Table 5. Other singleton novel rare CNVs.
| Chromosome | Sample | Gender | Size, bpa | CNV | Origin | Genesb | Other Rare Variantsc |
|---|---|---|---|---|---|---|---|
| 1p36.11 | 88253 | M | 16,863 | Loss | Maternal | WASF2 intronic | 9p21.3 (13.1 kb) loss KIAA1797;9q22.31 (10.7 kb) loss not in any gene |
| 1p34.1 | 94073 | F | 9205 | Loss | Paternal | PRDX1 exonic | 2q35 (6.8 kb) loss 40972;8p23.1 (74.5 kb) loss PINX1,MIR1322 |
| 2p21 | 115818L | M | 9068 | Loss | Paternal | PPM1B exonic | 16q22.3 (90.8 kb) gain not in any gene |
| 2p16.3 | 75420 | F | 10,491 | Gain | Maternal | STON1-GTF2A1L,STON1 | 2p16.3 (10.5 kb) gain STON1-GTF2A1L,STON1;2q14.1 (118.8 kb) gain DPP10;17q12 (84.3 kb) gain GPR179, MRPL45, LOC440434 |
| 2p12 | 100678L | F | 52,069 | Gain | Paternal | CTNNA2 exonic | 1p31.1 (53.5 kb) loss not in any gene;1q42.2 (5 kb) loss FAM89A;2p23.1 (7.4 kb) loss GALNT14;4p15.31 (19 kb) loss SLIT2;9p21.3 (65 kb) loss not in any gene;16q24.1 (12.4 kb) loss ATP2C2 |
| 2q11.2 | 47173L | F | 780,104 | Gain | Unknownd | 11 genes | 19q13.43 (843.3 kb) loss TRAPPC2P1, ZNF835,USP29,ZNF17, ZNF71, ZNF749, ZNF264, LOC147670, VN1R1, AURKC, PEG3-AS1, ZIM2, ZIM3, ZNF304, ZNF805, ZNF547, ZNF543, MIMT1, ZNF460, DUXA, ZNF548, PEG3;20q13.12 (15.1 kb) gain CD40 |
| 3p22.2 | 58016 | M | 38,181 | Gain | Paternal | LRRFIP2 exonic | 6p22.1 (9.5 kb) loss HIST1H2AG,HIST1H2BJ;19q13.31 (78.2 kb) gain TEX101;21q21.1 (70.9 kb) loss C21orf34 |
| 3p14.2 | L656 | M | 332,421 | Loss | Maternal | FHIT exonic | 1q32.1 (37 kb) loss MDM4;2p14 (26 kb) loss FBXO48,APLF;6q12 (16.3 kb) loss EYS;8q22.2 (38.3 kb) loss VPS13B;17q25.3 (46.2 kb) loss CYTH1;17q25.3 (32.7 kb) loss LOC100294362, ENDOV, RNF213;Xp11.3 (32.8 kb) loss CXorf36 |
| 3q13.31 | 52026 | M | 10,004 | Loss | Maternal | ZBTB20 intronic | 7p11.2 (81.7 kb) gain LOC650226, DKFZp434L192;7q36.2 (70.7 kb) loss DPP6;13q31.2,13q31.3 (74.9 kb) gain not in any gene |
| 3q13.33 | 55310 | M | 29,147 | Gain | Paternal | ARHGAP31 exonic | 7q21.12 (12.3 kb) loss not in any gene;10q23.1 (23.3 kb) loss NRG3;Xp22.2 (19.2 kb) gain SYAP1 |
| 3q25.1 | 50002 | F | 7969 | Gain | Unknownd | WWTR1 intronic | 1p36.22 (6.4 kb) loss UBE4B; 5p15.1,5p15.2 (300.2 kb) gain not in any gene;7p21.1 (20.7 kb) loss not in any gene;9p24.1 (10.2 kb) loss KDM4C;14q23.2 (8.4 kb) gain MTHFD1 |
| 3q26.2 | 46685 | M | 10,633 | Loss | Paternal | PRKCI exonic | 4q13.1 (32.6 kb) gain not in any gene |
