASD | None | 2q14.1 | chr2:116,548,326-116,675,350 | Gain | 127 kb | DPP10 | De novo |
| TM4-3 | M | Non-syndromic ASD | Macrocephaly | 3p26.3 | chr3:104972-264293 | Gain | 159 kb | CHL1 | De novo |
| PS12-3 | F | Non-syndromic ASD | None | 7q31.1 | chr7:111080241-111183610 | Loss | 103 kb | IMMP2L | NA |
| RA29 | M | ASD, ID | None | 15q13.3 | chr15:32,389,362-32,415,088 | Loss | 25 kb | CHRNA7 | NA (Not paternal) |
| AR12-3 | M | Non-syndromic ASD | Abnormal hearing test | 18q22.3 | chr18:72186404-72404396 | Gain | 217 kb | ZNF407, CNDP2, CNDP1 | De novo |
| C. VOUS, likely benign CNVs (N = 5 of 114) | |||||||||
| TM13-3 | M | Non-syndromic ASD | Macrocephaly | 4q24 | chr4:103560963-103658350 | Loss | 97 kb | MANBA | Paternal |
| PS37-3 | M | Non-syndromic ASD | seizures | 10q23.1 | chr10:84017608-84115017 | Loss | 97 kb | NRG3 (intronic) | Maternal |
| AR33-3 | M | Non-syndromic ASD | None | 17p13.3 | chr17:228978-440497 | Gain | 211 kb | FAM101B, VPS53 | Paternal |
| RA11 | M | ASD, ID | None | Xp11.4 | chrX:41252835-41363836 | Gain | 111 kb | NYX, (near CASK) | Maternal |
| RA32 | M | ASD, ID | None | Xq28 | chrX:148086944-148291691 | Loss | 204 kb | No gene (near AFF2) | Maternal |
| D. VOUS (no subclassification) (N = 10 of 114) | |||||||||
| AR91-3 | M | Non-syndromic ASD | None | 2q13 | chr2:112581082-112858485 | Gain | 277 kb | ANAPC1, MERTK | Maternal |
| RA15 | M | ASD, ID | None | 2q12.2-2q12.3 | chr2:106637427-107642482 | Gain | 1.0 Mb | C2orf40, USX1, PLGLA, RGPD3, ST6GAL2 | Maternal |
| TM35-3 | F | Non-syndromic ASD | None | 4q28.2 | chr4:128901402-130163564 | Gain | 1.26 Mb | SCLT1, PHF17, PGRMC2 | Paternal |
| 2546 | M | ASD, GDD, MCA | Generalized hypotonia, clenched hands, microphthalmia, large ear | 7q11.22 | chr7:69718336-69783020 | Loss | 64 kb | AUTS2 | Maternal |
| TM54-3 | M | Non-syndromic ASD | None | 8q24.3 | chr8:142,039,892-143,535,189 | Loss | 1.49 Mb | PTP4A3, GPR20 | Paternal |
| TU29 | F | ASD, ID | Facial dysmorphism, seizures | 15q26.2 | chr15:95048523-96519797 | Gain | 1.47 Mb | Reference genes: LOC440311, LINC00924 | Maternal |
| TU23 | F | ASD, ID MCA | Microcephaly, brain abnormalities, facial dysmorphism, congenital heart defect, abnormal hearing test, congenital cataract | 18q21.31-8q21.32 | chr18:55411917-56384192 | Gain | 972 kb | ATP8B1, NEDD4L, MIRN122A, MALT1 | Paternal |
| RA39 | M | ASD, ID | None | 20p12.1 | chr20:14562027-14714457 | Loss | 152 kb | MACROD2 | Paternal |
| TU4 | M | Non-syndromic ASD | Short philtrum, 2 hair whirls, small eyes | Xp22.31 | chrX:6449601-8141017 | Gain | 1.69 Mb | HDHD1A, STS, VCX, VCX2, VCX3 A, PNPLA4 | Maternal |
| RA6 | M | ASD, ID | None | Xq28 | chrX:154735698-155094135 | Gain | 358 kb | TMLHE, SPRY3 | Maternal |
Abbreviations: VOUS, variant of uncertain clinical significance; ASD, autism spectrum disorder; ID, intellectual disability; DD, developmental delay; GDD, global developmental delay; MCA, multiple congenital anomalies; NA, not available.