| 3q29 | 76066 | M | 27,516 | Loss | Unknownd | KIAA0226 exonic | 17q25.3 (13.4 kb) gain NARF;22q11.21 (2762.8 kb) gain encompassing 65 genes |
| 4p15.31 | 100678L | F | 19,015 | Loss | Maternal | SLIT2 intronic | 1p31.1 (53.5 kb) loss not in any gene;1q42.2 (5 kb) loss FAM89A;2p23.1 (7.4 kb) loss GALNT14;2p12 (52.1 kb) gain CTNNA2;9p21.3 (65 kb) loss not in any gene;16q24.1 (12.4 kb) loss ATP2C2 |
| 4q21.1 | 62345L | M | 8527 | Loss | Paternal | SHROOM3 intronic | 5q21.1 (20.8 kb) loss not in any gene;14q21.2 (59.5 kb) loss not in any gene |
| 4q32.1 | 55360 | M | 16,194 | Gain | Maternal | FGA exonic | 9p21.3 (18 kb) gain IFNA22P;12p12.1 (18.9 kb) loss not in any gene;15q13.3 (36.3 kb) loss MIR211,TRPM1 |
| 5p15.2 | 51119 | M | 12,982 | Loss | Unknownd | CTNND2 intronic | — |
| 5p14.3 | 167532 | F | 16,492 | Gain | Maternal | CDH18 intronic | 11p15.4 (98.4 kb) loss LOC283299, OR5E1P, OR5P3, OR5P2;12q24.12 (12.7 kb) loss ATXN2 |
| 5q14.3 | 55262-L | M | 665,114 | Gain | Maternal | LYSMD3,POLR3G,CETN3,MBLAC2, GPR98 | 2q37.1 (119.8 kb) gain NMUR1,C2orf57;4q21.21 (22.7 kb) gain ANTXR2;14q22.2 (26.4 kb) gain CDKN3;22q13.31 (54.2 kb) loss not in any gene |
| 5q22.2 | 59269L | F | 25,834 | Loss | Maternal | MCC exonic | 22q12.1 (225.1 kb) loss TTC28;Xq11.1 (308.9 kb) gain MTMR8 |
| 5q31.3 | 66559 | M | 19,794 | Gain | Unknownd | TAF7,SLC25A2 | 6q27 (307.6 kb) gain C6orf118, PDE10A;11q12.1 (24.3 kb) loss OR5B2, OR5B12;16q21 (81.9 kb) gain not in any gene |
| 5q33.1 | 60560L | M | 54,785 | Gain | Paternal | NDST1 exonic | 20p13 (22.4 kb) gain SNPH;22q12.3 (77.4 kb) gain SLC5A4 |
| 6p22.1 | 58016 | M | 9549 | Loss | Paternal | HIST1H2AG,HIST1H2BJ | 3p22.2 (38.2 kb) gain LRRFIP2;19q13.31 (78.2 kb) gain TEX101;21q21.1 (70.9 kb) loss C21orf34 |
| 6q26 | 75744 | M | 17,712 | Loss | Paternal | PARK2 intronic | 21q21.3 (8.1 kb) loss NCRNA00189 |
| 7p21.3 | 68687 | M | 258,183 | Loss | Maternal | NXPH1 exonic | 1q32.1 (145.7 kb) gain CAMSAP1L1, C1orf106, GPR25;13q33.2 (63.9 kb) loss not in any gene;13q33.2 (69.6 kb) gain not in any gene |
| 8p21.2 | 88810 | M | 28,281 | Gain | Paternal | ADAM7 exonic | 6p22.1 (17.3 kb) gain not in any gene;19q13.43 (24.1 kb) gain SLC27A5,ZBTB45 |
| 9p22.3 | 131240 | M | 8341 | Loss | Paternal | NFIB intronic | 5p13.2 (51.9 kb) gain PRLR,AGXT2;6q25.1 (20.8 kb) loss RAET1L;8p12 (66.6 kb) loss NRG1;16p13.3 (16.5 kb) loss HBM, HBA1, HBA2, HBQ1 |
| 9p22.1 | 61180-L | M | 7974 | Loss | Paternal | SLC24A2 exonic | 3p21.31 (20.4 kb) loss MIR425, DALRD3, MIR191, QRICH1, IMPDH2, NDUFAF3;6q22.31 (296.4 kb) gain C6orf204, PLN, BRD7P3 |
| 9p13.3 | 59641L | F | 190,658 | Gain | Maternal | PTENP1,PRSS3,UBE2R2 | 6q24.1 (13.2 kb) loss TXLNB;17q24.1 (5.9 kb) loss CEP112;Xp21.1 (15.4 kb) gain DMD |
| 10q25.1 | 115816L | M | 9442 | Loss | Maternal | SORCS3 intronic | 11q23.3 (9.2 kb) loss CBL;15q21.3 (58.8 kb) loss not in any gene |
| 11q12.2 | 72816L | M | 15,159 | Loss | Paternal | DAGLA exonic | 7q31.31 (19.4 kb) gain not in any gene;8q22.1 (19.8 kb) loss not in any gene;12q12 (25 kb) gain KIF21A;14q24.2 (8.5 kb) gain RGS6;22q12.1 (25.6 kb) loss MIR1302-1,MYO18B |
| 11q23.3 | 96280L | M | 19,424 | Gain | Paternal | VPS11 exonic | 3p12.3 (123 kb) loss not in any gene;13q33.1 (74.2 kb) loss FGF14;15q11.2 (25.7 kb) loss not in any gene;Xp11.4 (39 kb) gain GPR82,GPR34,CASK |
| 11q24.2 | 138952L | F | 11,398 | Loss | Maternal | KIRREL3 intronic | 4p13 (71.3 kb) gain not in any gene;11q14.1 (28.8 kb) gain not in any gene;14q31.2 (27.9 kb) loss not in any gene |
| 11q24.3 | 98320L | M | 8428 | Loss | Maternal | APLP2 exonic | 1q31.1 (321.4 kb) loss not in any gene;4q13.1 (1326.4 kb) gain not in any gene;5q23.1 (42 kb) loss not in any gene;7q31.1 (98.6 kb) loss IMMP2L |
| 12q15 | 59794L | M | 9279 | Loss | Maternal | RAP1B intronic | 5q35.2 (8 kb) loss ATP6V0E1;14q32.2 (8.9 kb) loss WDR25;20p11.22 (148.7 kb) gain not in any gene |
| 12q24.33 | 50280 | M | 202,302 | Gain | Maternal | LOC100130238, GALNT9 | 3q21.3 (6.1 kb) loss CCDC48;12q24.33 (77.8 kb) gain SFSWAP |
| 14q23.2 | 50002 | F | 8427 | Gain | Unknownd | MTHFD1 exonic | 1p36.22 (6.4 kb) loss UBE4B;3q25.1 (8 kb) gain WWTR1;5p15.1,5p15.2 (300.2 kb) gain not in any gene;7p21.1 (20.7 kb) loss not in any gene;9p24.1 (10.2 kb) loss KDM4C |
| 15q24.2 | 62261L | M | 12,936 | Loss | Paternal | PTPN9 intronic | 5q14.1 (15.3 kb) gain BHMT2;8q24.21 (45.3 kb) gain GSDMC |
| 15q25.1 | 68388 | F | 7142 | Loss | Paternal | IL16 exonic | 1p32.2 (567.4 kb) gain DAB1;10q22.3 (12.9 kb) gain C10orf11;22q12.1 (8.4 kb) loss not in any gene |
| 16p13.3 | 47378 | M | 13,736 | Loss | Maternal | TRAP1 intronic | 2p23.1 (42.7 kb) loss CAPN14,EHD3;3p25.1 (16.1 kb) loss CAND2;21q21.2,21q21.1 (75 kb) loss not in any gene |
| 16p11.2 | 100564 | F | 546,709 | Gain | Maternal | 27 genes | 8q12.3 (17.9 kb) loss ASPH;10q21.3 (47.3 kb) loss not in any gene;17p11.2 (186.2 kb) loss LOC162632, CCDC144A, FAM106CP, KRT16P2;Xq21.1 (130.3 kb) gain not in any gene |
| 16q24.1 | 100678L | F | 12,352 | Loss | Maternal | ATP2C2 exonic | 1p31.1 (53.5 kb) loss not in any gene;1q42.2 (5 kb) loss FAM89A;2p23.1 (7.4 kb) loss GALNT14;2p12 (52.1 kb) gain CTNNA2;4p15.31 (19 kb) loss SLIT2;9p21.3 (65 kb) loss not in any gene |
| 16q24.2 | 68711 | M | 17,969 | Loss | Maternal | KLHDC4 exonic | 2p23.1 (61.4 kb) loss LCLAT1;4p15.1 (48 kb) loss not in any gene;6q21 (14.6 kb) gain not in any gene;7p21.3 (87.4 kb) loss VWDE;12p13.2 (8 kb) gain KLRK1, KLRC4-KLRK1 |
| 17p13.1 | 47387 | M | 7758 | Gain | Maternal | NDEL1, MYH10 | 2p23.1 (7.4 kb) loss GALNT14;2q22.1 (299.4 kb) loss THSD7B;5q31.3 (29.9 kb) loss PCDHB9, PCDHB8, PCDHB7, PCDHB16 |
| 17q11.2 | 87042 | F | 14,177 | Loss | Maternal | NF1 exonic | − |
| 17q25.3 | 103818L | M | 48,984 | Gain | Maternal | TIMP2 exonic | 8q24.13 (54.1 kb) loss not in any gene |
| 19q13.32 | 85287L | M | 17,455 | Loss | Maternal | BBC3,MIR3190, MIR3191 | 16q22.1 (36.5 kb) gain DDX19A, DDX19B;16q23.1 (16.2 kb) loss WWOX |
| 19q13.33 | 168753 | M | 61,936 | Loss | Maternal | SHANK1,CLEC11A | 4p15.33 (5.4 kb) loss not in any gene |
| 20p13 | 92540L | M | 15,645 | Loss | Paternal | SLC23A2 exonic | 2q34 (23 kb) loss SPAG16 |
| 22q11.21 | 118909L | F | 7277 | Loss | Unknownd | CECR2 exonic | 7q22.2 (12.4 kb) gain not in any gene;10q21.3 (8.1 kb) loss CTNNA3 |
| 22q11.22-q11.23 | MM0177-3 | M | 656,280 | Gain | Maternal | RAB36,FBXW4P1,RTDR1,GNAZ,MIR650,IGLL5,BCR | − |
| 22q11.23 | 154266L | M | 6784 | Loss | Maternal | UPB1 | 11p14.3 (138.6 kb) loss not in any gene |
| Xq28 | 100676L | M | 123,871 | Gain | Maternal | ZNF185,CETN2, NSDHL | 3q22.3 (11.5 kb) loss not in any gene;5p14.2 (12.2 kb) loss not in any gene;22q12.3 (35.6 kb) gain not in any gene |
ASD, autism spectrum disorder; CNV, copy number variations; F, female; M, male; qPCR, quantitative polymerase chain reaction; UTR, untranslated region.
a
These CNVs were validated by qPCR. However accurate breakpoints have not been identified. The size of the CNVs shown is as detected by microarrays.
b
A CNV encompassing coding regions of the gene are defined as exonic, whereas those encompassing introns were defined as intronic.
c
Other rare variants present in the individual.
d
Inheritance is unknown if the parents DNA were unavailable.